BIO - TERMS - PROTEIN Flashcards
19S regulatory caps
Multisubunit component of the proteasome that functions to capture ubiquitinated proteins for degradation in the catalytic core.
20S catalytic core
Multisubunit component of proteasome responsible for protein degradation.
abatacept
An Fc fusion protein containing the CTLA-4 extracellular domain used in treating rheumatoid arthritis that blocks co-stimulation of T cells by binding B7 molecules.
adipose differentiation related protein
A protein that functions in the maintenance and storage of neutral lipid droplets in many types of cells.
Adrenodoxin
A mitochondrial iron-sulfur protein that participates in hydroxylation reactions of steroids.
Agrin
Signal protein released by an axonal growth cone during formation of the synapse between it and a muscle cell.
alefacept
Recombinant CD58–IgG1 fusion protein that blocks CD2 binding by CD58 used in treatment for psoriasis.
Allosteric effector
A ligand that affects the equilibrium between the alternative conformations of an allosteric protein.
Allosteric transition
A reversible interaction of a small molecule with a protein molecule that causes a change in the shape of the protein and a consequent alteration of the interaction of that protein with a third molecule.
allostery (adjective allosteric)
Change in a protein’s conformation brought about by the binding of a regulatory ligand (at a site other than the protein’s catalytic site), or by covalent modification. The change in conformation alters the activity of the protein and can form the basis of directed movement
amphitropic proteins
Proteins that associate reversibly with the membrane and thus can be found in the cytosol, in the membrane, or in both places.
Amyloid
Abnormally folded, insoluble proteins with β-pleated sheet structure.
amyloidoses
A variety of progressive conditions characterized by abnormal deposits of misfolded proteins in one or more organs or tissues.
angiotensin I
A liver protein produced from angiotensinogen through the actions of the kidney enzyme renin.
anti-apoptotic Bcl2 family proteins
Proteins (e.g., Bcl2, BclXL) on the cytosolic surface of the outer mitochondrial membrane that bind and inhibit pro-apoptotic Bcl2 family proteins and thereby help prevent inappropriate activation of the intrinsic pathway of apoptosis.
Antifreeze proteins
Proteins of animals, plants, fungi, and bacteria bind to ice crystals and inhibit their growth.They protect against freezing damages.
antiporter
Carrier protein that transports two different ions or small molecules across a membrane in opposite directions, either simultaneously or in sequence.
antiviral protein (AVP)
A protein made in response to interferon that blocks viral multiplication.
Apaf1
Adaptor protein of the intrinsic apoptotic pathway; on binding cytochrome c, oligomerizes to form an apoptosome.
ARF proteins
Monomeric GTPase in the Ras superfamily responsible for regulating both COPI coat assembly and clathrin coat assembly.
ARP (actin-related protein) complex (Arp 2/3 complex)
Complex of proteins that nucleates actin filament growth from the minus end.
ASC (PYCARD)
An adaptor protein containing pyrin and CARD domains involved in activating caspase 1 in the inflammasome.
ATP-binding cassette (ABC)
A large family of proteins containing a particular domain for nucleotide-binding that includes many transporters, such as TAP1 and TAP2, but also various NOD members.
Autocrine growth stimulation
Stimulation of cell growth by proteins produced and sensed by the same cell. (Chapter 6)
Avidin
A biotin-binding protein in egg white.
axoneme
Bundle of microtubules and associated proteins that forms the core of a cilium or a flagellum in eukaryotic cells and is responsible for their movements.
Backbone
The continuous chain of atoms running the length of a protein or other polymer.
Bak
A main effector Bcl2 family protein of the intrinsic pathway of apoptosis in mammalian cells that is bound to the mitochondrial outer membrane even in the absence of an apoptotic signal; activation is usually by activated pro-apoptotic BH3-only proteins.
Bax
A main effector Bcl2 family protein of the intrinsic pathway of apoptosis in mammalian cells; located mainly in the cytosol and translocates to the mitochondria only after activation, usually by activated pro-apoptotic BH3-only proteins.
Bcl-2 family
Family of intracellular proteins that includes members that promote apoptosis (Bax, Bak, and Bok) and members that inhibit apoptosis (Bcl-2, Bcl-W, and Bcl-XL).
Bcl2
Anti-apoptotic Bcl2 family protein of the outer mitochondrial membrane that binds and inhibits pro-apoptotic Bcl2 family proteins and prevents inappropriate activation of the intrinsic pathway of apoptosis.
Bcl2 family
Family of intracellular proteins that either promote or inhibit apoptosis by regulating the release of cytochrome c and other mitochondrial proteins from the intermembrane space into the cytosol.
BclXL
Anti-apoptotic Bcl2 family protein of the outer mitochondrial membrane that binds and inhibits pro-apoptotic Bcl2 family proteins and prevents inappropriate activation of the intrinsic pathway of apoptosis.
BH3-only proteins
The largest subclass of Bcl2 family proteins. Produced or activated in response to an apoptotic stimulus and promote apoptosis mainly by inhibiting antiapoptotic Bcl2 family proteins.
binding site
The crevice or pocket on a protein in which a ligand binds.
BiP
Endoplasmic reticulum (ER)-resident chaperone protein member of the family of hsp70-type chaperone proteins.
BLNK
B-cell linker protein. See SLP-65.
C2
Complement protein of the classical and lectin pathways that is cleaved by the C1 complex to yield C2b and C2a. C2a is an active protease that forms part of the classical C3 convertase C4bC2a.
C4
Complement protein of the classical and lectin pathways. C4 is cleaved by C1s to C4b, which forms part of the classical C3 convertase.
C4b-binding protein (C4BP)
A complement-regulatory protein that inactivates the classical pathway C3 convertase formed on host cells by displacing C2a from the C4bC2a complex. C4BP binds C4b attached to host cells, but cannot bind C4b attached to pathogens.
C6, C7, C8, C9
Complement proteins that act with C5b to form the membrane-attack complex, producing a pore that leads to lysis of the target cell.
Ca2+ pump (calcium pump, Ca2+ ATPase)
Transport protein in the membrane of sarcoplasmic reticulum of muscle cells (and elsewhere). Pumps Ca2+ out of the cytoplasm into the sarcoplasmic reticulum using the energy of ATP hydrolysis.
Ca2+/calmodulin-dependent kinase (CaM-kinase)
Serine/ threonine protein kinase that is activated by Ca2+/calmodulin. Indirectly mediates the effects of an increase in cytosolic Ca2+ by phosphorylating specific target proteins.
calcium-calmodulin-dependent protein kinase (CaMK)
A protein kinase activated by elevations of internal Ca²⁺ concentration.
CaM-kinase II
Multifunctional Ca2+/calmodulin-dependent protein kinase that phosphorylates itself and various target proteins when activated. Found in most animal cells but is especially abundant at synapses in the brain, and is involved in some forms of synaptic plasticity in vertebrates.
capsomere
A protein subunit of a viral capsid.
casein
Milk protein.
CD59, protectin
Cell-surface protein that protects host cells from complement damage by blocking binding of C9 to the C5b678 complex, thus preventing MAC formation.
Cdc25
Protein phosphatase that dephosphorylates Cdks and increases their activity.
Cdk inhibitor protein (CKI)
Protein that binds to and inhibits cyclin–Cdk complexes, primarily involved in the control of G1 and S phases.
Cdk-activating kinase (CAK)
Protein kinase that phosphorylates Cdks in cyclin–Cdk complexes, activating the Cdk.
cell-cycle control system
Network of regulatory proteins that governs progression of a eukaryotic cell through the cell cycle.
Ceruloplasmin
A copper-containing plasma protein.
channel (membrane channel)
Transmembrane protein complex that allows inorganic ions or other small molecules to diffuse passively across the lipid bilayer
channel rhodopsin
Photosensitive protein forming a cation channel across the membrane that opens in response to light. charge separation In photosynthesis, the light-induced transfer of a high-energy electron from chlorophyll to an acceptor molecule resulting in the formation of a positive charge on the chlorophyll and a negative charge on a mobile electron carrier.
chaperonin
One of two major classes of chaperones found in virtually all organisms; a complex of proteins that functions in protein folding, either GroES/GroEL in bacteria or Hsp60 in eukaryotes.
Chediak–Higashi syndrome
A defect in phagocytic cell function caused by a defect in a protein involved in intracellular vesicle fusion. Lysosomes fail to fuse properly with phagosomes, and killing of ingested bacteria is impaired.
Cholesterol ester transfer protein
A protein that transfers cholesterol esters from high-density lipoprotein (HDL) to other lipoproteins.
Chromophore
Chemical compound that can absorb light at a certain wavelength and therefore appears colored in bright light. cofactor of a protein that is responsible for the absorption of light.
circular dichroism spectroscopy
A method used to characterize the degree of folding in a protein, based on differences in the absorption of right-handed versus left-handed circularly polarized light.
cisternal maturation model
One hypothesis for how the Golgi apparatus achieves and maintains its polarized structure and how molecules move from one cisterna to another. This model views the cisternae as dynamic structures that mature from early to late by acquiring and then losing specific Golgiresident proteins as they move through the Golgi stack with cargo.
classical cadherins
Family of cadherin proteins, including E-cadherin, N-cadherin, and P-cadherin, that are closely related in sequence throughout their extracellular and intracellular domains.
Cluster-of-differentiation markers
Distinct surface proteins that are recognized by specifi c monoclonal antibodies; these antibodies bind to various cluster-of-diff erentiation markers and are used to distinguish diff erent cell types (e.g., CD4 on helper T cells). Also called CD markers. (Chapter 4)
co-translational
Occurring as translation proceeds. Examples include the import of a protein into the endoplasmic reticulum before the polypeptide chain is completely synthesized, and the folding of a nascent protein into its secondary and tertiary structure as it emerges from a ribosome.
co-transport
A transport mechanism in cells in which two compounds or substances are simultaneously transported across a membrane by the same carrier protein. Co-transport may or may not require ATP.
coated vesicle
Small membrane-enclosed organelle with a cage of proteins (the coat) on its cytosolic surface. Formed by the pinching off of a coated region of membrane (coated pit). Some coats are made of clathrin, others are made from other proteins.
cochlear amplifier
Outer hair cells, including the motor proteins in the outer hair cell membrane, that amplify displacements of the basilar membrane in the cochlea.
cohesin, cohesin complex
Complex of proteins that holds sister chromatids together along their length before their separation.
collagen fibers
Strong, flexible protein located within many connective tissues.
colloid
(kol′oyd) Opaque mixture composed of water and solute (usually protein); substance within thyroid follicles.
complement activation
The activation of the normally inactive proteins of the complement system that occurs on infection. See classical pathway, alternative pathway, lectin pathway.
complement regulatory proteins
Proteins that control complement activity and prevent complement from being activated on the surfaces of host cells.
condensin, condensin complex
Complex of proteins involved in chromosome condensation prior to mitosis. Target for M-Cdk.
conjugated protein
A protein containing one or more prosthetic groups.
connexon
Water-filled pore in the plasma membrane formed by a ring of six connexin protein subunits. Half of a gap junction: connexons from two adjoining cells join to form a continuous channel through which ions and small molecules can pass.
Constitutive proteins
Proteins that are synthesized at all times.
constitutive secretory pathway
Pathway present in all cells by which molecules such as plasma membrane proteins are continually delivered to the plasma membrane from the Golgi apparatus in vesicles that fuse with the plasma membrane. The default route to the plasma membrane if no other sorting signals are present.
corepressor
A molecule that binds to a repressor protein, enabling the repressor to bind to an operator.
CTR1
Copper transport protein 1; a membrane bound copper-binding protein that imports copper into cells.
cyclin–Cdk complex
Protein complex formed periodically during the eukaryotic cell cycle as the level of a particular cyclin increases. A cyclin-dependent kinase (Cdk) then becomes partially activated.
cyclophilins
A family of prolylisomerases that affect protein folding, that also bind cyclosporin A to produce a complex that associates with calcineurin, preventing its activation by calmodulin.
De novo sequencing
Determination of a new protein sequence not previously described in data bases.
death effector domain (DED)
Protein-interaction domain originally discovered in proteins involved in programmed cell death or apoptosis. As part of the intracellular domains of some adaptor proteins, death domains are involved in transmitting pro-inflammatory and/or pro-apoptotic signals.
Denatured
The physical changes that occur in a protein when secondary and tertiary structures are disrupted.
denatured protein
A protein that has lost enough of its native conformation by exposure to a destabilizing agent such as heat or detergent that its function is lost.
dephosphorylation
The removal of a phosphate group from a molecule, usually a protein.
divalent metal transporter 1 (DMT1)
A protein on the small-intestinal absorptive surface that is responsible for the absorption of iron and copper in their inorganic forms.
Duchenne muscular dystrophy
A severe inherited muscle disease caused by defects of the structural protein dystrophin.
dynamic instability
Sudden conversion from growth to shrinkage, and vice versa, in a protein filament such as a microtubule or actin filament.
E3 ubiquitin ligase
Proteins or protein complexes that specifically link ubiquitin polypeptides to lysine residues of target proteins.
Ectomycorrhizins
Symbiosis related proteins unique to ectomycorrhizae.
effector Bcl2 family proteins
Pro-apoptotic proteins of the intrinsic pathway of apoptosis that in response to an apoptotic stimulus become activated and aggregate to form oligomers in the mitochondrial outer membrane, inducing the release of cytochrome c and other intermembrane proteins. Bax and Bak are the main effector Bcl2 family proteins in mammalian cells.
Electrospray ionization (ESI)
Ion source technique in mass spectrometers for ionization of biomacromolecules (e.g., petides and proteins) present in a liquid phase.
endosome maturation
Process by which early endosomes mature to late endosomes and endolysosomes; in the conversion process, the endosome membrane protein composition changes, the endosome moves from the cell periphery to close to the nucleus, and the endosome ceases to recycle material to the plasma membrane and irreversibly commits its remaining contents to degradation.
Epidermolysis bullosa
A group of inherited skin-blistering diseases caused by abnormalities of proteins in the dermal-epidermal junction.
ER resident protein
Protein that remains in the endoplasmic reticulum (ER) or its membranes and carries out its function there, as opposed to proteins that are present in the ER only in transit.
ESCRT protein complexes
Four protein complexes (ESCRT-0, ESCRT-1, ESCRT-2, and ESCRT-3) that act sequentially to shepherd mono-ubiquitylated membrane proteins on endosomal membranes into intralumenal vesicles. ESCRT-3 complex catalyzes the pinching-off reaction.
Extracellular signal-regulated kinases (ERKs)
Serine/ threonine kinases of the mitogen-activated protein (MAP) kinase family.
ferroportin
A membrane protein that transports iron from inside a cell to the outside.
Fibrillin
Protein in microfibrils that is defective in Marfan syndrome.
flagellin
A protein that is the major constituent of the flagellum, the tail-like structure used in bacterial locomotion. TLR-5 recognizes intact flagellin protein that has dissociated from the flagellum.
flippases
Membrane proteins in the ABC transporter family that catalyze the movement of phospholipids from the extracellular leaflet to the cytosolic leaflet of a membrane bilayer.
floppases
Membrane proteins in the ABC transporter family that catalyze movement of phospholipids from the cytosolic leaflet to the extracellular leaflet of a membrane bilayer.
fluorescence recovery after photobleaching (FRAP)
Technique for monitoring the kinetic parameters of a protein by analyzing how fluorescent protein molecules move into an area of the cell bleached by a beam of laser light.
Fluorescent proteins
Have intrinsic fluorescence properties by containing covalently bonded chromophores build-up by a tripeptide (Ser–Tyr–Gly); the first one (green fluorescent protein GFP) has been isolated from the jellyfish Aequorea victoria and exhibits bright green fluorescence when exposed to blue to ultraviolet light; nowadays a great variety of engineered GFP derivatives and fluorescent proteins of different families exist.
formin
Dimeric protein that nucleates the growth of straight, unbranched actin filaments that can be cross-linked by other proteins to form parallel bundles.
fractionation
The process of separating the proteins or other components of a complex molecular mixture into fractions based on differences in properties such as solubility, net charge, molecular weight, or function.
FRAP (fluorescence recovery after photobleaching)
A technique used to quantify the diffusion of membrane components (lipids or proteins) in the plane of the bilayer.
gated transport
Movement of proteins between the cytosol and the nucleus through nuclear pore complexes in the nuclear envelope that function as selective gates.
geminin
Protein that prevents the formation of new prereplicative complexes during S phase and mitosis, thus ensuring that the chromosomes are replicated only once in each cell cycle.
gluten-sensitive enteropathy
Sometimes referred to as celiac disease. Inflammation of the small intestine due to an autoimmune inflammatory disease precipitated by the ingestion of the wheat protein, gluten.
Gq
Class of G protein that couples GPCRs to phospholipase C-β to activate the inositol phospholipid signaling pathway.
GTP (guanosine 5′-triphosphate)
Nucleoside triphosphate produced by the phosphorylation of GDP (guanosine diphosphate). Like ATP, it releases a large amount of free energy on hydrolysis of its terminal phosphate group. Has a special role in microtubule assembly, protein synthesis, and cell signaling.
Heat shock proteins
Chaperones that are induced by heat exposure.
Heinz bodies
Abnormal protein aggregates in erythrocytes.
Helper virus
A virus that provides viral proteins needed for the reproduction of a coinfecting defective virus or subviral agents. (Chapter 12) .
heme carrier protein (hcp1)
A protein in the small intestine mucosal cells that transports a heme molecule from the gut lumen into an enterocyte.
heme protein
A protein containing a heme as a prosthetic group.
Hemopexin
A heme-binding protein in serum.
hephaestin
A copper-containing protein that transports iron from the mucosal cells of the small intestine to the
High-density lipoprotein
A protein-rich lipoprotein that transports cholesterol to the liver.
Hill coefficient
A measure of cooperative interaction between protein subunits.
HLA-DO
An invariant MHC class II molecule that binds HLA-DM, inhibiting the release of CLIP from MHC class II molecules in intracellular vesicles. A homologous protein in mice is called H-2O or H2-DO.
homeodomain
The protein domain encoded by the homeobox; a regulatory unit that determines the segmentation of a body plan.
homologous proteins
Proteins having similar sequences and functions in different species; for example, the hemoglobins.
IFIT (IFN-induced protein with tetratricoid repeats)
A small family of host proteins induced by interferons that regulate protein translation during infection in part by interactions with eIF3.
IFITM (interferon-induced transmembrane protein)
A small family of host transmembrane proteins induced by interferons that function in the cell’s vesicular compartment to restrain various steps in viral replication.
IKK
The IkB kinase, IKK, is a multisubunit protein complex composed of IKKα, IKKβ, and IKKγ (or NEMO).
Inducible proteins
Proteins whose synthesis is regulated.
inhibitors of apoptosis (IAPs)
Intracellular protein inhibitors of apoptosis.
inner nuclear membrane
One of two concentric membranes comprising the nuclear envelope; continuous with the outer nuclear membrane; contains specific proteins as anchoring sites for chromatin and the nuclear lamina.
integral proteins
Proteins firmly bound to a membrane by hydrophobic interactions; as distinct from peripheral proteins.
Intermediate filament
A type of cytoskeletal fiber formed from proteins in a coiled coil conformation.
intrinsically disordered proteins
Proteins, or segments of proteins, that lack a definable three-dimensional structure in solution.
invasin
A surface protein produced by Salmonella Typhimurium and Escherichia coli that rearranges nearby actin filaments in the cytoskeleton of a host cell.
ion pump
A protein that transports ions across a membrane at the expense of metabolic energy.
IRAK1, IRAK4
Protein kinases that are part of the intracellular signaling pathways leading from TLRs.
IREG1
A membrane protein that transports iron from inside a cell to the outside. Also known as ferroportin.
IRGM3
A protein that functions in the maintenance and storage of neutral lipid droplets in many types of cells in association with adipose differentiation related protein.
iron–sulfur cluster
Electron-transporting group consisting of either two or four iron atoms bound to an equal number of sulfur atoms, found in a class of electron-transport proteins.
Isobaric tags for relative and absolute quantitation (iTRAQ)
Chemical labels with different masses for protein quantification in tandem mass spectrometry.
Isotope-coded affinity tags (ICAT)
Chemical labels containing 2H or 13C isotopes for protein quantification in mass spectrometry.
keratinization
(ker′ă-tin-i- zā′shŭn) Process during which keratinocytes fill with the protein keratin.
kinase cascade
Intracellular signaling pathway in which one protein kinase, activated by phosphorylation, phosphorylates the next protein kinase in the sequence, and so on, relaying the signal onward.
kinesin
Member of one of the two main classes of motor proteins that use the energy of ATP hydrolysis to move along microtubules.
kinesin-1
Motor protein associated with microtubules that transports cargo within the cell; also called “conventional kinesin.”
Klotho
A protein that works in tandem with FGF23 in lowering serum phosphate levels when elevated.
Kostmann’s disease
A form of severe congenital neutropenia, an inherited condition in which the neutrophil count is low. In Kostmann’s disease, this is due to a deficiency of the mitochondrial protein HAX1, which leads to apoptosis of developing myeloid cells and persistent neutropenia.
lactoferrin
One of several human iron-binding proteins that reduce iron available to a pathogen.
Lamin
A type of intermediate filament protein in the nucleus.
linker for activation of T cells
A cytoplasmic adaptor protein with several tyrosines that become phosphorylated by the tyrosine kinase ZAP-70. It helps to coordinate downstream signaling events in T-cell activation.
LIP10
A cleaved fragment of invariant chain retaining the transmembrane segments that remains bound to MHC class II proteins and helps target the complex to the endosome.
macrolide
An antibiotic that inhibits protein synthesis; for example, erythromycin.
MAdCAM-1
Mucosal cell-adhesion molecule-1. A mucosal addressin that is recognized by the lymphocyte surface proteins L-selectin and VLA-4, enabling the specific homing of lymphocytes to mucosal tissues.
major basic protein
Protein released by activated eosinophils that acts on mast cells and basophils to cause their degranulation.
MAL
An adaptor protein that associates with MyD88 in signaling by TLR‑2/1, TLR-2/6, and TLR-4.
MAP kinase module (mitogen-activated protein kinase module)
An intracellular signaling module composed of three protein kinases, acting in sequence, with MAP kinase as the third. Typically activated by a Ras protein in response to extracellular signals.
Marfan syndrome
Dominantly inherited disorder caused by abnormalities of the connective tissue protein fibrillin.
marginal zone B cells
A unique population of B cells found in the spleen marginal zones; they do not circulate and are distinguished from conventional B cells by a distinct set of surface proteins.
MAVS (mitochondrial antiviral signaling protein)
A CARD-containing adaptor protein attached to the outer mitochondrial membrane that signals downstream of RIG-I and MDA-5 to activate IRF3 and NFκB in response to viral infection.
MD-2
Accessory protein for TLR-4 activity.
Mdm2
A protein that inactivates the p53 protein.
Mediator
A large nuclear protein complex involved in transcriptional regulation.
membrane attack complex (MAC)
Complement proteins C5–C9, which together make lesions in cell membranes that lead to cell death.
membrane differentiation
A dense accumulation of protein adjacent to and within the membrane on either side of a synaptic cleft.
membrane protein
Amphiphilic protein of diverse structure and function that associates with the lipid bilayer of cell membranes.
membrane transport
Movement of a polar solute across a membrane via a specific membrane protein (a transporter).
membrane transport protein
Membrane protein that mediates the passage of ions or molecules across a membrane. The two main classes are transporters (also called carriers or permeases) and channels.
membrane-associated protein
Membrane protein not extending into the hydrophobic interior of the lipid bilayer but bound to either face of the membrane by noncovalent interactions with other membrane proteins.
membrane-attack complex (MAC)
Protein complex composed of C5b to C9 that assembles a membrane-spanning hydrophilic pore on pathogen surfaces, causing cell lysis.
membrane-bending proteins
Attach to specific membrane regions as needed and act to control local membrane curvature and thus confer on membranes their characteristic threedimensional shapes.
membrane-bound ribosome
Ribosome attached to the cytosolic face of the endoplasmic reticulum. The site of synthesis of proteins that enter the endoplasmic reticulum.
Membrane-spanning domain
A segment of an integral membrane protein that spans the lipid bilayer; often -helical. (Chapters 2 and 4)
metalloprotein
A protein with a metal ion as its prosthetic group.
MIC-A, MIC-B
MHC class Ib proteins that are induced by stress, infection, or transformation in many cell types and are recognized by NKG2D.
microtubule-associated protein (MAP)
Any protein that binds to microtubules and modifies their properties. Many different kinds have been found, including structural proteins, such as MAP2, and motor proteins, such as dynein. [Not to be confused with the “MAP” (mitogen-activated protein kinase) of “MAP kinase.”]
mitochondrial hsp70
Part of a multisubunit protein assembly bound to the matrix side of the TIM23 complex that acts as a motor to pull mitochondrial precursor proteins into the matrix space.
mitochondrial precursor proteins
Proteins first fully synthesized in the cytosol and then translocated into mitochondrial subcompartments as directed by one or more signal sequences.
mobiloferrin
A cytoplasmic protein in cells that is capable of binding and transporting iron.
molecular switch hypothesis
The idea that protein kinases can be switched “on” by autophosphorylation to a state in which they no longer require the presence of a specific second messenger to be active. Such persistently active kinases may hold the memory of an episode of strong synaptic activation. Initially proposed by John Lisman at Brandeis University.
motif
Any distinct folding pattern for elements of secondary structure, observed in one or more proteins. A motif can be simple or complex, and can represent all or just a small part of a polypeptide chain. Also called a fold or supersecondary structure.
motor protein
Protein that uses energy derived from nucleoside triphosphate hydrolysis to propel itself along a linear track (protein filament or other polymeric molecule).
MSH2, MSH6
Mismatch repair proteins that detect uridine and recruit nucleases to remove the damaged and several adjacent nucleotides.
mTORC1, mTORC2
Active complexes of mTOR formed with the regulatory proteins Raptor and Rictor, respectively.
mucus
Sticky solution of proteins (mucins) secreted by goblet cells of internal epithelia, forming a protective layer on the epithelial surface.
multipass transmembrane protein
Membrane protein in which the polypeptide chain crosses the lipid bilayer more than once.
Mx (myxoma resistant) proteins
Interferon-inducible proteins required for cellular resistance to influenza virus replication.
MyD88
An adaptor protein that functions in signaling by all TLR proteins except TLR3.
myofilament
(mı̄-ō-fil′ă-ment) A protein filament that makes up the myofibrils in both skeletal and cardiac muscle cells.
Myosin light-chain kinase
A calcium-calmodulin activated protein kinase that induces contraction in smooth muscle.
Na+-K+ pump (Na+-K+ ATPase)
Transmembrane carrier protein found in the plasma membrane of most animal cells that pumps Na+ out of and K+ into the cell, using energy derived from ATP hydrolysis.
NAIP2
An NLR protein that, together with NLRC4, recognizes the PrgJ protein of the Salmonella typhimurium type III injection system to activate an inflammasome pathway in response to infection.
negative cooperativity
A property of some multisubunit enzymes or proteins in which binding of a ligand or substrate to one subunit impairs binding to another subunit. negative feedback Regulation of a biochemical pathway in which a reaction product inhibits an earlier step in the pathway.
Nephrotic syndrome
A type of kidney disease with massive proteinuria.
neurofibril
(nūr-o-fi′bril) Filamentous protein structure in a neuron composed of neurofilaments and microtubules.
neuronal membrane
The barrier, about 5 nm thick, that separates the inside of a nerve cell from the outside; consists of a phospholipid bilayer with proteins embedded in it; encloses the intracellular organelles and vesicles.
Niemann-Pick C1-Like 1 (NPC1L1)
Refers to a protein on the brush border of the small intestine enterocyte that is thought to be responsible for cholesterol absorption. It is also thought to be present in hepatocytes.
nitrogen balance method
A method to determine the minimum amount of dietary protein needed to keep a subject in nitrogen equilibrium.
NOD subfamily
A subgroup of NLR proteins that contain a CARD domain which is used for activation of downstream signaling.
Non-invasive methods
Originally defined as a medical procedure in which no break in the skin is created; in cell-biology this term is used for visualization of intact and living cells/tissues/organs by use of fluorescent proteins or dyes.
nonclassical cadherins
Large family of cadherins that are more distantly related in sequence than classical cadherins and include proteins involved in adhesion (including protocadherins, desmocollins, and desmogleins) and signaling.
Nonhistone chromosomal proteins
All of the proteins in chromosomes except the histones.
nuclear lamin
Protein subunit of the intermediate filaments that form the nuclear lamina.
nuclear lamina
Fibrous meshwork of proteins on the inner surface of the inner nuclear membrane. It is made up of a network of intermediate filaments formed from nuclear lamins.
nucleoporin
Any of a number of different proteins that make up nuclear pore complexes.
nucleotide-binding oligomerization domain (NOD)
A type of conserved domain originally recognized in ATP-binding cassette (ABC) transporters present present in a large number of proteins, but which also mediates protein homooligomerization.
oligomeric protein
A multisubunit protein having two or more identical polypeptide chains.
Oligomerization
Association of polypeptide chains, which may be the same or different, to form a protein with multiple subunits. (Chapter 8)
Opa
A bacterial outer membrane protein; cells with Opa form opaque colonies.
OXA complex
Protein translocator in the inner mitochondrial membrane that mediates insertion of inner membrane proteins.
P-selectin glycoprotein ligand-1 (PSGL-1)
Protein expressed by activated effector T cells that is a ligand for P-selectin on endothelial cells, and may enable activated T cells to enter all tissues in small numbers.
P-type pumps
A class of ATP-driven pumps comprising structurally and functionally related multipass transmembrane proteins that phosphorylate themselves during the pumping cycle. The class includes many of the ion pumps responsible for setting up and maintaining gradients of Na+, K+, H+, and Ca2+ across cell membranes.
Patched
Transmembrane protein predicted to cross the plasma membrane 12 times; much is in intracellular vesicles and some is on the cell surface where it binds the Hedgehog protein.
PDZ domain
Protein-binding domain present in many scaffold proteins, and often used as a docking site for intracellular tails of transmembrane proteins.
pentraxin
A family of acute-phase proteins formed of five identical subunits, to which C-reactive protein and serum amyloid protein belong. pepsin A protease that cleaves several sites on the carboxy-terminal side of the disulfide linkages, producing the F(abʹ)2 fragment and several fragments of the Fc region.
perforin
Protein that makes a pore in a target cell membrane, released by cytotoxic T lymphocytes.
peroxins
Form a protein translocator that participates in the import of proteins into peroxisomes.
Pertussis toxin
A toxin produced by Bordetella pertussis; causes cyclic AMP accumulation by inactivation of the Gi protein.
phase variation
The random switching of phenotype and expression of proteins involved in infection at frequencies much higher than mutation rates.
Phosphoprotein
A protein containing covalently bound phosphate.
Phosphorylase kinase
A protein kinase that phosphorylates glycogen phosphorylase.
Pin-formed (PIN)-proteins
A family of membraneintegral auxin efflux carriers that mediate the efflux of auxin from cells to only one side thereby causing the directional distribution of auxins through tissues.
pleckstrin homology domain (PH domain)
Protein domain found in some intracellular signaling proteins. Some PH domains in intracellular signaling proteins bind to phosphatidylinositol 3,4,5-trisphosphate produced by PI 3-kinase, bringing the signaling protein to the plasma membrane when PI 3-kinase is activated.
polygenic
Containing several separate loci encoding proteins of identical function; applied to the MHC. Cf. polymorphic.
Polyubiquitylation
Addition of three or more ubiquitin polypeptides to lysine residues of target proteins; polyubiquitylation very often targets proteins to degradation in the proteasome.
PorA
Outer membrane protein of Neisseria meningitidis that binds C4BP, thereby inactivating C3b deposited on its surface.
positive cooperativity
A property of some multisubunit enzymes or proteins in which binding of a ligand or substrate to one subunit facilitates binding to another subunit.
Posttranslational processing
Chemical modification of proteins.
PrgJ
A protein component of the Salmonella typhimurium type III secretion system inner rod used by the bacterium to infect eukaryotic cells. This protein is detected by NLR proteins NAIP2 and NLRC4.
primary cilium
Short, single, nonmotile cilium lacking dynein that arises from a centriole and projects from the surface of many animal cell types. Some signaling proteins are concentrated in the primary cilium.
prion disease
Transmissible spongiform encephalopathy— such as Kuru and Creutzfeldt–Jakob disease (CJD) in humans, scrapie in sheep, and bovine spongiform encephalopathy (BSE, or “mad cow disease”) in cows—that is caused and transmitted by an infectious, abnormally folded protein (prion).
profilin
An actin-binding protein that sequesters monomeric actin. Protozoan profilins contain sequences recognized by TLR-11 and TLR-12.
Protamines
Small basic proteins that replace the histones in the chromosomes of some sperm cells.
protein activity control
The selective activation, inactivation, degradation, or compartmentalization of specific proteins after they have been made. One of the means by which a cell controls which proteins are active at a given time or location in the cell.
Protein Data Bank
A worldwide online repository of X-ray and NMR structural data for biological macromolecules. To access the Protein Data Bank, go to http://www.rcsb.org/pdb/.
protein efficiency ratio (PER)
A method of evaluating protein quality by the weight gain of a growing animal in relation to its protein intake when energy is ample and a protein source is fed at an adequate level.
Protein kinase G
The cyclic GMP-activated protein kinase.
Protein NMR
Nuclear magnetic resonance spectroscopy of proteins for the determination of the three-dimensional protein structure requiring aqueous solutions of highly purified proteins.
protein structure
One of the four basic structures that the polypeptide chains of proteins assume to achieve their intended function: primary, secondary, tertiary, and quaternary.
protein subunit
An individual protein chain in a protein composed of more than one chain.
protein targeting
The process by which newly synthesized proteins are sorted and transported to their proper locations in the cell.
protein translocation
Process of moving a protein across a membrane.
protein translocator
Membrane-bound protein that mediates the transport of another protein across a membrane.
protein-interaction domains, protein-interaction modules
Protein domains, usually with no enzymatic activity themselves, that have binding specificity for particular sites (such as phosphorylated tyrosines, proline-rich regions, or membrane phospholipids) on other proteins or cellular structures.
Proton-coupled folate transporter (PCFT)
A large intestine transport protein for folate absorption.
pyogenic arthritis, pyoderma gangrenosum, and acne (PAPA)
Autoinflammatory syndrome that is caused by mutations in a protein that interacts with pyrin.
pyrin
One of several protein interaction domains, structurally related to but distinct from CARD, TIR, DD, and DED domains.
Rab effectors
Molecules that bind activated, membranebound Rab proteins and act as downstream mediators of vesicle transport, membrane tethering, and fusion.
Rab proteins
Monomeric GTPase in the Ras superfamily present in plasma and organelle membranes in its GTP-bound state, and as a soluble cytosolic protein in its GDP-bound state. Involved in conferring specificity on vesicle docking.
Rab proteins into
Rab domains on membranes, which changes the identity of an organelle and reassigns membrane dynamics.
RAET1
A family of 10 MHC class Ib proteins that are ligands for NKG2D, and includes several UL16-binding proteins (ULBPs).
Raf
A protein kinase in the Raf–MEK1–Erk signaling cascade that is the first protein kinase in the pathway, and is activated by the small GTPase Ras.
Ran (Ran protein)
Monomeric GTPase of the Ras superfamily present in both cytosol and nucleus. Required for the active transport of macromolecules into and out of the nucleus through nuclear pore complexes.
random coil
A section of a protein’s secondary structure that has less regular patterns than alpha-helixes or beta-pleated sheets.
Ras superfamily
Large superfamily of monomeric GTPases (also called small GTP-binding proteins) of which Ras is the prototypical member.
Ras superfamily of G proteins
Small (Mr ~20,000), monomeric guanosine nucleotide– binding proteins that regulate signaling and membrane trafficking pathways. Inactive with GDP bound, they are activated by displacement of GDP by GTP, then inactivated by their intrinsic GTPase. Also called small G proteins.
Ras-GAPs
Ras GTPase-activating proteins; increase the rate of hydrolysis of bound GTP by Ras, thereby inactivating Ras.
Receiver domain proteins
Proteins that function as downstream components of two-component signaling systems; protein activity is regulated by the transfer of a phosphate residue from histidine kinase sensor proteins to an aspartate residue of the receiver domain.
reference protein
A high-quality protein, such as milk or egg, that is used to compare the quality of other proteins.
RegIIIγ
An antimicrobial protein of the C-type lectin family, produced by Paneth cells in the gut in mice.
regulatory cascade
A multistep regulatory pathway in which a signal leads to activation of a series of proteins in succession, with each protein in the succession catalytically activating the next, such that the original signal is amplified exponentially.
reticular fibers
Proteins that form a flexible network in tissues; found in some connective tissues.
Retinol-binding protein
A plasma protein that carries retinol from the liver to other tissues.
retrotranslocation complex
The return of endoplasmic reticulum proteins to the cytosol.
Rett syndrome
A neurodevelopmental disorder caused by mutations in a methylcytosine-binding protein.
RFVT1, RFVT2, RFVT3
different intestinal riboflavin transport proteins.
Ribbon diagram
Display of the three-dimensional protein structure with structural parts (α-helices and β-sheets) of the secondary structure.
S-protein (vitronectin)
Plasma protein that binds incompletely formed MAC complexes, such as C5b67, preventing bystander complement damage to host membranes.
SAM complex
Protein translocator that helps β-barrel proteins to fold properly in the outer mitochondrial membrane.
Sar1 protein
Monomeric GTPase responsible for regulating COPII coat assembly at the endoplasmic reticulum membrane.
Scaffold
The central core structure of condensed chromosomes. The scaffold is composed of nonhistone chromosomal proteins.
SCF complex
A class of E3 ubiquitin ligase complexes that consists of a CULLIN1 backbone, a small RING-box protein, an adaptor protein, and an F-box protein; the F-box protein mediates specific recognition of target proteins.
scramblases
Membrane proteins that catalyze the movement of phospholipids across the membrane bilayer, leading to uniform distribution of a lipid between the two membrane leaflets.
Secretion
The release of proteins or other molecules from the cell by the fusion of cargo-vesicles with the plasma membrane; also an important step for the insertion of integral membrane proteins into the plasma membrane.
secretion system
Specialized bacterial systems that secrete effector proteins that interact with host cells.
securin
Protein that binds to the protease separase and thereby prevents its cleavage of the protein linkages that hold sister chromatids together in early mitosis. Securin is destroyed at the metaphase-to-anaphase transition.
selenoprotein P
A selenium containing protein that transports and stores selenium and is thought to function as an antioxidant. It appears to be involved in selenium homeostasis in both brain and testes.
Selenoprotein W
A selenium containing protein that is critical in preventing certain muscle disease in cattle and sheep.
separase
Protease that cleaves the cohesin protein linkages that hold sister chromatids together. Acts at anaphase, enabling chromatid separation and segregation.
serine protease inhibitor (serpin)
Class of proteins that inhibit various proteases, originally referring to those specific to serine proteases.
SHP (SH2-containing phosphatase)
An SH2-containing protein phosphatase.
signal patch
Protein-sorting signal that consists of a specific three-dimensional arrangement of atoms on the folded protein’s surface.
single-pass transmembrane protein
Membrane protein in which the polypeptide chain crosses the lipid bilayer only once.
Slit
Signal protein, secreted by cells of the neural tube floor plate, responsible for repelling the growth cones of commissural axons after they have crossed the midline, thereby ensuring these neurons do not re-cross the midline.
small G proteins
Single-subunit G proteins, such as Ras, that act as intracellular signaling molecules downstream of many transmembrane signaling events. Also called small GTPases.
SNARE proteins (SNAREs)
Members of a large family of transmembrane proteins present in organelle membranes and the vesicles derived from them. SNAREs catalyze the many membrane fusion events in cells. They exist in pairs—a v-SNARE in the vesicle membrane that binds specifically to a complementary t-SNARE in the target membrane.
sodium dodecyl sulfate polyacrylamide-gel electrophoresis (SDS-PAGE)
Type of electrophoresis used to separate proteins by size. The protein mixture to be separated is first treated with a powerful negatively charged detergent (SDS) and with a reducing agent (β-mercaptoethanol), before being run through a polyacrylamide gel. The detergent and reducing agent unfold the proteins, free them from association with other molecules, and separate the polypeptide subunits.
sorting signal
Signal sequence or signal patch that directs the delivery of a protein to a specific location, such as a particular intracellular compartment.
Spongiform encephalopathies
Rapidly progressive neurodegenerative diseases caused by misfolded prion protein.
SREBP cleavage-activating system (SCAP)
A protein located in the endoplasmic reticulum that responds to cell cholesterol levels. When cell cholesterol levels decline, SCAP will escort SREBP to the cell nucleus in order to enhance expression of enzymes involved with cholesterol biosynthesis.
staphylococcal complement inhibitor (SCIN)
Staphylococcal protein that inhibits the activity of the classical and alternative C3 convertases, promoting the evasion of destruction by complement.
STIM1
A transmembrane protein that acts as a Ca2+ sensor in the endoplasmic reticulum. When Ca2+ is depleted from the endoplasmic reticulum, STIM1 is activated and induces opening of plasma membrane CRAC channels.
storage vesicle
Organelles that form from the Golgi complex; contain proteins made in the rough ER and processed in the Golgi complex.
Streptokinase
A plasmin-activating bacterial protein.
surfactant proteins A and D (SP-A and SP-D)
Acute-phase proteins that help protect the epithelial surfaces of the lung against infection.
symporter
Carrier protein that transports two types of solute across the membrane in the same direction.
talin
An intracellular protein involved in the linkage of activated integrins, such as LFA-1, to the cytoskeleton to allow changes in cellular motility and migration, such as in the diapedesis of neutrophils across the vascular endothelium.
Tannins
Secondary metabolites with several phenolic OH-groups that can form hydrogen- and ionic bonds with proteins thereby altering their conformation; distinguished are gallotannins and catechol tannins which derive from catechin or epicatechin.
tapasin
TAP-associated protein. A key molecule in the assembly of MHC class I molecules; a cell deficient in this protein has only unstable MHC class I molecules on the cell surface.
Thrombomodulin
An anticoagulant protein on endothelial cells.
THTR1, THTR2
Small intestinal transport proteins for thiamin.
thylakoid membrane
Chloroplast membrane system that contains the large membrane protein complexes for photosynthesis and photophosphorylation.
thyroglobin
The storage form of iodine, in which iodine is incorporated into the globulin protein.
TIM complexes
Protein translocators in the mitochondrial inner membrane. The TIM23 complex mediates the transport of proteins into the matrix and the insertion of some proteins into the inner membrane; the TIM22 complex mediates the insertion of a subgroup of proteins into the inner membrane.
TOM complex
Multisubunit protein complex that transports proteins across the mitochondrial outer membrane.
TOR
Large, serine/threonine protein kinase that is activated by the PI-3-kinase–Akt signaling pathway and promotes cell growth.
TRAM
An adaptor protein that pairs with TRIF in signaling by TLR-4. transcytosis The active transport of molecules, such as secreted IgA, through epithelial cells from one face to the other.
trans Golgi network (TGN)
Network of interconnected tubular and cisternal structures closely associated with the trans face of the Golgi apparatus and the compartment from which proteins and lipids exit the Golgi, bound for the cell surface or another compartment.
Transcortin
A cortisol-binding protein in plasma.
transfer vesicle
Membrane-bound sacs that move proteins from the Golgi complex to specific areas in the cell.
Transmembrane helix
A membrane-spanning, hydrophobic α-helix in integral membrane proteins.
transporter ZIP4
A protein in the mucosal cells of the small intestine that transports zinc from the gut lumen into an enterocyte.
Transthyretin (“Prealbumin”)
A plasma protein that binds thyroxine and retinol-binding protein.
treadmilling
Process by which a polymeric protein filament is maintained at constant length by addition of protein subunits at one end and loss of subunits at the other.
TRIF
An adaptor protein that alone is involved in signaling by TLR-3, and that when paired with TRAM, functions in signaling by TLR-4.
TRPM7
A magnesium channel protein that is expressed ubiquitiously on most cells for magnesium absorption. It is similar to TRPM6.
TSC
Protein complex that acts as a GTPase-activating protein (GAP) for Rheb in its non-phosphorylated state. TSC is inactivated when phosphorylated by Akt.
Two-component sensor
Histidine kinases that carry protein modules regulating phosphate transfer rates on the binding of small molecules or light-absorption by attached chromophors.
type IV collagen
An essential component of mature basal laminae consisting of three long protein chains twisted into a ropelike superhelix with multiple bends. Separate molecules assemble into a flexible, felt-like network that gives the basal lamina tensile strength.
ubiquitin–proteasome system (UPS)
A quality control system in the cell that involves K48-linked ubiquitination of target proteins that are then recognized by the proteasome for degradation.
ubiquitination
The process of attachment of one or many subunits of ubiquitin to a target protein, which can mediate either degradation by the proteasome, or formation of scaffolds used for signaling, depending on the nature of the linkages.
UNC93B1
A mutlipass transmembrane protein that is necessary for the normal transport of TLR-3, TLR-7, and TLR-9 from the ER, where they are assembled, to the endosome, where they function.
uniporter
Carrier protein that transports a single solute from one side of the membrane to the other.
vectorial
Describes an enzymatic reaction or transport process in which the protein has a specific orientation in a biological membrane such that the substrate is moved from one side of the membrane to the other as it is converted into product.
vesicle transport model
One hypothesis for how the Golgi apparatus achieves and maintains its polarized structure and how molecules move from one cisterna to another. This model holds that Golgi cisternae are long-lived structures that retain their characteristic set of Golgi-resident proteins firmly in place, and cargo proteins are transported from one cisterna to the next by transport vesicles.
vesicular transport
Transport of proteins from one cell compartment to another by means of membrane-bounded intermediaries such as vesicles or organelle fragments.
Viroporin
Hydrophobic viral protein that forms pores in cellular membranes; many facilitate release of progeny virus particles. ( Chapter 13)
Virtual screening
Computational methods for iterative docking of chemical compounds into a chosen site in a protein target to identify drug leads. (Chapter 9)
voltage-gated calcium channel
A membrane protein forming a pore that is permeable to Ca²⁺ and gated by depolarization of the membrane.
voltage-gated sodium channel
A membrane protein forming a pore that is permeable to Na+ and gated by depolarization of the membrane.
Western blot
The transfer of proteins from an electrophoretic gel to a cellulose or nylon membrane by means of an electric force.
Zeitlupe-like proteins
Family of blue/UV-A light photoreceptors that use a LOV domain as light sensor module; function as components of SCF E3 ubiquitin ligase complexes that regulate photoperiodic flowering and entrainment of the endogenous clock.
α-Fetoprotein
A fetal plasma protein, levels of which are elevated in serum of patients with liver cancer and in amniotic fluid if the fetus has an open neural tube defect.
β conformation
An extended, zigzag arrangement of a polypeptide chain; a common secondary structure in proteins.
β2-microglobulin
The light chain of the MHC class I proteins, encoded outside the MHC. It binds noncovalently to the heavy or α chain.
γ-tubulin ring complex (γ-TuRC)
Protein complex containing γ-tubulin and other proteins that is an efficient nucleator of microtubules and caps their minus ends.
