Lecture 2 Reading Flashcards
What determines the folding of a protein chain?
Weak noncovalent Bonds
H bonds, electrostatic attractions, van der waals attractions. The combined strength of these bonds determines stability of folded shape.
Polypeptide backbone
Repeating sequence of atoms along the core of the polypeptide chain. Attached to repetitive chain are side chains.
Hydrophobic clustering force
Has a central role in determining shape of protein. Distribution of polar and nonpolar amino acids. Nonpolar cluster in interior.
How do most proteins fold up
Into one stable conformation that can change slightly when the protein interacts with other molecules in the cell.
Molecular chaperones
Assist in protein folding. Bind to partly folded polypeptide chains and help them progress along most energetically favorable folding pathway.
Protein domains
Structural units that fold more or less independently of each other
Common folding patterns
Alpha helix and beta sheet
Coiled coil
Stable alpha helix structure, firms when two alpha helices have most of their nonpolar side chains on one side, so they can twist around each other with three side chains facing inward
Different functions of domains
Signaling pathways
Regulation
Why do so many proteins form stable conformations
Natural selection
What makes up protein families
Each family member has an amino acid sequence and a 3d conformation that resembles those of other family members
Protein folds
Ways in proteins fold up in nature
Domain shuffling
Many large proteins have evolved through the joining of oreexsiting domains in new combinations
Protein modules
A subset of protein domains with versatile structures
Protein modules built from
Stable core structure formed from strands of beta sheets
Multi domain proteins
Have more than one domain
Binding site
Any region of a proteins surface that can interact with another molecule thorough sets of noncovalent bonds
Globular proteins
Chain folds up into ball
Fibrous proteins
Have simple, elongated three d structures
Intermediate filaments
Component of cytoskeleton
Disordered polypeptide chains
Rubber elastic mesh work that allows for flexibility of skin, for example
What do disordered regions do
Form binding sites
Tether protein domains
Restrict diffusion
Disulfide bonds
Disulfide structures. Act as atomic staples rot reinforce favored conformation
Advantages of using small subunits to build larger structures
Needs only small amt of genetic info
Assembly and disassembly readily controlled
Synthesis errors avoided more frequently
Rings, tubes and spheres add
Stability
Two categories of protein interaction with amino acid side chains
Restricting access to water
Altering reactivity of amino acids
Why is regulating water access important?
Water molecules form hydrogen bonds that can compete with ligands for sites on protein surface. A ligand will form tighter h bonds and electrostatic interactions with a protein if water molecules are kept away.
How can clustering of neighboring polar amino acid chains alter the reactivity if these amino acids?
If protein folding forces together a bunch of negative side chains against their will, this will make a more attractive site for something that is positively charged. Amino acid chains that are normally not reactive will become reactive when they interact with one another through h bonds, so they can make or break covalent bonds
What does chemical reactivity of protein surface depend on?
Which amino acid side chains are exposed
Their exact orientation to one another
Evolutionary tracing purpose
Identify sites in a protein’s domain that are most crucial to the domain’s function.
Evolutionary tracing method
Amino acids that are unchanged, or nearly unchanged, when all of the known family members are mapped onto a model of the three d structure of one family member. Most invariant positions often cluster on protein surface. Cluster generally corresponds to binding site.
Types of protein-protein interfaces
Surface-string interaction
Coiled -coil
Surface-surface
Surface-string interaction
Portion of surface of protein contacts an extended loop of polypeptide chain on a second protein
Coiled-coil
When two alpha helices, one from each protein pair together. Seen in gene regulatory proteins
Surface-surface interactions
Precise matching of one rigid surface to another. Extremely specific.
Antibodies
Immunoglobulins, produced by immune system in response to foreign molecules, bind to target molecules, either inactivate molecule or mark it for destruction.
Equilibrium constant (k)
Calculates strength of binding
How does phosphorylation affect a protein?
Conformational change
Affect bindings, changing activity
Form part of structure that binding sites recognize
When are phosphate groups added or removed ?
In response to signals that specify change in a cells state.
What does protein phosphorylation involve
Enzyme catalyzed transfer of terminal phosphate group of ATP molecule to hydroxy ply group in do serine , threonine, or tyrosine side chains of the proteins
Protein kinase
Catalyzes phosphorylation
Protein phosphatase
Catalyzes the reverse reaction of phosphate removal, or de phosphorylation.
How are phosphates useful?
They activate and deactivate protein processes
How does a kinase work?
It transfers a phosphate group from an ATP molecule to an amino acid side chain of a target protein
How do GTP-binding proteins work?
Phosphate is not attached directly to protein. It’s par of a guanine nucleotide GTP. This binds tightly to a class of proteins known as GTP-binding proteins. Proteins regulated in this way are in their active conformations with GTP bound. Loss of phosphate group when bound GTP is hydrolyzed to GDPin a reaction catalyzed by protein itself. In its GDP bonus state protein is inactive. Aka as GTPases.
GTPase activating protein
Regulatory protein that controls whether GTP or GDP is bound. GAP will bind to a protein and induce it to hydrolyzed its bound GTP
Guanine nucleotide exchange factor
Binds to GDP bound protein and causes it to release its GDP. Site is immediately filled by GTP. Activates protein.
Proteomics
Research focused on the analysis of large sets of proteins
