Lecture 13 Flashcards
Helix-Turn-Helix
- motif
- two small helices connected by a turn
- DNA binding-structure
- common to the group of small proteins called transcription factors which are involved in the transcription of genetic information
Transcription factors
- involved in the transcription of genetic information
- Bind the major groove of DNA thereby either activating or suppressing the transcription of an adjacent gene
HTH structure details
- HTH assembly is held together by dispersion forces
- Most H-bonds maintain the two helices, but the cross-helix gln-gln interaction makes a strong contribution to the structure
- The turn is ALWAYS a short segment and always contains at least one gly (the smallest and most flexible AA)
Calmodulin
- Calcium sensing and signaling protein that consists of 7 alpha helices
- Shape changes dramatically when Ca2+ binds; forming 2 hydrophobic clefts that allows calmodulin to bind to a range of other calcium processing proteins
- binds Ca2+ in specific HTH known as EF hand
four helix bundles
- Domain
- helices cross one another at angles ~20º which allows R groups to mesh together efficiently
- Alpha helices are often amphipathic
- Four helix bundles align together to give a hydrophobic core
The Globin Fold
More complex arrangement of alpha helices
-usually consists of several helices packed against each other with larger angles, ~50º and ~90º so helices form a hydrophobic packer for the heme active site
Greek Key
Consists of four antiparallel beta strands and the loops that connect them
- strands 1,2,3 connected by hairpin turns
- strand four connected by a longer loop
- resembles greek art
beta-alpha-beta motif
- basically two parallel beta strands with an alpha helix in the middle
- almost always right handed crossover loop
- stabilized by a hydrophobic core
The Rossman Fold
-A motif often found in nucleic acid binding proteins
beta-alpha-beta-alpha-beta
The beta barrel
- antiparallel beta are often arranged as two beta sheets that stack against each other to form a distorted barrel structure
- several structural variations of beta barrels
beta meander
Simple set of 2 or more antiparallel beta strands connected by hairpin turns
Omega loop
A catch all term for a loop of several residues that has no specific internal hydrogen bonding
Domains
- segment of a polypeptide that can fold, function, and evolve independently of the rest of the protein
- each has its own characteristic tertiary structure
- one domain may appear in several different proteins
- vary from 25-500 AA’s
Porins
membrane protein that allow movement of solutes in and out of cells
Fibrous proteins
Structural molecules used for muscle fiber, bone matrix, tendons and connective tissue
- found only in animals
- usually insoluble in water
- includes keratin, collagen, and fibroin
Fibroin
-Fibrous protein that forms silk
Keratins
- fibrous protein
- hair skin and nails
Collagen
Fibrous protein that basically is what holds an animal together
Membrane proteins
Span the lipid bilayer and have several major functions including transport of molecules across the membrane, enzymatic activity, signal transduction and cell-cell recognition
-usually bundles of alpha helices with hydrophobic exterior surfaces
Globular proteins
Act as catalysts, messengers, transporters, and regulators
- approximately spherical in shape, important for keeping proteins in solution by maximizing hydrogen bonding to water
- hemoglobin is a globular protein
