Chapter 3 - Proteins

Test Your Knowledge About Basic Protein Structure Name one polar and one nonpolar amino acid, then make a list of all the additional amino acids that you remember. What are the four weak (noncovalent) interactions that determine the conformation of a protein? (True/False) A protein is at a near entropy minimum (point of lowest disorder, or greatest order) when it is completely stretched out like a string and when it is properly folded up. Explain. (True/False) Loops of polypeptide that protrude from the surface of a protein often form the binding sites for other molecules. Explain. (True/False) For a family of related genes that do not match genes of known function in the sequence database, it should be possible to deduce their function using “evolutionary tracing” to see where conserved amino acids cluster on their surfaces. Explain.

Also Pro, Phe, Met, Trp, Gly, Cys

Reactions that promote protein folding

Adapted from L. Wu et al. , 1995, Nature Struc. Biol Adapted from L. Wu et al., 1995, Nature Struc. Biol. 2:281; courtesy of J. Harris and P. S. Kim

Molecular chaperones Chaperones Video – chaperone-aided protein folding

Average length ≈ 10 residues ≈ 15 Å. Minimum length = 4 residues: how many H-bonds? Maximum length = 40 residues.

Pleated - look edge-on Strands ~ 5 Å apart Note direction of H-bonds will differ in anti-parallel & mixed sheets

Loops & Turns Connect secondary structural elements. Loops often carry the functional groups. Hairpin turns: Shortest possible loops (2 residues). Gly often in tight turns.

Motifs (protein folds) Domains/Modules Beta-Hairpins I Beta-Hairpins II Beta Corners Beta Barrels Helix Hairpins Alpha-Alpha Corners E-F Hand Helix-Turn-Helix Beta-Alpha-Beta Motifs Greek Key Motifs Most domains can be classified into a smaller number of "folds". Many domains are not unique to the proteins produced by one gene or one gene family but instead appear in a variety of proteins. The domains found most commonly are often called promiscuous. Structural domains vary in length from between about 25 amino acids up to 500 amino acids in length. The shortest domains such as zinc fingers are stabilised by metal ions or disulphide bridges. Domains often are named and singled out because they play an important role in the biological function of the protein they belong to; for example, the "calcium-binding" domain of calmodulin. Because they are self-stabilizing, domains can be "swapped" by genetic engineering between one protein and another to make chimera proteins. A domain may be composed of none, one, or many structural motifs. Some simple combinations of secondary structure elements have been found to frequently occur in protein structure and are referred to as 'super-secondary structure' or motifs. For example, the β-hairpin motif consists of two adjacent antiparallel β-strands joined by a small loop. Pyruvate kinase

B sheet core with protruding loops Loops for binding interactions N and C terminals at opposite poles or form “plug-ins” Domain shuffling

Families/Clans Pyruvate kinase This is a member of the Pyruvatekinase-likeTIM barrel superfamily Other families GP120 Family Envelope glycoprotein GP120 RVT_1 Reverse transcriptase (RNA-dependent DNA polymerase) COX1 Cytochrome C and Quinol oxidase polypeptide I Oxidored_q1 NADH-Ubiquinone/plastoquinone (complex I), various chains MFS_1 Major Facilitator Superfamily HCV_NS1 Hepatitis C virus non-structural protein E2/NS1

Serine Protease family

Other Important Protein Structural Features Subunits Dimers, tetramers, large assemblies of monomers Filamentous proteins Globular proteins Video – clathrin assembly

Test Your Knowledge Now Amino Acid Side Chain Proportion Buried I = Ile 0.60 V=Val 0.54 C=Cys 0.50 F=Phe L=Leu 0.45 M=Met 0.40 A=Ala 0.38 G=Gly 0.36 W=Trp 0.27 T=Thr 0.23 S=Ser 0.22 E=Glu 0.18 P=Pro H=His 0.17 D=Asp 0.15 Y=Tyr N=Asn 0.12 Q=Gln 0.07 K=Lys 0.03 R=Arg 0.01 Small proteins may have only one or two amino acid side chains that are totally inaccessible to solvent. Even in large proteins, only about 15% of the amino acids are fully buried. A list of buried side chains from a study of twelve proteins is shown in Table 1. The list is ordered by the proportion of amino acids of each type that are fully buried. What types of amino acids are most commonly buried? Least commonly buried? Are there any surprises? If so, why? Table 1. Proportions of amino acids that are inaccessible to solvent in a study of twelve proteins.