1. Structure and Function
PROTEINS
Structure and Function

2. Introduction
Proteins are a diverse and versatile group of biomolecules that provide the functional units of nearly all biochemical processes
Diversity comes from large variety of building blocks and large number of permutations by which they can be arranged, and the resulting conformations that they assume.
Structure and function are closely linked

3. Protein Synthesis
DNA
mRNA
maturation
transport
splicing
PROTEIN

4. Protein Synthesis PROTEINS Compartmentalization
Noncovalent interactions
Folding
Covalent Modification

5. Protein Function
Short list : catalytic, structural, transport, mechanical, signal
Large number of functions are a result of structures that have evolved to take on functions

6. Amino Acids Building blocks
20 or so in number, posses biochemical properties that protein exploit to generate that proper structure and resulting function

7. Amino Acids – The generic amino acid

8. Amino Acids – R groups provide large variety of functionality

9. Peptides and the primary structure of proteins

10. Forces influencing structure and function
covalent bonds
hydrophobic interactions
hydrogen bonds
van der Waal’s interaction

11. Forces: van der Waal’s - + + - - - + - + + - + - - + + -

12. Forces: electrostatic interactions- +

13. Forces: Hydrogen bonds+ +

14. Forces: Hydrogen bonds

15. Forces: Covalent bonds

16. Other considerations: bond lengths and angles

17. Other considerations: steric hindrances

18. Other considerations: hydrophobic interactions
Oil
Hydrophobic residues
Water
Hydrophilic portion

19. Protein Structure
Primary structure is the unique sequence of amino acids linked by peptide bonds. The sequence is determined by the DNA sequence of the gene which coded for it.
/translation="MAVFLLATSTIMFPTKIEAADCNGACSPFEVPPCRSRDCRCVPILFVGFCIHPTGLSSVAKMIDEHPNLCQSDDECMKKGSGNFCARYPNNYIDYGWCFDS DSEALKGFLAMPRATTK"

20. Protein Structure
Secondary structure : regular structures that polypeptide chains assume
Alpha helix
Beta sheets
Turns
Loops

21. The Alpha helix
3.6 residues/turn; 1.5 A rise/residue; typically right hand turn; alpha-helix formers: A,C,L,M,Glu,Gln,H,K

22. Beta Sheets
hydrogen bonds between protein strands, rather than within a strand; The amino acids are more extended than in a helices, with 3.5 Å between adjacent residues; The side chains of the amino acids alternate above and below the sheet. ; As mentioned above, hydrogen bonds are formed between the amine and carbonyl groups across strands ; strong beta formers: V,I,P,T,W

23. Beta Turns and Loops
A beta-turn is a short secondary structure, only 4 residues in length, which enables the overall structure to have 180 degree turns. Turns are characterized by a hydrogen bond between the CO group of residue n and the NH group of residue n+3 (i.e, between the first and the fourth residue of the turn). Since a beta-turn has several unsaturated back-bone hydrogen bond donors and acceptors, it is polar, and is usually found near the surface of the protein.
Turners: S,D,N,P,R
More Elaborate turn are called loops, unlike alpha helices and beta strands, loops do not have regular periodic structures

24. Tertiary Structures
Tertiary structure is the overall course of the polypeptide chain
General features:
Hydrophobic residues inside
Charged chains on the outside
Hydrophobic residues
Hydrophilic portion

25. Tertiary Structure – example: myoglobin

26. Tertiary Structure – example: myoglobin

27. Quarternary Structure – protein subunit assembly into higher order structures
to contribute functionality
to control activity
add to structure

28. Quarternary Structure – contribution of functionality by subunit – RNA polymerase
beta subunits bind to DNA
sigma factor determines specificity

29. Quarternary Structure – control of activity – multimerization controls binding affinity to oxygen

30. Protein Folding
Renaturation experiments indicate that amino acid sequences contain the necessary information to dictate resulting tertiary structures
Caveat: not all proteins fold as efficiently as others. In the cell, refolding is assisted by chaperone proteins

31. Protein Folding – prediction of secondary structure formation
experimental vs predicted secondary structure that an oligo peptide will form based on the propensity of the amino acid moieties gave about 60 – 70% success rates
some amino acids have close propensities for two structure – Glu alpha vs. beta sheet only by a factor of 2
The context is critical in determining outcome

32. Protein Folding – a cooperative process
sharp transition between native and denatured states with increasing denaturant
% unfolded
[ denaturant]

33. Protein Folding – process of progressive stabilization vs random search
“the essence of protein folding is the retention of partly correct intermediates”

34. Protein Folding
Prediction of three dimensional structure from sequence remains a great challenge
Two approaches:
ab initio prediction – minimization of free energy in the structure
knowledge based

35. Structure-Function relationships – catalysis
Active site of AdoMet synthetase with AdoMet, PPi, Pi and 2Mg2+. The subunits that form the active site are shaded differently.

36. Structure-Function relationships – transmembrane transport and signaling
Porin, the exception that proves the rule

37. Structure-Function relationships – transport
hemoglobin contains hemes to carry oxygen

38. Structure-Function relationships nucleic acid metabolism
DNA polymerase beta subunit complex for clasping DNA

39. Protein Structure and function determination – Data
gene sequencing
chemical characterization
molecular biology methods
genetics

40. Protein Structure and function determination – Data

41. Protein Structure and function determination – Data: NMR

42. Some protein databases on the web
NCBI
ExProt – proteins with experimentally-verified functions
SWISS-Prot – curated protein sequences
BRENDA -- extensive functional data on enzymes
BLOCK – multiple alignments of conserved regions of protein families
PROSITE – biologically significant protein patterns and profiles