Structure and Function PROTEINS Structure and Function

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

Protein Synthesis DNA mRNA maturation transport splicing PROTEIN

Protein Synthesis PROTEINS Compartmentalization Noncovalent interactions Folding Covalent Modification

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

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

Amino Acids – The generic amino acid

Amino Acids – R groups provide large variety of functionality

Peptides and the primary structure of proteins

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

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

Forces: electrostatic interactions - +

Forces: Hydrogen bonds + +

Forces: Hydrogen bonds

Forces: Covalent bonds

Other considerations: bond lengths and angles

Other considerations: steric hindrances

Other considerations: hydrophobic interactions Oil Hydrophobic residues Water Hydrophilic portion

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"

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

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

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

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

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

Tertiary Structure – example: myoglobin

Tertiary Structure – example: myoglobin

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

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

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

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

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

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

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

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

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.

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

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

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

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

Protein Structure and function determination – Data

Protein Structure and function determination – Data: NMR

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