Chapter 4 The Three Dimensional Structure of Proteins In this chapter there are five themes o The three dimensional structure of a protein is determined by its o The function of a protein depends on its structure o An isolated protein usually exists in one or a small number of stable amino acid sequence structural forms o The most important forces stabilizing the specific structures maintained by a given protein are non covalent interactions o We can recognize some common structural patterns that help to organize our understanding of protein architecture 4 1 Overview of Protein Structure Conformation the spatial arrangement of atoms in a protein o Possible conformations include any structural state it can achieve without breaking covalent bonds o Changes can occur by rotation about single bonds o One or a few conformations predominate under biological conditions The ones that are thermodynamically the most stable i e have Native proteins are proteins in any of their functional folded the lowest Gibbs free energy conformations A Protein s Conformation Is Stabilized Largely by Weak Interactions the tendency to maintain a native conformation The high entropy and hydrogen bonding interactions of a polypeptide chain Stability favor the unfolded state of a protein but disulfide bonds and the weak noncovalent interactions counteract this Many proteins do not have disulfide bonds especially in bacterial proteins the dominating interactions that contribute to Hydrophobic interactions the stability of proteins Solvation layer surrounds a hydrophobic molecule a highly structured shell of water that forms when water o Solvation layers can form around polar molecules The interaction of oppositely charged groups that form an ion pair a salt bride and can be stabilizing or destabilizing o The strength of a salt bridge increases as it moves to an environment of lower dielectric constant from the polar aqueous solvent to the nonpolar protein interior o This means salt bridges can provide significant stabilization to protein structure The structural patterns discussed reflect two rules o Hydrophobic residues are largely buried in the protein interior away from water o The number of hydrogen bonds and ionic interactions within the protein is maximized reducing the number of hydrogen bonding and ionic groups that aren t paired with a partner The Peptide Bond Is Rigid and Planar Pauling and Corey discovered that peptide C N bonds have slight resonance with a double bond and so cannot rotate freely Peptides have three dihedral angles called phi psi and omega o In theory phi and psi can have any value between 180 and 180 o Ramachandran plot but due to steric hindrance some values are prohibited allowed values for these angles when psi is plotted versus phi to determine the 4 2 Protein Secondary Structure The Helix Is a Common Protein Secondary Structure Helix the simplest arrangement a polypeptide chain can assume o The R groups protrude outward from the helical backbone o Phi 57 o Psi 47 o Each helical turn includes 3 6 amino acids o The helical twist is right handed o The helix makes optimal use of internal hydrogen bonds Amino Acid Sequence Affects Stability of the Helix Alanine shows the greatest tendency to form helices The position of an amino acid relative to its neighbors affects whether or not a polypeptide will form a helix Critical interactions occur between an amino acid side chain and the side chain three or four amino acids away on either side because of the twist of the helix Proline introduces a destabilizing kink in an helix because of the ring in the R group The identity of the amino acids near the ends of an helix also affect the stability o Negatively charged amino acids are found near the N terminus o Positively charged amino acids are found near the C terminus Summary of factors that affect the stability of an helix o The intrinsic propensity of an amino acid to form one o The interactions between R groups o The bulkiness of adjacent R groups o The occurrence of Pro and Gly residues o Interactions between amino acid residues at the ends of the helical segment and the electric dipole inherent to the helix The Conformation Organizes Polypeptide Chains into Sheets Conformation o Sheet the backbone of a polypeptide chain is extended in a zigzag when the zigzag polypeptide chains are arranged side by side and connected by hydrogen bonds o The chains can be either parallel or antiparallel o Phi 119 parallel o Psi 135 antiparallel o R groups must be relatively small Turns Are Common in Proteins reversals in direction in a polypeptide that connect the ends of two Turns adjacent segments of an antiparallel sheet o 180 turn involving four amino acids o Proline and Glycine residues usually occur o There is a hydrogen bond between the first and fourth residue Common Secondary Structures Have Characteristic Dihedral Angles Common Secondary Structures Can Be Assessed by Circular Dichroism measuring the difference in Circular dichroism CD spectroscopy absorption of left handed versus right handed plane polarized light Using CD spectroscopy chemists can o Determine whether a protein is properly folded o Estimate the fraction of the protein that is folded in either of the common secondary structures o Monitor transitions between the folded and unfolded states 4 3 Protein Tertiary and Quaternary Structures Tertiary structure in a protein dimensional complexes Quaternary structure the overall three dimensional arrangement of all atoms the arrangement of protein subunits in three There are two major groups of proteins o Fibrous proteins have polypeptide chains arranged in long strands or sheets Usually consist largely of a single type of secondary structure Have a relatively simple tertiary structure Proteins that provide support shape and external protection have polypeptide chains folded into a spherical or o Globular proteins globular shape Often contain several types of secondary structure Most enzymes and regulatory proteins Fibrous Proteins Are Adapted for a Structural Function All fibrous proteins are insoluble in water due to a high concentration of hydrophobic amino acid residues Keratin o Found only in mammals o Hair wool nails claws quills horns hooves skin o Part of the intermediate filament IF protein family o Right handed helix that is a coiled coil supercoil o Rich in hydrophobic residues Ala Val Leu Ile Met and Phe o Strength is enhanced by covalent cross links disulfide bonds