Understanding Protein Structure: Amino Acids, pKa, and Protein Formation, Study notes of Biochemistry

Download Understanding Protein Structure: Amino Acids, pKa, and Protein Formation and more Study notes Biochemistry in PDF only on Docsity! Protein Structure Amino Acids Amino acids are the building blocks of proteins. All AA’s have the same basic structure: Carboxyl Group Amino Group Alpha Carbon Side Chain Nonpolar Residues Oo 0 Rae moh Bal HAC] HH C How Ga oe CHECK 6 Br 5 oO H.CHE- “oO “oH CH Oo He ie ; > NHI NH, NH; NH, NH; : c Alanine (Ala) Glycine (Gly) Valine (Val) Isoleucine (lle) Proline (Pro) Hy HCH a i H Ul S He ; oe ao ; H “ ns “eA Oe ne + i. CH, NH, 2 \ ut Ge Leucine (Leu) Methionine (Met) Tryptophan (Trp) Phenylalanine (Phe) Acidic Residues Aspartic Acid (Asp) o H Oo a= a i Co HEC, - H i O z + NH, Glutamic Acid (Glu) Basic Residues Lysine (Lys) Amino Acid Properties pKa • You know that the pH is defined in terms of the proton concentration pH = -log[H+] and that this is based on an equilibrium that is reached between an acid (or base) and it constituent parts HA ↔ H+ + A- pKa • The equilibrium constant for this reaction is given by • If we solve this equation for [H+] we get ][ ]][[ HA AHKa −+ = ][ ][][ HA AKH a − + = Histidine Since the pKa of histidine is close to neutral, its protonation state depends strongly on its local environment. This feature is often exploited and histidine is used as a molecular switch. The Peptide Bond To make a protein, these amino acids are joined together in a polypeptide chain through the formation of a peptide bond. Polypeptides • Proteins are nothing more than long polypeptide chains. • Chains that are less than 40-50 amino acids or residues are often referred to as polypeptide chains since they are too smal to form a functional domain. • Larger than this size, they are called proteins • The structure, function and general properties of a protein are all determined by the sequence of amino acids that make up its primary sequence. (φ,ψ) Angles The Ramachandran Plot The (φ,ψ) angles of amino acids in a polypeptide chain or protein are restricted, largely because of steric interactions (glycine is an exception). Secondary Structure • The primary sequence or main chain of the protein must organize itself to form a compact structure. This is done in an elegant fashion by forming secondary structure elements • The two most common secondary structure elements are alpha helices and beta sheets, formed by repeating amino acids with the same (φ,ψ) angles • There are other secondary structure elements such as turns, coils, 310 helices, etc. Disulfide Bonds • Pairs of cysteines can form disulfide bonds between different parts of the main chain • This adds stability and is common in extracellular proteins Tertiary Structure • To make the protein look like a protein, the secondary structure elements come together to form the tertiary structure • Most often, the secondary structure elements form motifs – Greek key – EF hand – Beta hairpin – … Quaternary Structure • Folded proteins then bind together to form dimer, trimers, or higher order structures • The functional form of hemoglobin is a tetramer Hydrogen Bonds • Hydrogen bonds are formed by the sharing of a proton between donor and acceptor groups • The strength is around 2-5 kcal/mol and the ideal distance is 2.8-3 Å van der Waals Interactions • Electrostatic interactions cannot account for all the non-covalent interactions observed between molecules (especially uncharged ones) • Atoms with dipoles (and higher order multipoles) induce and interact with dipoles in other atoms via dispersion forces (1/r6) Hydrophobic Interactions • Hydrophobic interactions are not attractive interactions, but results from the inability of water to form hydrogen bonds with certain side chains Diffraction • If successful in forming a regular crystal, the hope is that they now diffract to a high enough resolution • This scattering density is then transformed in real space coordinates 10 Å 5 Å3 Å Resolution of Structures Hydrogens are typically too small to be resolved except in the highest resolution structures (< 1 Å) • 5 Å structures resolve some secondary structure and can be useful • 2.5 – 3 Å is more typical – constrains (φ,ψ) angles • less that 1.5 Å is a very good structure - (φ,ψ) angles are well defined Sequence to Structure • Even with the highest resolution structures it is difficult or impossible to tell the difference between a N, O or C. Thus you need to know the sequence to thread the structure and judge the atom based on the local environment N O O X ASP: X=O (charged) ASN: X=N (polar) Could it be LEU ??