Principles of Protein Structure PHAR 201/Bioinformatics I Philip E. Bourne School of Pharmacy & Pharm. Sci., UCSD Prerequisite Reading: Structural Bioinformatics Chapters 1-2 Thanks to Eric Scheeff and Lynn Fink PHAR201 Lecture 1 2012

Remember .. The first 2 lectures are not so much to teach/refresh your knowledge of protein/DNA/RNA structure, but for you to conceptualize, describe and subsequently analyze complex biological data Assignment 1 will test this PHAR201 Lecture 1 2012

Remember.. All which we study is an abstraction to make comprehension of a complex entity more straightforward We think of structures as static entities, but they are dynamic, sometimes to the point of being ill-definable – function requires this flexibility The more we have the more we should know and use – contrast Kendrew to the PDB today PHAR201 Lecture 1 2012

Primary Structure - Amino Acids It is the amino acid sequence (1940) that “exclusively” determines the 3D structure of a protein 20 amino acids – modifications do occur post translationally 2,3,4 completely encoded by primary structure Linear polymer theory Set of 20 amino acids not determined until 1940 PHAR201 Lecture 1 2012

Amino Acids Continued… It is the properties of the R group that determine the property of the aa and ultimately the protein Different schemes exist for describing the properties Willie Taylor’s scheme is often employed in bioinformatics analyses Hydrophobicity, polarity and charge are common measures Learn the amino acid codes, structures and properties! Subclasses – Aromatic or aliphatic; large and small Static properties of the amino acid Primary Structure PHAR201 Lecture 1 2012

Amino Acids Continued… Chirality – amino acids are enatiomorphs, that is mirror images exist – only the L(S) form is found in naturally forming proteins. Some enzymes can produce D(R) amino acids Think about a data structure for this information – annotation and a validation procedure should be included Think about systematic versus common nomenclature Primary Structure PHAR201 Lecture 1 2012

Peptide Bond Formation Individual amino acids form a polypeptide chain Such a chain is a component of a hierarchy for describing macromolecular structure The chain has its own set of attributes The peptide linkage is planar and rigid Primary Structure PHAR201 Lecture 1 2012

Geometry of the Chain A dihedral angle is the angle between two planes defined by 4 atoms – 123 make one plane; 234 the other Omega is the rotation around the peptide bond Cn – Nn+1 – it is planar and is 180 under ideal conditions Phi is the angle around N – Calpha Psi is the angle around Calpha C’ The values of phi and psi are constrained to certain values based on steric clashes of the R group. Thus these values show characteristic patterns as defined by the Ramachandran plot PHAR201 Lecture 1 2012 Secondary Structure From Brandon and Tooze

Ramachandran Plot Shows allowed and disallowed regions Gly and Pro are exceptions: Gly has no limitation; Pro is constrained by the fact its side chain binds back to the main chain Gray = allowed conformations. βA, antiparallel b sheet; βP, parallel b sheet; βT, twisted b sheet (parallel or anti-parallel); α, right-handed α helix; L, left-handed helix; 3, 310 helix; p, Π helix. PHAR201 Lecture 1 2012 Secondary Structure

Secondary Structure The chemical nature of the carboxyl and amino groups of all amino acids permit hydrogen bond formation (stability) and hence defines secondary structures within the protein. The R group has an impact on the likelihood of secondary structure formation (proline is an extreme case) This leads to a propensity for amino acids to exist in a particular secondary structure conformation Helices and sheets are the regular secondary structures, but irregular secondary structures exist and can be critical for biological function Alpha and beta predicted by Pauling Stabiliz PHAR201 Lecture 1 2012 Secondary Structure

Alpha Helix A helix can turn right or left from N to C terminus – only right-handed are observed in nature as this produces less clashes All hydrogen bonds are satisfied except at the ends = stable PHAR201 Lecture 1 2012 Secondary Structure

Alpha Helix Continued There are 3.6 residues per turn A helical wheel will outline the surface properties of the helix PHAR201 Lecture 1 2012 Secondary Structure

Other (Rarer) Helix Types - 310 Less favorable geometry 3 residues per turn with i+3 not i+4 Hence narrower and more elongated Usually seen at the end of an alpha helix PHAR201 Lecture 1 2012 4HHB Secondary Structure

Other (Very Rare) Helix Types - Π Less favorable geometry 4 residues per turn with i+5 not i+4 Squat and constrained PHAR201 Lecture 1 2012 Secondary Structure

Beta Sheets PHAR201 Lecture 1 2012 Secondary Structure

Beta Sheets Continued Between adjacent polypeptide chains Phi and psi are rotated approximately 180 degrees from each other Mixed sheets are less common Viewed end on the sheet has a right handed twist that may fold back upon itself leading to a barrel shape (a beta barrel) Beta bulge is a variant; residue on one strand forms two hydrogen bonds with residue on other – causes one strand to bulge – occurs most frequently in parallel sheets PHAR201 Lecture 1 2012 Secondary Structure

Other Secondary Structures – Loop or Coil Often functionally significant Different types Hairpin loops (aka reverse turns) – often between anti-parallel beta strands Omega loops – beginning and end close (6-16 residues) Extended loops – more than 16 residues 1AKK PHAR201 Lecture 1 2012 Secondary Structure

Tertiary Structure Myoglobin (Kendrew 1958) and hemoglobin (Perutz 1960) gave us the proven experimental insights into tertiary structure as secondary structures interacting by a variety of mechanisms While backbone interactions define most of the secondary structure interactions, it is the side chains that define the tertiary interactions PHAR201 Lecture 1 2012 Tertiary Structure

Components of Tertiary Structure Fold – used differently in different contexts – most broadly a reproducible and recognizable 3 dimensional arrangement Domain – a compact and self folding component of the protein that usually represents a discreet structural and functional unit Motif (aka supersecondary structure) a recognizable subcomponent of the fold – several motifs usually comprise a domain Like all fields these terms are not used strictly making capturing data that conforms to these terms all the more difficult PHAR201 Lecture 1 2012 Tertiary Structure

Tertiary Structure as Dictated by the Environment Proteins exist in an aqueous environment where hydrophilic residues tend to group at the surface and hydrophobic residues form the core – but the backbone of all residues is somewhat hydrophilic – therefore it is important to have this neutralized by satisfying all hydrogen bonds as is achieved in the formation of secondary structures Polar residues must be satisfied in the same way – on occasion pockets of water (discreet from the solvent) exist as an intrinsic part of the protein to satisfy this need Ion pairs (aka salt bridge) form important interactions Disulphide linkages between cysteines form the strongest (ie covalent tertiary linkages); the majority of cysteines do not form such linkages 5EBX PHAR201 Lecture 1 2012 Tertiary Structure

Tertiary Structure as Dictated by Protein Modification To the amino acid itself eg hydroxyproline needed for collagen formation Addition of carbohydrates (intracellular localization) Addition of lipids (binding to the membrane) Association with small molecules – notably metals eg hemoglobin PHAR201 Lecture 1 2012 Tertiary Structure

There are Different Forms of Classification apart from Structural Biochemical Globular Membrane Fibrous myoglobin Bacteriorhodopsin Collagen PHAR201 Lecture 1 2012

Quaternary Structure The biological function of some molecules is determined by multiple polypeptide chains – multimeric proteins Chains can be identical eg homeodimer or different eg heterodimer The interactions within multimers is the same as that found in tertiary and secondary structures PHAR201 Lecture 1 2012

Cooperativity Co-location of Function Combination Structural Assembly Hemoglobin: Enhanced binding capability of oxygen Cooperativity Glutamine sythetase: Controlled use of Nitrogen from Multiple active sites Co-location of Function Combination Immunoglobulin: Multiple receptor responses Structural Assembly Actin: Giving the cell shape and form PHAR201 Lecture 1 2012 Quaternary Structure

Quaternary Structure: Ferritin - The Bodies Iron Storage Protein PHAR201 Lecture 1 2012 Quaternary Structure

PHAR201 Lecture 1 2012

Disorder? PHAR201 Lecture 1 2012

Additional Reading Branden and Tooze (1999) Introduction to Protein Structure (2nd Edition) Garland Publishing. An excellent introduction Richardson (1981) The Anatomy and Taxonomy of Protein Structure Adv. Protein Chem. 34: 167-339 Good historical perspective PHAR201 Lecture 1 2012