PHAR201 Lecture 1 2012 1

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

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

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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

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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

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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!

Primary Structure

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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

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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

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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

From Brandon and ToozeSecondary Structure

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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.

Secondary Structure

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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

Secondary Structure

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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

Secondary Structure

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Alpha Helix Continued

• There are 3.6 residues per turn

• A helical wheel will outline the surface properties of the helix

Secondary Structure

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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

Secondary Structure 4HHB

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Other (Very Rare) Helix Types - Π

• Less favorable geometry

• 4 residues per turn with i+5 not i+4

• Squat and constrained

Secondary Structure

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Beta Sheets

Secondary Structure

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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

Secondary Structure

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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

Secondary Structure

1AKK

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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

Tertiary Structure

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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

Tertiary Structure

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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

Tertiary Structure5EBX

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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

Tertiary Structure

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There are Different Forms of Classification apart from Structural

• Biochemical– Globular

– Membrane

– Fibrous

myoglobin

Collagen

Bacteriorhodopsin

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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

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Cooperativity

Co-location of Function

Combination

Structural Assembly

Hemoglobin:Enhanced bindingcapability of oxygen

Glutamine sythetase:Controlled use ofNitrogen from Multiple active sites

Immunoglobulin:Multiple receptorresponses

Actin:Giving the cell shape and form

Quaternary Structure

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Quaternary Structure: Ferritin - The Bodies Iron Storage Protein

Quaternary Structure

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Disorder?

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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