phar201 lecture 1 20121 principles of protein structure phar 201/bioinformatics i philip e. bourne...
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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