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
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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 illdefinable – 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
Secondary Structure
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From Brandon and Tooze
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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 antiparallel); α, right-handed α helix; L, lefthanded 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 righthanded 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
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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)
1AKK
– Extended loops – more than 16 residues
Secondary Structure
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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 Structure
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5EBX
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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
Bacteriorhodopsin
Collagen
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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
Quaternary Structure
Hemoglobin:
Enhanced binding
capability of oxygen
Glutamine sythetase:
Controlled use of
Nitrogen from
Multiple active sites
Immunoglobulin:
Multiple receptor
responses
Actin:
Giving the cell shape
and form
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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
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