protein folds and structure

8/6/2019 Protein Folds and Structure

1/19


2/19

The central dogma

DNA ------- RNA ---------- Protein

{A,C,T,G} {A,C,G,U} {A,D,..Y}

Guanine, Cytosine TU

Thymine, Adenine


3/19

Biology/Chemistry of Protein Structure

Primary

Secondary

Tertiary

Quaternary

Assembly

Folding

Packing

InteractionS

TR

U

C

TU

R

E P

RO

C

E

SS


4/19

Primary Structure

linearordered

1 dimensional

sequence of amino acid polymer

by convention, written from amino end to carboxyl enda perfectly linear amino acid polymer is neitherfunctional nor energetically favorable folding!


5/19

Protein Folding

tumbles towards

conformations that reduce E (this process is thermodynamically favorable)

yields secondary structure

occurs in the cytosol

involves localized spatialinteraction among primarystructure elements, i.e. theamino acids

may or may not involvechaperone proteins


6/19

Secondary Structure non-linear

3 dimensional

localized to regions of an

amino acid chain

formed and stabilized by

hydrogen bonding,

electrostatic and van der

Waals interactions


7/19

Ramachandran Plot

Pauling built models based on the followingprinciples, codified by Ramachandran:

(1) bond lengths and angles should besimilar to those found in individualamino acids and small peptides

(2) peptide bond should be planer

(3) overlaps not permitted, pairs of atomsno closer than sum of their covalent radii

(4) stabilization have sterics that permithydrogen bonding

Two degrees of freedom:

(1 ) (phi) angle = rotation about N C(2) (psi) angle = rotation about C C A linear amino acid polymer with some folds

is better but still not functional nor

completely energetically favorable packing!


8/19

Protein Packing

occurs in the cytosol (~60% bulk

water, ~40% water of hydration) involves interaction between

secondary structure elementsand solvent

may be promoted bychaperones, membrane proteins

tumbles into molten globulestates

overall entropy loss is smallenough so enthalpy determinessign of E, which decreases(loss in entropy from packingcounteracted by gain fromdesolvation and reorganizationof water, i.e. hydrophobic effect)

yields tertiary structure


9/19

Tertiary Structure

non-linear

3 dimensional

global but restricted to the

amino acid polymer

formed and stabilized by

hydrogen bonding, covalent

(e.g. disulfide) bonding,

hydrophobic packing toward

core and hydrophilic

exposure to solvent

A globular amino acid

polymer folded and

compacted is somewhat

functional (catalytic) and

energetically favorableinteraction!


10/19

Protein Interaction

occurs in the cytosol, in close proximity to other

folded and packed proteins

involves interaction among tertiary structure

elements of separate polymer chains may be promoted by chaperones, membrane

proteins, cytosolic and extracellular elements aswell as the proteins own propensities

E decreases further due to furtherdesolvation and reduction of surface area

globular proteins, e.g. hemoglobin,largely involved in catalytic roles

fibrous proteins, e.g. collagen,

largely involved in structural roles

yields quaternary structure


11/19

Quaternary Structure

non-linear

3 dimensional

global, and across

distinct amino acid

polymers

formed by hydrogen

bonding, covalent

bonding, hydrophobic

packing and hydrophilic

exposure favorable, functional

structures occur

frequently and have been

categorized


12/19

Class/Motif

class = secondary structurecomposition,

e.g. all , all , segregated + , mixed / motif = small, specific

combinations of secondarystructure elements,

e.g. - - loop both subset of

fold/architecture/domains


13/19

Fold/Architecture/Domains

fold = architecture = the

overall shape andorientation of the secondarystructures, ignoringconnectivity between thestructures,

e.g. / barrel, TIM barrel domain = the

functional property

of such a fold or

architecture,

e.g. binding, cleaving,spanning sites

subset of topology/fold

families/superfamilies


14/19

Experimental Determination and Analysis

Repositories

Protein Data Bank

Molecular Modeling DataBase

Resolution

X-Ray Crystallography

NMR Spectroscopy

Mass Spectroscopy (next week)

Fluorescence Resonance Energy Transfer


15/19

A repository for 3-D biological macromolecularstructure. Established in 1971 at Brookhaven National Lab (7

structures)

It includes proteins, nucleic acids and viruses. Obtained by X-Ray crystallography (80%) or NMR

spectroscopy (16%). Submitted by biologists and biochemists from

around the world.

Protein Data bank (PDB)


16/19

Computational Determination and Analysis

Databases

CATH (Class, Architecture, Topology, Homologoussuperfamily)

SCOP (Structural Classification Of Proteins)

FSSP (Fold classification based on Structure-Structure

alignment of Proteins)

Prediction

Ab-initio, theoretical modeling, and conformation spacesearch

Homology modeling and threading

Energy minimization, simulation and Monte Carlo


17/19

CATH a combination of manual and automated

hierarchical classification

four major levels:

Class (C) based on secondarystructure content

Architecture (A) based on grossorientation of secondary structures

Topology (T) based on connectionsand numbers of secondary structures

Homologous superfamily (H) basedon structure/function evolutionarycommonalities

provides useful geometric information (e.g.architecture)

partial automation may result in examples

near fixed thresholds being assignedinaccurately


18/19

SCOP a purely manual hierarchical classification three major levels:

Family based on clear evolutionaryrelationship (pairwise residue identitiesbetween proteins are >30%)

Superfamily based on probableevolutionary origin (low sequenceidentity but common structure/functionfeatures

Fold based on major structuralsimilarity (major secondary structuresin same arrangement and topology

provides detailed evolutionary information

manual process influences updatefrequency and equally exhaustiveexamination


19/19

FSSP a purely automated

hierarchical classification

three major levels: representative set 330

protein chains (less than 30%sequence identity)

clustering based onstructural alignment into fold

families convergence cutting at a

high statistical significancelevel increases the number ofdistinct families, graduallyapproaching one family per

protein chain continually updated, presentsdata and lets user assess

Without sufficient knowledge,user may not assess dataappropriately

list of representative set

clustering dendogram

protein folds and structure

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