PROTEINSPROTEINS

PROTEINSPROTEINS

Wood, brick, nails, glass Materials Amino acids, cofactors

Temperature, earthquakes Environmental Factors Temperature, solubility

How many people? Population Factors # partner proteins, # reactants

How many doors and windows? Portals Passages for substrates and reactants

Spanish, Victorian, Motifs/Styles Conserved domains or protein folds

1950's blocky science building

Julia Morgan Architect Evolution

Traditional Architecture Molecular ArchitectureFormfits

function

Levels of Protein Structure

Primary structure = order of amino acids in the protein chain

Charged and polar R-groups tend to map to protein surfaces

Non-polar R-groups tend to be buried in the cores of proteins

MyoglobinBlue = non-polarR-group

Red = Heme

Amino Acids Are Joined By Peptide Bonds In Peptides

- -carboxyl of one amino acid is joined to -amino of a second amino acid (with removal of water)

- only -carboxyl and -amino groups are used, not R-group carboxyl or amino groups

Chemistry of peptide bond formation

The peptide bond is planar

This resonance restricts the number of conformations in proteins -- main chain rotations are restricted to and

Primary sequence reveals important clues about a protein

DnaG E. coli ...EPNRLLVVEGYMDVVAL...DnaG S. typ ...EPQRLLVVEGYMDVVAL...DnaG B. subt ...KQERAVLFEGFADVYTA...gp4 T3 ...GGKKIVVTEGEIDMLTV...gp4 T7 ...GGKKIVVTEGEIDALTV...

: *: :: * * : :

small hydrophobiclarge hydrophobicpolarpositive chargenegative charge

• Evolution conserves amino acids that are important to protein structure and function across species. Sequence comparison of multiple “homologs” of a particular protein reveals highly conserved regions that are important for function.

• Clusters of conserved residues are called “motifs” -- motifs carry out a particular function or form a particular structure that is important for the conserved protein.

motif

Secondary structure = local folding of residues into regular patterns

The -helix• In the -helix, the carbonyl oxygen of residue “i” forms a hydrogen bond with the amide of residue “i+4”.

• Although each hydrogen bond is relatively weak in isolation, the sum of the hydrogen bonds in a helix makes it quite stable.

• The propensity of a peptide for forming an -helix also depends on its sequence.

The -sheet • In a -sheet, carbonyl oxygens and amides form hydrogen bonds.

• These secondary structures can be either antiparallel (as shown) or parallel and need not be planar (as shown) but can be twisted.

• The propensity of a peptide for forming -sheet also depends on its sequence.

Why do Secondary Structures form

Tertiary structure = global folding of a protein chain

Tertiary structures are quite varied

Quaternary structure = Higher-order assembly of proteins

Examples of other quaternary structures

Tetramer Hexamer Filament

SSB DNA helicase Recombinase Allows coordinated Allows coordinated DNA binding Allows complete DNA binding and ATP hydrolysis coverage of an

extended molecule

Quaternary Structures

Classes of proteinsFunctional definition:Enzymes: Accelerate biochemical reactions

Structural: Form biological structures

Transport: Carry biochemically important substances

Defense: Protect the body from foreign invaders

Structural definition:Globular: Complex folds, irregularly shaped tertiary structures

Fibrous: Extended, simple folds -- generally structural proteins

Cellular localization definition:Membrane: In direct physical contact with a membrane; generally

water insoluble.

Soluble: Water soluble; can be anywhere in the cell.

Protein Overview

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from sequence to structure

Function

to dynamics

Need to understand physical principles underlie the passage

LEVINTHAL PARADOXLEVINTHAL PARADOX

100 a.a in general

If there are 10 states/a.a 10100 conformations

Three Folding Problems

• Computational:Computational: Protein structure prediction from an amino acid sequence.

• .Folding speed: “Levinthal paradox” the kinetic question how can a protein fold so fasts

• The folding code: The folding code: The ”thermodynamic” question of how a native structure results from interatomic forces acting on an amino acid sequence

What if proteins misfold?• Diseases such as Alzheimer's disease, cystic fibrosis,

BSE (Mad Cow disease), and even many cancers are believed to result from protein misfolding.

• When proteins misfold, they can clump together ("aggregate"). These clumps can often gather in the brain, where they are believed to cause the symptoms of Mad Cow or Alzheimer's disease.

Experimental Structure PredictionExperimental Structure Prediction

• Electron Microscopy:Structural information for large macromolecules at low resolution

• NMR (Nuclear Magnetic Resonance) Spectroscopy: A solution of protein is placed in a magnetic field and the effects of different radio frequencies on the resonance of different atoms in proteins.

• X-ray crystallography: The beam of x-rays are passed through a crystal of protein. Atoms in the protein crystal scatter the x-rays, which produce a diffraction pattern on a photographic film.

Pros and ConsPros and Cons

• None of them is high throughput technology• NMR

– Size of protein limited (about 200 residues)– Protein must be soluble– can provide the structure in near physiological condition– can provide informations about dynamics

• X-ray Crystallography– Must be able to crystallize protein– Accurate

X-ray crystallographyX-ray crystallography

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NMRNMR

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Why Predict Protein Structures?

High Resolution Structures better than 3Å

To eliminate protein structure determination

To speed up drug discovery

Sequence --------------> StructureSequence --------------> Structure

FunctionFunction

‘Protein folding problem’

Bioinformatics. Sequence

alignments

A fundamental paradigm of protein science: The amino acid sequence encodes the structure; the structure determines

the function

Mod

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d

sim

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Dill & Chan

From a computational point of view:

What is a molecular dynamics simulation?

• Simulation that shows how the atoms in the system move with time

• Typically on the nanosecond timescale

• Atoms are treated like hard balls, and their motions are described by Newton’s laws.

Molecular Dynamics Theory

MD as a tool for minimizationEnergy

positionEnergy minimizationstops at local minima

Molecular dynamicsuses thermal energyto explore the energysurface

State A

State B

Folding Energy Landscape

The Folding @ Home initiative(Vijay Pande, Stanford University)

http://folding.stanford.edu/

The Folding @ Home initiative