Computational Biophysics

& Systems Biology

Biomolecular modeling of proteins
Instructor:Prof.JessA.Izaguirre
Textbook:TamarSchlick,MolecularModelingand
Simulation:AnInterdisciplinaryGuide,Springer
Verlag,BerlinNewYork,2002,Chapters24
References:
C.Brooks,M.Karplus,B.Pettitt,Proteins:A
TheoreticalPerspectiveofDynamics,Structure,and
Thermodynamics,Wiley,1988
Variouswebsitesindicatedinthetext

Outline
1. Historical perspective
2. Review of protein
structure
3. Review of protein
dynamics

What is biomolecular modeling?

Application of computational models to
understand the structure, dynamics, and
thermodynamics of biological molecules
The models must be tailored to the question at
hand: Schrodinger equation is not the answer to
everything! Reductionist view bound to fail!
This implies that biomolecular modeling must be
both multidisciplinary and multiscale

Historical Perspective
1.
2.
3.
4.
5.
a.
b.

1946 MD calculation
1960 force fields
1969 Levinthals paradox on protein folding
1970 MD of biological molecules
1971 protein data bank
1998 ion channel protein crystal structure
1999 IBM announces blue gene project

Theoretical Foundations
1. Born-Oppenheimer approximation (fixed nuclei)
2. Force field parameters for families of chemical
compounds
3. System modeled using Newtons equations of
motion
4. Examples: hard spheres simulations (alder and
Wainwright, 1959); Liquid water (Rahman and
Stillinger, 1970); BPTI (McCammon and
Karplus); Villin headpiece (Duan and Kollman,
1998)

Experimental Foundations I
1.

X-ray crystallography

2.

Analysis of the X-ray diffraction pattern produced when a

beam of X-rays is directed onto a well-ordered crystal. The
phase has to be reconstructed.
Phase problem solved by direct method for small
molecules
For larger molecules, sophisticated Multiple Isomorphous
Replacement (MIR) technique used
Current resolution below 2 \AA

Protein crystallography

Difficult to grow well-ordered crystals

Early success in predicting alpha helices and beta sheets
(Pauling, 1950s)

Experimental Foundations II
3. NMR Spectroscopy

Nuclear Magnetic Resonance provides

structural and dynamic information about
molecules. It is not as detailed as X-ray,
somewhat limited in size
Distances between neighboring hydrogens
are used to reconstruct the 3D structure
using global optimization
Relaxation rates give dynamics (slow and
fast)

Proteins I
Polypeptide chains made up of amino
acids or residues linked by peptide bonds
Peptide bond is a partial double bond; limited
rotation 2kcal/mole for rotations 10-20; 3.2
kcal/mole for rotations 20 out of the plane

20 aminoacids

Proteins I
50-500 residues, 1000-10000 atoms
Native structure believed to correspond to
energy minimum, since proteins unfold
when temperature is increased

Protein Functions

Enzymes synthetic and degradative

Hormones
Receptors
Membrane structural proteins
Aquaporin and Ion Channels
Transporters
Photosynthesis
APT/energy generators
Photoreceptors

Protein Functions
Replicases and polymerase
Globular structural proteins tubulin,
flagellin
Fibrous structural proteins collagens,
keratin
Motor proteins kinesins, myosin

Source: MIT OCW (MIT 791)

Protein Structure

Protein Structure


Source: MIT OCW
(MIT 791)


Source: MIT OCW
(MIT 791)


Source: MIT OCW
(MIT 791)


Source: MIT OCW
(MIT 791)


Source: MIT OCW
(MIT 791)


Source: MIT OCW
(MIT 791)


Source: MIT OCW
(MIT 791)


Source: MIT OCW
(MIT 791)


Source: MIT OCW
(MIT 791)

Model Molecule: Hemoglobin

Heme Groups in Hemoglobin

Hemoglobin: Background
Protein in red blood cells
Composed of four subunits, each
containing a heme group: a ring-like
structure with a central iron atom that
binds oxygen
Picks up oxygen in lungs, releases it in
peripheral tissues (e.g. muscles)

Hemoglobin Quaternary
Structure

Two alpha subunits and two beta subunits

beta)
(141
AA per alpha, 146 AA per

Hemoglobin Tertiary Structure

One beta subunit (8 alpha helices)

Proteins III
Protein motions of importance are torsional
oscillations about the bonds that link groups
together
Substantial displacements of groups occur over
long time intervals
Collective motions either local (cage structure)
or rigid-body (displacement of different regions)
What is the importance of these fluctuations for
biological function?
See http://www.molmovdb.org

Proteins IV
Effect of fluctuations:
Thermodynamics: equilibrium behavior
important; examples, energy of ligand binding
Dynamics: displacements from average
structure important; example, local sidechain
motions that act as conformational gates in
oxygen transport myoglobin, enzymes, ion
channels

Proteins V: Local Motions

0.01-5 AA, 1 fs -0.1s
Atomic fluctuations
Small displacements for substrate binding in enzymes
Energy source for barrier crossing and other
activated processes (e.g., ring flips)

Sidechain motions
Opening pathways for ligand (myoglobin)
Closing active site

Loop motions
Disorder-to-order transition as part of virus formation

Proteins VI: Rigid-Body Motions

1-10 AA, 1 ns 1 s
Helix motions
Transitions between substrates (myoglobin)

Hinge-bending motions
Gating of active-site region (liver alcohol
dehydroginase)
Increasing binding range of antigens
(antibodies)

Proteins VII: Large Scale Motion

> 5 AA, 1 microsecond 10000 s
Helix-coil transition
Activation of hormones

Dissociation
Formation of viruses

Folding and unfolding transition

Synthesis and degradation of proteins

Role of motions sometimes only inferred from

two or more conformations in structural studies

Study of Dynamics I
The computational study of atomic
fluctuations in BPTI and other proteins has
shown that :
Directional character of active-site fluctuations
in enzymes contributes to catalysis
Small amplitude fluctuations are lubricant
It may be possible to extrapolate from short
time fluctuations to larger-scale protein
motions

Study of Dynamics II
Collective motions particularly important
for biological function, e.g., displacements
for transition from inactive to active
Extended nature of these motions makes
them sensitive to environment: great
difference between vacuum and solution
simulations
Collective motions transmit external solvent
effects to protein interior

Study of Dynamics III

For the related storage protein, myoglobin:
Fluctuations in the globin are essential to
binding: the protein matrix in X-ray is so tightly
packed that there is no low energy path for
the ligand to enter or leave the heme pocket
Only through structural fluctuations can the
barriers be lowered sufficiently
Demonstrated through energy minimization
and molecular dynamics

Study of Dynamics IV
For the transport protein hemoglobin there are
several important motions:
Oxygen binding produces tertiary structural change
A quaternary structural change from deoxy (low
oxygen affinity) to oxy configuration takes place.
This transmits information over a long distance
From the X-ray deoxy and oxy structures, a
stochastic reaction path has been found. Detailed
ligand binding has been performed using MD. A
statistical mechanical model has provided coupling
between these two processes

Lengthening Scales: SRP

Enzyme simulation of
a ms using stochastic
reaction path
disadvantage: need
initial and final
configuration
Finds a trajectory
where global energy
is minimized

Protein Folding

Source: Folding@Home

Source:
Gruebele 2002, Fig. 1

Folding from Simulation

Predicting kinetic rates

Atomistic simulations (MD)

microsecond resolution
so far for 2 state folders
Solvent representation
Ensemble kinetics

Transition state identification e.g. Unfolding simulations

reaction coordinates
transition path sampling
reaction path methods
Free energy landscape

F(q) = -ln P(q)

replica exchange
thermodynamic
integration

Folding Coordinates
Fraction of native contacts (difficult
experimentally)
Radius of gyration (not universal)
Global coordinates
Local coordinates
Thermodynamic coordinates (measure
barrier changes w. small change in T, etc.)