Biochemistry 300 Introduction to Structural Biology

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Biochemistry 300Introduction to Structural
Biology
Jan. 10, 2007

• Walter Chazin
• 5140 BIOSCI/MRBIII
• E-mail Walter.Chazin_at_vanderbilt.edu
• http//structbio.vanderbilt.edu/chazin/classnotes/
  

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Biology is Organized into Structures
Organ ? Tissue ? Cell ? Molecule ? Atoms

• A cell is an organization of millions of
  molecules
• Proper communication between these molecules is
  essential to the normal functioning of the cell
• To understand communication
  Determine the arrangement of atoms

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What is Structural Biology?
Sequence
Structural Scales
MESDAMESETMESSRSMYNAMEISWALTERYALLKINCALLMEWALLYIP
REFERDREVILMYSELFIMACENTERDIRATVANDYINTENNESSEEILI
KENMRANDDYNAMICSRPADNAPRIMASERADCALCYCLINNDRKINASE
MRPCALTRACTINKARKICIPCDPKIQDENVSDETAVSWILLWINITALL
polymerase
SSBs
Complexes
helicase
primase
Assemblies
Cell Structures
System Dynamics
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Atomic Resolution Structural Biology

• Determine atomic structure to analyze why
  molecules interact

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The Reward Understanding?Control
Shape
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Atomic Structure in Context
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Current Strategy for Atomic Resolution Structural
Biology

• Break down complexity so that the system can be
  understood at a fundamental level
• Build up a picture of the whole from the
  reconstruction of the high resolution pieces
• Understanding basic governing principles enables
  prediction, design, control
• Pharmaceuticals, biotechnology

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Build-up Quaternary Structure
70AB
14/32D/70C
X-ray
Zn
B
A
C
D
RPA70 RPA32 RPA14
NTD
NMR
14
CTD
70NTD
32CTD
quaternary structure?
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Put Structure Into Context
MBP-tagged Siah-1
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Approaches to Atomic Resolution Structural Biology

• NMR Spectroscopy X-ray
  Crystallography
• Computation

• Determine experimentally or model 3D structures
  of biomolecules
• ESR/Fluorescence to measure distances when
  traditional methods fail
• EM/Scattering to get snapshots of whole
  molecular structures
• (Cryo-EM starts to approach atomic resolution!)

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Inserting High Resolution Structures Into Low
Resolution Envelopes
Mesh DAMMIN Ribbon 1QUQ
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Why Structure in silico?

• A good guess is better than nothing!
• Enables the design of experiments
• Potential for high-throughput
• Crystallography and NMR dont always work!
• Many important proteins do not crystallize
• Size limitations with NMR

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Computational ApproachesMolecular Simulations

• Convert experimental data into structures
• Predict effects of mutations, changes in
  environment
• Insight into molecular motions
• Interpret structures- characterize the chemical
  properties (e.g. surface) to infer function

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Computational ApproachesStructure Prediction

• Secondary structure (only sequence)
• Homology modeling (using related structure)
• Fold recognition
• Ab-initio 3D prediction The Holy Grail

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Complementarity of theAtomic Resolution Methods

• X-ray crystallography- highest resolution
  structures faster than NMR
• NMR- enables widely varying solution conditions
  characterization of motions and dynamic, weakly
  interacting systems
• Computation- fundamental understanding of
  structure, dynamics and interactions (provides
  the why answers) models without experiment very
  fast

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Representations of 3D Structures
Both accuracy and precision are important
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THE STRUCTURE?

• To correctly represent 3D structure (not a
  model), the uncertainty in each atomic coordinate
  must be represented
• Polypeptides are dynamic and therefore occupy
  more than one conformation

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Accuracy/Precision Determined Differently for
X-ray and NMR
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Variability Uncertainty and Flexibility in
Experimental Structures
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Representation of Structure Conformational
Ensemble

• Neither crystal nor solution structures can be
  properly represented by a single conformation
• Intrinsic motions
• Imperfect data

Variability reflected in the RMSD of the ensemble
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Challenges For Understanding The Meaning of
Structure

• Structures determined by NMR, computation, and
  X-ray crystallography are static snapshots of
  highly dynamic molecular systems

• Biological process (recognition, interaction,
  chemistry) require molecular motions (from
  femto-seconds to minutes)
• New methods are needed to comprehend and
  facilitate thinking about the dynamic structure
  of molecules visualization

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Visualization of Structures
Intestinal Ca2-binding protein!

• Need to incorporate 3D and motion

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Center for Structural Biology
Dedicated to furthering biomedical research and
education involving 3D structures at or near
atomic resolution http//structbio.vanderbilt.edu