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GRC - Protein Folding Dynamics


									Protein Folding - Results and

                 Charles L. Brooks III
             The Scripps Research Institute
                  La Jolla, California

                N+N Meeting, DC 04/04
Protein Folding - Results and

    • Basic elements of protein folding free
      energy landscape calculations
    • Folding studies predict folding
      pathways/mechanisms and inform new
    • Computational requirements and
      experiences with the GRID

               N+N Meeting, DC 04/04
General issues in condensed phase
• Sampling, sampling, sampling
   – Anecdotal observations of individual events are
     exactly that - anecdotes, not a basis for discovery
   – Failures of high temperature unfolding studies linked
     to poor sampling of non-equilibrium events
   – Suspect AIMD simulations linked to non-
     convergence of statistical sampling
• Non-equilibrium “experiments”must be run 10s
  of times
• Statistical errors must be quantified

                      N+N Meeting, DC 04/04

N+N Meeting, DC 04/04
Constructing folding free
energy landscapes
• Solvated molecular dynamics
trajectories at several temperatures yield
multiple unfolding pathways connecting
native and unfolded states

                                                  • Clustering in the
                                                  space of r and Rg
                                                  provide spanning
                                                  initial conditions for
                                                  biased free energy

                          N+N Meeting, DC 04/04
Funneled landscapes visualized and
• Ideas from simulation have helped
  “evolve” our thinking about protein
  folding funnels and free energy

                          N+N Meeting, DC 04/04
Small helical proteins fold via multiple
pathways on a funnel-like landscape

                                        Helix formation and
                                        collapse occur via
                                        at least two

                                        collapse and helix

                                        type mechanism

                N+N Meeting, DC 04/04
Folding is Downhill

 • Microsecond folding dynamics of the F13W G29A mutant of the
   B domain of staphylococcal protein A by laser-induced
   temperature jump. George Dimitriadis, Adam Drysdale, Jeffrey
   K. Myers, Pooja Arora, Sheena E. Radford, Terence G. Oas,
   and D. Alastair Smith, PNAS, 101, 3809 (2004).
    – “The data suggest, therefore, that helix II is formed in the rate-
      limiting transition state, consistent with theoretical models of how
      this protein folds (27).”
    – “Using this value, the DG† for F13W* at 37°C is ~3/4kBT … in the
      regime of downhill folding.”
    – 27. Guo, Brooks and Boczko, PNAS, 94, 10161 (1997)

                            N+N Meeting, DC 04/04
And centered around the HII/HI

 • Testing protein-folding simulations by experiment: B domain of
   protein A Satoshi Sato, Tomasz Religa, Valerie Daggett, and
   Alan R. Fersht. PNAS, in the press (2004).
    – “The rate-determining transition state for the folding of the B
      domain is constructed around a nearly fully formed H2, which is
      stabilized by hydrophobic interactions from H1. H1 itself is only
      weakly structured…”
    – “Boczko and Brooks (27) and Guo et al. (28) used a biased-
      sampling method and concluded that the interface between H1 and
      H2 forms first, starting around the T1 region, and then the H2-H3
      interface forms later with mostly concomitant secondary and tertiary
      structure formation.”
    – 27. Boczko and Brooks, Science, 269, 393 (1995).
    – 28. Guo, Brooks and Boczko, PNAS, 94, 10161 (1997).

                           N+N Meeting, DC 04/04
New paradigms for experiment - single
molecules, fast folding

• Exciting new experiments begin
  to elucidate the nature of folding
• Simulation and theory suggest
  many single domain proteins
  may fold in downhill or nearly
  downhill fashion
• Simulation and experiment
  converge in characterizing
  folding timescales for small
                          • Nearly barrier-less folding free energy
                              landscapes observed in simulations under
                              native-supporting conditions
                          • Experiment confirms small (~ a few kBT) free
                              energy barriers
                          N+N Meeting, DC 04/04
Folding of a/b protein G involves
significant water participation
   • Nature of the collapsed state involves
     – Significant solvent “lubrication”
     – Final barrier associated with solvent expulsion

                               Water in core of collapsed state

                               Barrier for final assent to
                               native state

                     N+N Meeting, DC 04/04
Function and form - folding and
assembly, folding and function
• New ideas are emerging from
  experiment and theory that link protein
  function to folding mechanism
• Protein assembly and folding too may • PIN and YAP domain
  be coupled                                bind different consensus
                                          • FBP binds two
                                            consensus sequence

                                                  • Multiphase folding as a
                                                    hallmark of functional
                                                    substates in protein

                          N+N Meeting, DC 04/04
 Computational Requirements:

• Requirements
   – 100-200 sequential runs on ~64 processors for total
     resource requirement of ~3 months 512 T3E processor
• GRID computing with Legion/Globus
   – 100-200 simultaneous runs of ~16-64 PEs of available
     machines on computational grid - each run of duration 8-12
• Application software
   – CHARMM ports to T3E, O2000, Alpha, Linux, - utilizing
     CHARMM-MPI, MPI or Legion-MPI, Globus, MMTSB Tool

                         N+N Meeting, DC 04/04
Constructing folding free energy
landscapes via GRID “parameter-space”
• Different conformational
  regions are mapped to different
  regions on the grid
• Tightly coupled parallelism (16-
  64 nodes) exploited for each
  region of conformational space
• Loose coupling exploited to
  distribute calculations across
  geographically distributed
  GRID nodes.

                      N+N Meeting, DC 04/04
GRID “parameter-space” scans: the reality

• Persistence in middleware platform focus is sketchy at
  best: Legion, Globus, OGSI?
   – The flavor de jour is a continually moving target
• Implementing new features to enable calculations within
  middleware framework is painful
   – Providing access to site-specific features, e.g., archival/retrieval
• Persistence of middleware infrastructure across sites is
  poor/non-existent across many sites
   – Demonstration projects seem to work because coherence in
     site-specific attention can be maintained, long-term solutions
     have not existed.

                           N+N Meeting, DC 04/04
Building a portal for the National
computational grid

                N+N Meeting, DC 04/04
N+N Meeting, DC 04/04
N+N Meeting, DC 04/04
Grid Portal is a good idea to bring
computing resource to broader

 • Lack of persistence in Globus behind portal makes it
   difficult to provide robust portal
 • Little involvement of “application scientist” diminishes
   usefulness of final product.
 • NSF needs to re-embrace the idea that application
   science and scientists should be driving the development
   of cyber-infrastructure

                     N+N Meeting, DC 04/04
Other solutions: Ensemble Computing
with the MMTSB Tool Set
• The ensemble computing paradigm is tightly integrated
  into the Tool Set
   – Ensemble data structures support repeated analysis on
     ensembles of biopolymer conformations or molecular structures
       • Energy and scoring of protein-ligand docking runs
       • 100’s - 1000’s of PB/GB-SA calculations
       • Use your imagination!
   – Master/slave parallel replica exchange simulations (see later
       • Ab initio protein and peptide folding
       • Loop modeling and homology modeling
       • Refinement and scoring of predicted structures
   – Ensemble construct integrated into much functionality of
     CHARMM, Amber, MONSSTER and other analysis tasks
                         N+N Meeting, DC 04/04
  Harnessing computational grids for
  biomolecular simulation studies
Characterization of Desktop Grids
                       • Large numbers of heterogeneous desktop PCs
                         connected to the Internet and Intranets
                       • Utilization of otherwise unused compute power
                          80%-90% of CPU time is idle time
                       • Nodes join and leave the grid frequently
                       • Unreliable, loosely-coupled interconnections
                       • Intrusive users and malicious attacks
  Desktop grid

Challenges using Desktop Grids

          • How can we optimally utilize a large amount of desktop PCs to stage
            high-quality, large-scale simulations?
          • How can we deal with the heterogeneity of desktop grid platforms?
          • Do the characteristics of the system (i.e. kind of resource, compute
            paradigms) affect the quality of the simulation results?
                            N+N Meeting, DC 04/04
A Distributable Desktop Grid Environment
for Macromolecular Modeling Built Around
• Protein-ligand docking applications
  implemented and useful
• Protein folding calculations (for structure
  prediction) ongoing for CASP6
• New “volunteer” resource for protein structure
  prediction, StructurePrediction@home

                   N+N Meeting, DC 04/04

 • People: M. Crowley, M. Taufer, A. Grimshaw,
   M. Humphrey, J. Karanicolas, M.Feig
 • Money: NIH (NCRR and others), NSF (CTBP,
 • Resources: TSRI, SDSC/NPACI, PSC

                  N+N Meeting, DC 04/04

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