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Why Do Protein Folding Rates Correlate with Metrics of Native Topology?

By Patrícia F. N. Faísca, Rui D. M. Travasso, Andrea Parisi and Antonio Rey

Abstract

For almost 15 years, the experimental correlation between protein folding rates and the contact order parameter has been under scrutiny. Here, we use a simple simulation model combined with a native-centric interaction potential to investigate the physical roots of this empirical observation. We simulate a large set of circular permutants, thus eliminating dependencies of the folding rate on other protein properties (e.g. stability). We show that the rate-contact order correlation is a consequence of the fact that, in high contact order structures, the contact order of the transition state ensemble closely mirrors the contact order of the native state. This happens because, in these structures, the native topology is represented in the transition state through the formation of a network of tertiary interactions that are distinctively long-ranged

Topics: Research Article
Publisher: Public Library of Science
OAI identifier: oai:pubmedcentral.nih.gov:3338708
Provided by: PubMed Central
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    1. (2010). A
    2. (2005). A critical assessment of the topomer search model of protein folding using a continuum explicit-chain model with extensive conformational sampling.
    3. (1989). A lattice statistical mechanics model of the conformational and sequence spaces of proteins.
    4. (1999). A simple model for calculating the kinetics of protein folding from three-dimensional structures.
    5. (1996). Chain length scaling of protein folding time.
    6. (2003). Contact order dependent protein folding rates: Kinetic consequences of a cooperative interplay between favorable nonlocal interactions and local conformational preferences. Proteins: Struct Func
    7. (2003). Contact order revisited: Influence of protein size on the folding rate.
    8. (1998). Contact order, transition state placement and the refolding rates of single domain proteins.
    9. (1998). Cooperativity in protein folding: From lattice models with side chains to real proteins.
    10. (2011). Cooperativity, local-nonlocal coupling, and nonnative interactions: principles of protein folding from coarsegrained models.
    11. (2010). Coordinate-dependent diffusion in protein folding.
    12. (2006). Do proteins with similar folds have similar transition state structures? a diffuse transition state of the 169 residue apoflavodoxin.
    13. (2003). Fersht A
    14. (1994). Free energy landscape for protein folding kinetics: intermediates, traps, and multiple pathways in theory and lattice model simulations.
    15. (2002). How the folding rate constant of simple, single-domain proteins depends on the number of native contacts.
    16. (2008). Identifying critical residues in protein folding: Insights from w-value and pfold analysis.
    17. (2008). Kinetic barriers and the role of topology in protein and rna folding.
    18. (1993). Kinetics and thermodynamics of folding in model proteins.
    19. (2000). Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus.
    20. (1998). Lattice models for proteins reveal multiple folding nuclei for nucleation-collapse mechanism.
    21. (2008). Loop-closure principles in protein folding.
    22. (2010). Non-native interactions play an effective role in protein folding dynamics.
    23. (2005). Nucleation and the transition state of the sh3 domain.
    24. (1998). On the transition coordinate for protein folding.
    25. (2006). P versus q: Structural reaction coordinates capture protein folding on smooth landscapes.
    26. (1995). Principles of protein folding – a perspective from simple exact models.
    27. (2005). Protein folding and the organization of the protein topology universe.
    28. (1994). Proteins with selected sequences fold into unique native conformation.
    29. (2007). Rate determining factors in protein model structures.
    30. (2003). Self-consistent determination of the transition state for protein folding: Application to a fibronectin type iii domain.
    31. (1994). Specific nucleus as the transition state for protein folding: evidence from the lattice model.
    32. (2003). The topomer search model: a simple, quantitative theory of two-state protein folding kinetics.
    33. (1996). The topomer-sampling model of protein folding.
    34. (2002). Thermodynamic control and dynamical regimes in protein folding.
    35. (2001). Three key residues form a critical contact network in a protein folding transition state.
    36. (2000). Topology, stability, dequence, and length: Defining the determinants of two-state protein folding kinetics.
    37. (2004). Transition states for protein folding have native topologies despite high structural variability.
    38. (2000). Transition-state structure as a unifying basis in protein-folding mechanisms: Contact order, chain topology, stability, and the extended nucleus mechanism.
    39. (1996). Universality and diversity of the protein folding scenarios: a comprehensive analysis with the aid of a lattice model.
    40. (2007). Use of the weighted histogram analysis method for the analysis of simulated and parallel tempering simulations.
    41. (2009). What have we learned from the studies of two-state folders, and what are the unanswered questions about two-state protein folding?

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