Predicting protein folding rates from geometric contact and amino acid sequence

Protein folding speeds are known to vary over more than eight orders of magnitude. Plaxco, Simons, and Baker (see References) first showed a correlation of folding speed with the topology of the native protein. That and subsequent studies showed, if the native structure of a protein is known, its folding speed can be predicted reasonably well through a correlation with the “localness” of the contacts in the protein. In the present work, we develop a related measure, the geometric contact number, N α, which is the number of nonlocal contacts that are well‐packed, by a Voronoi criterion. We find, first, that in 80 proteins, the largest such database of proteins yet studied, N α is a consistently excellent predictor of folding speeds of both two‐state fast folders and more complex multistate folders. Second, we show that folding rates can also be predicted from amino acid sequences directly, without the need to know the native topology or other structural properties.

[1]  Oxana V Galzitskaya,et al.  Entropy capacity determines protein folding , 2006, Proteins.

[2]  Jie Liang,et al.  Protein folding dynamics via quantification of kinematic energy landscape. , 2006, Physical review letters.

[3]  K. Dill,et al.  Phi values in protein-folding kinetics have energetic and structural components. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[4]  Marco Punta,et al.  Protein folding rates estimated from contact predictions. , 2005, Journal of molecular biology.

[5]  M. Michael Gromiha,et al.  A Statistical Model for Predicting Protein Folding Rates from Amino Acid Sequence with Structural Class Information , 2005, J. Chem. Inf. Model..

[6]  Athi N. Naganathan,et al.  Scaling of folding times with protein size. , 2005, Journal of the American Chemical Society.

[7]  A. Finkelstein,et al.  Prediction of protein folding rates from the amino acid sequence-predicted secondary structure , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[8]  A. Poupon.  Voronoi and Voronoi-related tessellations in studies of protein structure and interaction. , 2004, Current opinion in structural biology.

[9]  Ken A Dill,et al.  Cooperativity in two‐state protein folding kinetics , 2003, Protein science : a publication of the Protein Society.

[10]  Z. Zeng,et al.  A SEQUENCE FUNCTION REVEALS NEW FEATURES IN β-PROTEIN FOLDING , 2003 .

[11]  Ken A Dill,et al.  Folding kinetics of two-state proteins: effect of circularization, permutation, and crosslinks. , 2003, Journal of molecular biology.

[12]  Igor B Kuznetsov,et al.  Class‐specific correlations between protein folding rate, structure‐derived, and sequence‐derived descriptors , 2003, Proteins.

[13]  Kevin W Plaxco,et al.  Contact order revisited: Influence of protein size on the folding rate , 2003, Protein science : a publication of the Protein Society.

[14]  Nicole Sips,et al.  Structural determinants of the rate of protein folding. , 2003, Journal of theoretical biology.

[15]  K. Dill,et al.  Folding rates and low-entropy-loss routes of two-state proteins. , 2003, Journal of molecular biology.

[16]  Z. Zeng,et al.  A Simple Parameter Relating Sequences with Folding Rates of Small α Helical Proteins , 2003 .

[17]  Dmitry N Ivankov,et al.  Chain length is the main determinant of the folding rate for proteins with three‐state folding kinetics , 2003, Proteins.

[18]  Jie Liang,et al.  Simplicial edge representation of protein structures and alpha contact potential with confidence measure , 2003, Proteins.

[19]  A. Roitberg,et al.  Smaller and faster: the 20-residue Trp-cage protein folds in 4 micros. , 2002, Journal of the American Chemical Society.

[20]  S. Takada,et al.  Roles of native topology and chain-length scaling in protein folding: a simulation study with a Go-like model. , 2001, Journal of molecular biology.

[21]  Ivet Bahar,et al.  Transition states and the meaning of Φ-values in protein folding kinetics , 2001, Nature Structural Biology.

[22]  M. Gromiha,et al.  Comparison between long-range interactions and contact order in determining the folding rate of two-state proteins: application of long-range order to folding rate prediction. , 2001, Journal of molecular biology.

[23]  D Baker,et al.  Topology, stability, sequence, and length: defining the determinants of two-state protein folding kinetics. , 2000, Biochemistry.

[24]  J R Bienkowska,et al.  Filtered neighbors threading , 1999, Proteins.

[25]  D. Baker,et al.  Contact order, transition state placement and the refolding rates of single domain proteins. , 1998, Journal of molecular biology.

[26]  W. Taylor,et al.  Multiple sequence threading: an analysis of alignment quality and stability. , 1997, Journal of molecular biology.

[27]  A V Finkelstein,et al.  Rate of protein folding near the point of thermodynamic equilibrium between the coil and the most stable chain fold. , 1997, Folding & design.

[28]  D. Thirumalai,et al.  From Minimal Models to Real Proteins: Time Scales for Protein Folding Kinetics , 1995 .

[29]  K. Dill,et al.  Cooperativity in protein-folding kinetics. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[30]  K. Dill,et al.  Protein core assembly processes , 1993 .

[31]  Akira Ishihama,et al.  Stimulation of the phage λ pL promoter by integration host factor requires the carboxy terminus of the α-subunit of RNA polymerase , 1992 .

[32]  T. Salakoski,et al.  Selection of a representative set of structures from brookhaven protein data bank , 1992, Proteins.

[33]  F M Richards,et al.  Areas, volumes, packing and protein structure. , 1977, Annual review of biophysics and bioengineering.

[34]  Hongyi Zhou,et al.  Folding rate prediction using total contact distance. , 2002, Biophysical journal.

[35]  Hue Sun Chan,et al.  Compact Polymers , 2001 .

[36]  B. Noble.  Applied Linear Algebra , 1969 .