Biomedical Engineering Reference
In-Depth Information
the process of molecular evolution. The three current research trajectories have
developed more independently than would be desirable, as models from each
subfield can be useful in other subfields. Further, incorporation of population
genetic models into molecular evolution is more advanced than the incorporation of
structural and functional considerations. However, it is with this growing multiscale
modeling trajectory that a key understanding of the evolution of cell and molecular
systems can be generated, both in the details and in the processes.
Acknowledgements D.A.L. is funded by NSF DBI-0743374 and NIH-INBRE award P20
RR016474. A.I.T. is supported by the aforementioned NSF award, while J.A.G. is supported by
the aforementioned NIH-INBRE award.
References
1. Gillespie, J.H.: Some properties of finite populations experiencing strong selection and weak
mutation. Am. Nat. 121 , 691-708 (1983)
2. Bornberg-Bauer, E., Chan, H.S.: Modeling evolutionary landscapes: Mutational stability,
topology, and superfunnels in sequence space. PNAS. 96 , 10689-10694 (1999)
3. Melin, R., Li, H., Wingreen, N.S., Tang, C.: Designability, thermodynamic stability, and
dynamics in protein folding: a lattice model study. J. Chem. Phys. 110 , 1252-1262 (1999)
4. Sali, A., Shakhnovich, E., Karplus, M.: How does a protein fold? Nature. 369 , 248-251 (1994)
5. Miyazawa, S., Jernigan, R.: Estimation of effective interresidue contact energies from protein
crystal structures- Quasi-chemical approximation. Macromol. 18 , 534-552 (1985)
6. Levinthal, C.: Are there pathways for protein folding? J. Chim. Phys. 65 , 44-45 (1968)
7. Li, L., Mirny, L.A., Shakhnovich, E.I.: Kinetics, thermodynamics and evolution of non-native
interactions in a protein folding nucleus. Nat. Struct. Mol. Biol. 7 , 336-342 (2000)
8. Williams, P., Pollock, D., Goldstein, R.: Evolution of functionality in lattice proteins. J. Mol.
Graph. Model. 19 , 150-156 (2001)
9. Bloom, J., Wilke, C., Arnold, F.A.C.: Stability and the evolvability of function in a model
protein. Biophys. J. 86 , 2758-2764 (2004)
10. Rastogi, S., Liberles, D.: Subfunctionalization of duplicated genes as a transition state to
neofunctionalization. BMC Evol. Biol. 5 , 28 (2005)
11. He, X., Zhang, J.: Rapid Subfunctionalization accompanied by prolonged and substantial
neofunctionalization in duplicate gene evolution. Genetics. 169 , 1157-1164 (2005)
12. Massey, S.E., Churbanov, A., Rastogi, S., Liberles, D.A.: Characterizing positive and negative
selection and their phylogenetic effects. Gene. 418 , 22-26 (2008)
13. Castoe, T.A., de Koning, A.P.J., Kim, H.M., Gu, W., Noonan, B.P., Naylor, G., Jiang, Z.J.,
Parkinson, C.L., Pollock, D.D.: Evidence for an ancient adaptive episode of convergent
molecular evolution. PNAS. 106 , 8986-8991 (2009)
14. Taverna, D., Goldstein, R.: Why are proteins marginally stable? Proteins. 46 , 105-109 (2002)
15. Bastolla, U., Farwer, J., Knapp, E.W., Vendruscolo, M.: How to guarantee optimal stability
for most representative structures in the protein data bank. Protein. Struct. Funct. Bioinf. 44 ,
79-96 (2001)
16. Robinson, D.M., Jones, D.T., Kishino, H., Goldman, N., Thorne, J.L.: Protein evolution with
dependence among codons due to tertiary structure. Mol. Biol. Evol. 20 , 1692-1704 (2003)
17. Parisi, G., Echave, J.: Structural constraints and emergence of sequence patterns in protein
evolution. Mol. Biol. Evol. 18 , 750-756 (2001)
18. Bastolla, U., Porto, M., Eduardo Roman, M.H., Vendruscolo, M.H.: Connectivity of neutral
networks, overdispersion, and structural conservation in protein evolution. J. Mol. Evol. 56 ,
243-254 (2003)
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