Understanding Protein Evolution: From Protein Physics to Darwinian Selection Export

@article{citeulike:4013312, abstract = {Efforts in whole-genome sequencing and structural proteomics start to provide a global view of the protein universe, the set of existing protein structures and sequences. However, approaches based on the selection of individual sequences have not been entirely successful at the quantitative description of the distribution of structures and sequences in the protein universe because evolutionary pressure acts on the entire organism, rather than on a particular molecule. In parallel to this line of study, studies in population genetics and phenomenological molecular evolution established a mathematical framework to describe the changes in genome sequences in populations of organisms over time. Here, we review both microscopic (physics-based) and macroscopic (organism-level) models of protein-sequence evolution and demonstrate that bridging the two scales provides the most complete description of the protein universe starting from clearly defined, testable, and physiologically relevant assumptions.}, author = {Zeldovich, Konstantin B. and Shakhnovich, Eugene I.}, citeulike-article-id = {4013312}, citeulike-linkout-0 = {http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.physchem.58.032806.104449}, citeulike-linkout-1 = {http://dx.doi.org/10.1146/annurev.physchem.58.032806.104449}, doi = {10.1146/annurev.physchem.58.032806.104449}, journal = {Annual Review of Physical Chemistry}, keywords = {lattice, modeling, protein\_evolution}, number = {1}, pages = {105--127}, posted-at = {2009-11-08 11:00:55}, priority = {2}, title = {Understanding Protein Evolution: From Protein Physics to Darwinian Selection}, url = {http://dx.doi.org/10.1146/annurev.physchem.58.032806.104449}, volume = {59}, year = {2008} }

TY - JOUR ID - citeulike:4013312 L3 - citeulike-article-id:4013312 N2 - Efforts in whole-genome sequencing and structural proteomics start to provide a global view of the protein universe, the set of existing protein structures and sequences. However, approaches based on the selection of individual sequences have not been entirely successful at the quantitative description of the distribution of structures and sequences in the protein universe because evolutionary pressure acts on the entire organism, rather than on a particular molecule. In parallel to this line of study, studies in population genetics and phenomenological molecular evolution established a mathematical framework to describe the changes in genome sequences in populations of organisms over time. Here, we review both microscopic (physics-based) and macroscopic (organism-level) models of protein-sequence evolution and demonstrate that bridging the two scales provides the most complete description of the protein universe starting from clearly defined, testable, and physiologically relevant assumptions. IS - 1 JF - Annual Review of Physical Chemistry EP - 127 TI - Understanding Protein Evolution: From Protein Physics to Darwinian Selection VL - 59 SP - 105 KW - lattice KW - modeling KW - protein_evolution AU - Zeldovich, Konstantin AU - Shakhnovich, Eugene PY - 2008/// UR - http://dx.doi.org/10.1146/annurev.physchem.58.032806.104449 ER -