Flexibility and packing in proteins Export

@article{citeulike:543543, abstract = {10.1073/pnas.032522499 Structural flexibility is an essential attribute, without which few proteins could carry out their biological functions. Much information about protein flexibility has come from x-ray crystallography, in the form of atomic mean-square displacements (AMSDs) or factors. Profiles showing the AMSD variation along the polypeptide chain are usually interpreted in dynamical terms but are ultimately governed by the local features of a highly complex energy landscape. Here, we bypass this complexity by showing that the AMSD profile is essentially determined by spatial variations in local packing density. On the basis of elementary statistical mechanics and generic features of atomic distributions in proteins, we predict a direct inverse proportionality between the AMSD and the contact density, i.e., the number of noncovalent neighbor atoms within a local region of ∼1.5 nm volume. Testing this local density model against a set of high-quality crystal structures of 38 nonhomologous proteins, we find that it accurately and consistently reproduces the prominent peaks in the AMSD profile and even captures minor features, such as the periodic AMSD variation within α helices. The predicted rigidifying effect of crystal contacts also agrees with experimental data. With regard to accuracy and computational efficiency, the model is clearly superior to its predecessors. The quantitative link between flexibility and packing density found here implies that AMSDs provide little independent information beyond that contained in the mean atomic coordinates.}, author = {Halle, Bertil}, citeulike-article-id = {543543}, citeulike-linkout-0 = {http://dx.doi.org/10.1073/pnas.032522499}, citeulike-linkout-1 = {http://www.pnas.org/content/99/3/1274.abstract}, citeulike-linkout-2 = {http://www.pnas.org/content/99/3/1274.full.pdf}, citeulike-linkout-3 = {http://www.pnas.org/cgi/content/abstract/99/3/1274}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/11818549}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=11818549}, day = {5}, doi = {10.1073/pnas.032522499}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, keywords = {free\_energy, gnm, protein\_dynamics, protein\_flexibility}, month = {February}, number = {3}, pages = {1274--1279}, posted-at = {2009-09-19 15:55:12}, priority = {2}, title = {Flexibility and packing in proteins}, url = {http://dx.doi.org/10.1073/pnas.032522499}, volume = {99}, year = {2002} }

TY - JOUR ID - citeulike:543543 L3 - citeulike-article-id:543543 N2 - 10.1073/pnas.032522499 Structural flexibility is an essential attribute, without which few proteins could carry out their biological functions. Much information about protein flexibility has come from x-ray crystallography, in the form of atomic mean-square displacements (AMSDs) or factors. Profiles showing the AMSD variation along the polypeptide chain are usually interpreted in dynamical terms but are ultimately governed by the local features of a highly complex energy landscape. Here, we bypass this complexity by showing that the AMSD profile is essentially determined by spatial variations in local packing density. On the basis of elementary statistical mechanics and generic features of atomic distributions in proteins, we predict a direct inverse proportionality between the AMSD and the contact density, i.e., the number of noncovalent neighbor atoms within a local region of ∼1.5 nm volume. Testing this local density model against a set of high-quality crystal structures of 38 nonhomologous proteins, we find that it accurately and consistently reproduces the prominent peaks in the AMSD profile and even captures minor features, such as the periodic AMSD variation within α helices. The predicted rigidifying effect of crystal contacts also agrees with experimental data. With regard to accuracy and computational efficiency, the model is clearly superior to its predecessors. The quantitative link between flexibility and packing density found here implies that AMSDs provide little independent information beyond that contained in the mean atomic coordinates. IS - 3 JF - Proceedings of the National Academy of Sciences of the United States of America EP - 1279 TI - Flexibility and packing in proteins VL - 99 SP - 1274 KW - free_energy KW - gnm KW - protein_dynamics KW - protein_flexibility AU - Halle, Bertil PY - 2002/02/05/ UR - http://dx.doi.org/10.1073/pnas.032522499 ER -