DNA sequence-dependent deformability deduced from proteinâDNA crystal complexes Export

@article{citeulike:622015, abstract = {The deformability of double helical DNA is critical for its packaging in the cell, recognition by other molecules, and transient opening during biochemically important processes. Here, a complete set of sequence-dependent empirical energy functions suitable for describing such behavior is extracted from the fluctuations and correlations of structural parameters in DNA\^{a}€“protein crystal complexes. These elastic functions provide useful stereochemical measures of the local base step movements operative in sequence-specific recognition and protein-induced deformations. In particular, the pyrimidine-purine dimers stand out as the most variable steps in the DNA\^{a}€“protein complexes, apparently acting as flexible \^{a}€œhinges\^{a}€ fitting the duplex to the protein surface. In addition to the angular parameters widely used to describe DNA deformations (i.e., the bend and twist angles), the translational parameters describing the displacements of base pairs along and across the helical axis are analyzed. The observed correlations of base pair bending and shearing motions are important for nonplanar folding of DNA in nucleosomes and other nucleoprotein complexes. The knowledge-based energies also offer realistic three-dimensional models for the study of long DNA polymers at the global level, incorporating structural features beyond the scope of conventional elastic rod treatments and adding a new dimension to literal analyses of genomic sequences.}, address = {Department of Chemistry, Rutgers University, New Brunswick, NJ 08903, USA. olson@rutchem.rutgers.edu}, author = {Olson, Wilma K. and Gorin, Andrey A. and Lu, Xiang-Jun and Hock, Lynette M. and Zhurkin, Victor B.}, citeulike-article-id = {622015}, citeulike-linkout-0 = {http://www.pnas.org/content/95/19/11163.long.abstract}, citeulike-linkout-1 = {http://www.pnas.org/content/95/19/11163.long.full.pdf}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/9736707}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=9736707}, day = {15}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, keywords = {dna, programmi}, month = {September}, number = {19}, pages = {11163--11168}, posted-at = {2009-09-14 16:20:30}, priority = {2}, title = {DNA sequence-dependent deformability deduced from protein\^{a}€“DNA crystal complexes}, url = {http://www.pnas.org/content/95/19/11163.long.abstract}, volume = {95}, year = {1998} }

TY - JOUR ID - citeulike:622015 L3 - citeulike-article-id:622015 N2 - The deformability of double helical DNA is critical for its packaging in the cell, recognition by other molecules, and transient opening during biochemically important processes. Here, a complete set of sequence-dependent empirical energy functions suitable for describing such behavior is extracted from the fluctuations and correlations of structural parameters in DNA–protein crystal complexes. These elastic functions provide useful stereochemical measures of the local base step movements operative in sequence-specific recognition and protein-induced deformations. In particular, the pyrimidine-purine dimers stand out as the most variable steps in the DNA–protein complexes, apparently acting as flexible “hinges” fitting the duplex to the protein surface. In addition to the angular parameters widely used to describe DNA deformations (i.e., the bend and twist angles), the translational parameters describing the displacements of base pairs along and across the helical axis are analyzed. The observed correlations of base pair bending and shearing motions are important for nonplanar folding of DNA in nucleosomes and other nucleoprotein complexes. The knowledge-based energies also offer realistic three-dimensional models for the study of long DNA polymers at the global level, incorporating structural features beyond the scope of conventional elastic rod treatments and adding a new dimension to literal analyses of genomic sequences. IS - 19 JF - Proceedings of the National Academy of Sciences of the United States of America SN - 0027-8424 AD - Department of Chemistry, Rutgers University, New Brunswick, NJ 08903, USA. olson@rutchem.rutgers.edu EP - 11168 TI - DNA sequence-dependent deformability deduced from protein–DNA crystal complexes VL - 95 SP - 11163 KW - dna KW - programmi AU - Olson, Wilma AU - Gorin, Andrey AU - Lu, Xiang-Jun AU - Hock, Lynette AU - Zhurkin, Victor PY - 1998/09/15/ UR - http://www.pnas.org/content/95/19/11163.long.abstract ER -