PMC:1867812 / 31154-32564 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/1867812","sourcedb":"PMC","sourceid":"1867812","source_url":"https://www.ncbi.nlm.nih.gov/pmc/1867812","text":"As BBA5 and GSGS fold, the dynamics among their residues is constantly changing until it reaches an equilibrium. This means that two residues previously in contact may become out of contact later. As a result, bit-patterns present in one conformation may be absent in the next. The evolving nature of contacting residues and in turn bit-patterns, is essentially the consequence of a variety of weak interactions among amino acids at different levels. Such weak interactions include hydrogen bonds, electrostatic interactions, van der Waal's packing and hydrophobic interactions [24]. To capture these (potential) interactions, a simple yet effective method is to consider how close two amino acids are located from each other in 3D. We also adopt this method here. Specifically, we consider interactions between local 3D motifs captured by labeled bit-patterns. We denote such interactions as \"interactions among bit-patterns\". Let pi and pj be two bit-patterns in a protein conformation, and pi.listCα and pj.listCα be the list of α-carbons involved in pi and pj, respectively. We define piand pj as interacting bit-patterns if at least one pair of α-carbons, each from pi.listCα and pj.listCα are located within a short distance δ. Note that the value of δ should be greater than the distance that is being used to identify contacting α-carbons when generating contact maps. In our analysis, we set δ = 10 Å.","tracks":[]}