PMC:1867812 / 10038-13109 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":"2.1 Protein Folding Trajectories\nAdvances in high-performance computing technologies and molecular dynamics have led to successful simulations of folding dynamics for (small) proteins at the atomistic level [8]. Such simulations result in a large number of folding trajectories, each of which consists of a series of 3D conformations of the protein under simulation. These conformations are usually sampled regularly (e.g., every 200fs) during a simulation. In this article, we also refer to each conformation as a folding frame or simply a frame. Furthermore, to represent a protein conformation, we adopt one of the commonly adopted representation schemes, where a conformation is represented as a sequence of α-carbons (Cα) located in 3D space.\nIn this article, we focus on the folding trajectories of two mini proteins: BBA5 (Protein Data Bank ID) [9] and GSGS (orBeta3s) [10,11]. Such trajectories were produced by the Folding@ home research group at Stanford University [12].\nBBA5 is a 23-residue protein that folds at microsecond timescale. The native structure (or fold) of BBA5 shows a β-hairpin involving residues 1–10 and centering about residues 4–5. It also includes an α-helix involving the remaining residues 11–23. By convention, residues are numbered increasingly from the N-terminal to C-terminal of a protein. Figure 1(a) illustrates the native conformation of BBA5. The two folding trajectories, referred to as T23 and T24 respectively, are of different length. T23 consists of a series of 192 conformations (or frames), while T24 has 150 frames. Each conformation is described at atomistic level in PDB format adopted by the Protein Data Bank programs. GSGS (or Beta3s) is a 20-residue peptide with an average folding rate of microseconds. Its NMR conformation shows a three-stranded anti-parallel β-sheet with turns at residues 6 – 7 and 14 – 15. Figure 2(a) depicts this native conformation. There are a total of 5 GSGS folding trajectories: T1, T2, T3, T4, and T5. The number of conformations in each trajectory is listed in Table 1. Similar to BBA5, each conformation corresponds to one PDB file. Pande et al. explained in detail on the simulation model and methods employed to produce such trajectories [8,9].\nFigure 1 Different conformations of the small protein BBA5, where only the Cα atoms are shown. (a)The native NMR structure of BBA5 based on data from the SCOP website. (b)The initial conformation of both folding trajectories. (c)The last conformation in the first trajectory. (d)The last conformation in the second trajectory.\nFigure 2 Different conformations of the GSGS peptide, where only the Cα atoms are shown. (a)The native NMR conformation of GSGS. (b)The initial conformation in all the five folding trajectories. (c)The last conformation in the 1st trajectory. (d)The last conformation in the 3rd trajectory. (e)The last conformation in the 5th trajectory.\nTable 1 A brief description of the GSGS folding trajectories.\nTrajectory ID Total number of conformations\nT 1 25,664\nT 2 30,075\nT 3 19,649\nT 4 25,263\nT 5 25,664","divisions":[{"label":"title","span":{"begin":0,"end":32}},{"label":"p","span":{"begin":33,"end":747}},{"label":"p","span":{"begin":748,"end":981}},{"label":"p","span":{"begin":982,"end":2235}},{"label":"figure","span":{"begin":2236,"end":2563}},{"label":"label","span":{"begin":2236,"end":2244}},{"label":"caption","span":{"begin":2246,"end":2563}},{"label":"p","span":{"begin":2246,"end":2563}},{"label":"figure","span":{"begin":2564,"end":2903}},{"label":"label","span":{"begin":2564,"end":2572}},{"label":"caption","span":{"begin":2574,"end":2903}},{"label":"p","span":{"begin":2574,"end":2903}},{"label":"label","span":{"begin":2904,"end":2911}},{"label":"caption","span":{"begin":2913,"end":2966}},{"label":"p","span":{"begin":2913,"end":2966}},{"label":"tr","span":{"begin":2967,"end":3011}},{"label":"td","span":{"begin":2967,"end":2980}},{"label":"td","span":{"begin":2982,"end":3011}},{"label":"tr","span":{"begin":3012,"end":3023}},{"label":"td","span":{"begin":3012,"end":3016}},{"label":"td","span":{"begin":3017,"end":3023}},{"label":"tr","span":{"begin":3024,"end":3035}},{"label":"td","span":{"begin":3024,"end":3028}},{"label":"td","span":{"begin":3029,"end":3035}},{"label":"tr","span":{"begin":3036,"end":3047}},{"label":"td","span":{"begin":3036,"end":3040}},{"label":"td","span":{"begin":3041,"end":3047}},{"label":"tr","span":{"begin":3048,"end":3059}},{"label":"td","span":{"begin":3048,"end":3052}},{"label":"td","span":{"begin":3053,"end":3059}},{"label":"td","span":{"begin":3060,"end":3064}}],"tracks":[{"project":"2_test","denotations":[{"id":"17407611-12422224-1692915","span":{"begin":853,"end":854},"obj":"12422224"},{"id":"17407611-10984515-1692916","span":{"begin":877,"end":879},"obj":"10984515"},{"id":"17407611-11243792-1692917","span":{"begin":880,"end":882},"obj":"11243792"},{"id":"17407611-12422224-1692918","span":{"begin":2232,"end":2233},"obj":"12422224"}],"attributes":[{"subj":"17407611-12422224-1692915","pred":"source","obj":"2_test"},{"subj":"17407611-10984515-1692916","pred":"source","obj":"2_test"},{"subj":"17407611-11243792-1692917","pred":"source","obj":"2_test"},{"subj":"17407611-12422224-1692918","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#93ec97","default":true}]}]}}