Instantaneous normal modes as an unforced reaction coordinate for protein conformational transitions.

We present a novel sampling approach to explore large protein conformational transitions by determining unique substates from instantaneous normal modes calculated from an elastic network model, and applied to a progression of atomistic molecular dynamics snapshots. This unbiased sampling scheme allows us to direct the path sampling between the conformational end states over simulation timescales that are greatly reduced relative to the known experimental timescales. We use adenylate kinase as a test system to show that instantaneous normal modes can be used to identify substates that drive the structural fluctuations of adenylate kinase from its closed to open conformations, in which we observe 16 complete transitions in 4 mus of simulation time, reducing the timescale over conventional simulation timescales by two orders of magnitude. Analysis shows that the unbiased determination of substates is consistent with known pathways determined experimentally.

Antimutagenic efficacy of some natural compounds on cyclophosphamide-induced p53 alterations.

Mutations in the p53 tumour suppressor gene have been associated with chemical carcinogens. Natural antimutagens are promising modulators for reducing the cancer risk. The present study was carried out to assess the protective efficacy of some natural antimutagens against p53 alterations. We investigated the ability of curcumin (100 mg/kg BW) and chlorophyllin (3 mg/kg BW) pretreatment, for three times per week for three successive weeks, to inhibit mutations induced by intraperitoneal injection of a single dose of 40 mg/kg BW of cyclophosphamide (CP). Forty male albino rats were assigned into four groups: control nontreated group, CP-treated group, curcumin-CP-treated group, and chlorophyllin-CP-treated group. Liver samples were collected for DNA isolation two days after CP injection. The isolated DNA was used in single-strand conformational polymorphism (SSCP) analysis of polymerase chain reaction (PCR)-amplified products of four regions: two in exon 5, one in exon 6, and one in exon 7. The amplified products of p53 different regions were found to be in the expected molecular size of the designed primers. SSCP analysis of these amplified products showed that CP-induced mutation in the p53 gene was found only in exon 7 shifting its electrophoretic mobility. Chlorophyllin treatment prior to CP injection had a more potent protective efficacy (80%) than that with curcumin (33.3%).