Replica-exchange conformational

Figure 10-5. Representative conformations of the (5 amyloid peptide (10-42) under different pH conditions. The conformations were obtained as centroids of the most populated clusters from the replica-exchange CPHMD folding simulations [43, 44]. The N-terminal residues 10-28 are shown in blue the C-terminal residues 29-42 are shown in red. In the most aggregation-prone state (pH 6), the side chains of the central hydrophobic cluster Leu-17, Val-18, Phe-19, Phe-20 and Ala-21 are shown as van der Waals spheres in pink, grey, cyan, purple and green, respectively...

Molecular dynamics has also been used to replace the MC moves for conformational advancement [43]. In the molecular dynamics version of parallel tempering, often referred to as replica exchange molecular dynamics, momenta are used in the propagation scheme such that a constant temperature is maintained between the swaps. After the swap in conformational space (with the same acceptance criterion as in the MC implementation), a readjustment in momentum space is also needed. This is done by renewing the momenta for replica i by the transformation... 

QUANTIFYING SOLVATION EFFECTS ON PEPTIDE CONFORMATIONS A QM/MM REPLICA EXCHANGE STUDY... 

Abstract We present replica exchange molecular dynamics calculations of the conformational space... 

We applied replica exchange molecular dynamics (REMD) calculations for conformational sampling of the AD in explicit water, where the AD is treated quantum mechanically and the water molecules classically, using the TIP3P [29] model. For comparison purposes, the same calculation is done where the AD is treated by a classical force field, using our recently developed AMBER ff99SB [30] parameters. 

This chapter highlighted the use of replica exchange molecular dynamics calculations for the investigation of the performance of the PM3, PDDG/PM3 and PM3PC Hamiltonians as applied for the conformational equilibrium of alanine dipeptide in the gas phase and water solution, a convenient model system for the study of biological molecules. 

NMR residual dipolar couplings (RDCs), in the form of the projection angles between the respective internuclear bond vectors, have been used by Haliloglu et as structural restraints in the ab initio structure prediction of a test set of six proteins. The restraints have been applied using a recently developed SICHO (5/de CHain Only) lattice protein model that employs a replica exchange Monte Carlo algorithm to search conformational space. The proteins studied were ACP (77 residues), rubredoxin (53 residues), NSl, a 73 residue RNA binding/dimeriz-ation domain, Nodf (35 residues), Crd (137 residues) and Bret domain with 92 residues. 

As discussed in Section II. D, the replica exchange Monte Carlo method appears to be an efficient tool for searching the conformational space of reduced protein... 

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