Premium
A molecular dynamics analysis of protein structural elements
Author(s) -
Post Carol Beth,
Dobson Christopher M.,
Karplus Martin
Publication year - 1989
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.340050409
Subject(s) - lysozyme , molecular dynamics , dihedral angle , chemistry , crystallography , substrate (aquarium) , loop (graph theory) , helix (gastropod) , chemical physics , protein structure , active site , dynamics (music) , protein secondary structure , molecular physics , physics , computational chemistry , molecule , biology , enzyme , hydrogen bond , mathematics , ecology , biochemistry , organic chemistry , combinatorics , snail , acoustics
The relation between protein secondary structure and internal motions was examined by using molecular dynamics to calculate positional fluctuations of individual helix, β‐sheet, and loop structural elements in free and substrate‐bound hen egg‐white lysozyme. The time development of the fluctuations revealed a general correspondence between structure and dynamics; the fluctuations of the helices and β‐sheets converged within the 101 psec period of the simulation and were lower than average in magnitude, while the fluctuations of theloop regions were not converged and were mostly larger than average in magnitude. Notable exceptions to this pattern occurred in the substrate‐bound simulation. A loop region (residues 101–107) of the active site cleft had significantly reduced motion due to interactions withthe substrate. Moreover, part of a loop and a 3 10 helix (residues of 67–88) not in contact with the substrate showeda marked increase in fluctuations. That these differences in dynamics of free and substrate‐bound lysozyme did not result simply from sampling errors was established by an analysis of the variations in the fluctuationsof the two halves of the 101 psec simulation of free lysozyme. Concerted transitions of four to five mainchain ϕ and ψ angles between dihedral wells were shown to be responsible for large coordinate shifts in the loops. These transitions displaced six or fewer residues and took place eitherabruptly, in 1 psec or less, or with a diffusive character over 5–10 psec. Displacements of rigid secondary structures involved longer timescale motions in bound lysozyme; a 0.5 Å rms change in the position of a helix occurred over the 55 psec simulation period. This helix reorientation within the protein appears to be a response to substrate binding. There was little correlation between the solvent accessible surface areaand the dynamics of the different structural elements.