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Analysis of the loop-helix interaction in bundle motif protein structures (1995)

Thompson, Thomas B. ; Chou, Kuo-Chen ; Zheng, Chong

Springer

The protein journal 14 (1995), S. 559-566

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ISSN: 1573-4943

Keywords: Bovine somatotropin ; methemerythrin ; cytochrome b-562 ; cytochrome c′ ; CHARMM ; GROMOS ; UHBD

Source: Springer Online Journal Archives 1860-2000

Topics: Chemistry and Pharmacology

Notes: Abstract Molecular dynamics simulations and energy analysis have been carried out to study the structural mobility and stability of the four α-helix bundle motifs. The simulation results as well as the X-ray data show that the atomic RMS fluctuation is larger at the loop region for four representative proteins investigated: methemerythrin, cytochrome b-562, cytochrome c′, and bovine somatotropin. The loop-loop, helix-helix, and loop-helix interactions are computed for the unfolded and folded proteins. In the folded and solvated protein structures the loop-helix interaction is stronger than the helix-helix interaction, especially in the electrostatic component. But the stabilization energies of both the loop-helix and the helix-helix interactions relative to the those of an unfolded structure are of the same order of magnitude. The stabilization due to protein-solvent interaction is greater in the helix region than in the loop region. The percentage of hydrophilic solvent accessible area for the four proteins studied was calculated with the method of Eisenberg and McLachlan. The percentage of the hydrophilic area is greater in the loops than in the helices. A Poisson-Boltzmann calculation shows that the potential from the loops acting on a helix is generally more negative than that from other helices.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/BF01886882

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Effects of the cutoff center on the mean potential and pair distribution functions in liquid water (1995)

Gabdoulline, Razif R. ; Zheng, Chong

New York, NY [u.a.] : Wiley-Blackwell

Journal of Computational Chemistry 16 (1995), S. 1428-1433

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ISSN: 0192-8651

Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry

Source: Wiley InterScience Backfile Collection 1832-2000

Topics: Chemistry and Pharmacology , Computer Science

Notes: Molecular dynamics simulations of extended simple point charge (SPC/E) water have been performed to study the effects of the truncation of long-range interactions on some calculated bulk properties of the liquid. The mean potential calculated in liquid water is sensitive to the choice of the cutoff center in the water molecule. The pair distribution function is also dependent on this choice, although not as strongly as the mean potential. An analysis is carried out to understand the origin of these effects. A common cutoff center is at the oxygen atom in the water molecule, but our study shows that this choice does not yield a mean potential value consistent with a more accurate estimate when no cutoff is applied. © 1995 John Wiley & Sons, Inc.

Additional Material: 6 Ill.