Theoretical Methods in the Analysis of Peptide Conformation

Zimmerman, S. Scott

doi:10.1016/b978-0-12-304207-1.50010-2

Cited by 3 publications

(5 citation statements)

References 190 publications

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“…The results from experimental and computational studies of the structure and conformation of GnRH analogs emphasize the importance of a complete exploration of the conformational space of the peptides (176). Whether the analogs are conformationally constrained or linear, the complete structural characterization is necessary before a reliable consensus on the structural features most important for receptor interaction can be reached (174).…”

Section: Exploration Of the Entire Conformation Space Of Gnrh Analogsmentioning

confidence: 98%

“…In spite of the significant limitations of the methods for energy-based evaluation of peptide conformations (for a review of methods see Ref. 176) that were available at the time for studies of peptide molecules of the size of GnRH, the early studies identified the central characteristic of the bioactive conformation of GnRH, the ␤-bend involving the Tyr-Gly-Leu-Arg in positions 5-8 (see Fig. 9).…”

Section: A Early Studies Of Gnrh Conformationmentioning

confidence: 99%

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Molecular Mechanisms of Ligand Interaction with the Gonadotropin-Releasing Hormone Receptor

1997

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Section: Exploration Of the Entire Conformation Space Of Gnrh Analogsmentioning

confidence: 98%

Section: A Early Studies Of Gnrh Conformationmentioning

confidence: 99%

Molecular Mechanisms of Ligand Interaction with the Gonadotropin-Releasing Hormone Receptor

1997

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“…A contour plot of the configurational energy levels in Nacetyl-/V-methylalaninamide has been previously published. 8,9 Since that plot was made, the parameters used in PepCAD have been modified to give results more closely approximating empirically observed energies. 10,11 In the earlier work,8,9 the dihedral angle of the side-chain methyl group was fixed at 60°.…”

Section: Resultsmentioning

confidence: 99%

CONTOUR, a general contour-plotting program for IBM-compatible microcomputers, and its application to peptides

Davidson¹,

Zimmerman²

1990

J. Chem. Inf. Comput. Sci.

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A computer program, CONTOUR, was developed for displaying contour plots on an IBM-compatible microcomputer. The program interpolates between abscissa and ordinate data values to display lines of constant elevation on a rectangular grid. The contour plot can be printed on a dot-matrix or laser printer using the MS-DOS Print Screen feature or using a graphics "capture" program. CONTOUR was used to create conformational energy contour plots of N-formylalanine, Nacetylalanine, and N-acetyl-N'-methylalaninamide.

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“…The use of empirical potential energy functions to describe peptide conformations (7) began with the work of Sasisekharan and Ramachandran (8), Scheraga (9), Lifson and co-workers (lo), Gelin and Karplus (1 I), Hagler (l2), and Levitt (13). The early work initially employed a hard sphere model, which was gradually improved to include van der Waals and electrostatic interactions, and a cosine term for torsional interactions (14,15). The computational procedure ECEPP (Empirical Conformation Energy Program for Peptides) (16) was then documented and distributed by Scheraga.…”

Section: Rconh C02r1mentioning

confidence: 99%

“…An STO-3G optimization of propane was used to obtain C-H (type 1-5) bond lengths for the side chains of amino acids such as valine and leucine. Finally, a 3-21G* optimization of 2-mercaptoethanol provided the S-H (type [15][16][17][18][19][20][21][22][23][24][25] bond length of cysteine.…”

Section: Atom Types Of Mmpepmentioning

confidence: 99%

MMPEP: Development and evaluation of peptide parameters for Allinger's MMP2(85) programme, including calculations on crambin and insulin

Wolfe¹,

Weaver²,

Yang³

1988

Can. J. Chem.

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SAUL WOLFE, DONALD FREDRIC WEAVER, and KIYULL YANG. Can. J. Chem. 66, 2687Chem. 66, (1988. Allinger's MMP2(85) program has been converted to an IBM environment, and the dimensions expanded to a current maximum of 999 atoms. Substantial additional expansion will be possible. An all-atom set of parameters, which permit Allinger's comprehensive force field to be applied to the molecular mechanics treatment of peptides, has been determined. These parameters, termed MMPEP, contain 21 atom types: 5 for carbon, 6 for hydrogen, 5 for nitrogen, 4 for oxygen, and 1 for sulfur, and are based on crystallographic heavy atom bond lengths and bond angles, vibrational and microwave spectra, and ab initio calculations. To minimize the conformational energy of a peptide from an initial starting geometry, all internally stored parameters are released, and replaced by PEPCON, a 360-line external file containing the MMPEP parameters.The ability of the MMPEP parameterization of MM85 to reproduce experimental crystal structures has been tested on several peptides and polypeptides, and the use of a dielectric constant E = 78.5 D leads to the following results: Ala-Ala-Gly (rms = 0.261); Gly-Gly-Val (rms = 0.349); glutathione (rms = 0.417); crambin (327 heavy atoms; rms = 0.310 for all heavy atoms); insulin (389 heavy atoms; rms = 0.646 for all heavy atoms); the origins of deviations can be interpreted. No problems have been encountered in the application of the Newton-Raphson minimization procedure to such large molecules as crambin and insulin, even though all possible nonbonded interactions have been retained. On the IBM 3081 computer, real time minimization of tripeptides requires 1-2 min, crambin requires 250 min, and insulin 200 min. Since hydrogen bonding in Allinger's force field is a natural result of electrostatic and van der Waals interactions, in MMPEP hydrogen bonding is taken into account through the large number of hydrogen atom types and their different bond moments and van der Waals radii. Afin de vkrifier les possibilites du programme MM85 incorporant les paramttres MMPEP de reproduire les structures cristallines expkrimentales, on a utilisk plusieurs peptides et polypeptides; utilisant une constante diklectrique E = 78,5 D, on obtient les rksultats suivants : Ala-Ala-Gly (rms = 0,261); Gly-Gly-Val (rms = 0,349); glutathion (rms = 0,417); crambine (327 atomes lourds; rms = 0,3 10 pour tous les atomes lourds); insuline (389 atomes lourds; rms = 0,646 pour les atomes lourds); on peut interpriter les causes des dbviations. On n'a pas rencontrC de problemes dans I'application de la mkthode de minimisation de Newton-Raphson a des molkcules de la taille de la crambine et l'insuline, m&me si toutes les interactions non-likes ont kt6 conservkes. Sur un ordinateur IBM 3081, le temps rkel de minimisation des tripeptides est de 1 a 2 min; celui de la crambine est de 250 min et celui de l'insuline est de 200 min. Dans le champ de force d'Allinger, les liaisons hydrogtnes sont un rksultat nature1 des interactions klectrostatiques...

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Theoretical Methods in the Analysis of Peptide Conformation

Cited by 3 publications

References 190 publications

Molecular Mechanisms of Ligand Interaction with the Gonadotropin-Releasing Hormone Receptor

Molecular Mechanisms of Ligand Interaction with the Gonadotropin-Releasing Hormone Receptor

CONTOUR, a general contour-plotting program for IBM-compatible microcomputers, and its application to peptides

MMPEP: Development and evaluation of peptide parameters for Allinger's MMP2(85) programme, including calculations on crambin and insulin

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