Energy functions for peptides and proteins. I. Derivation of a consistent force field including the hydrogen bond from amide crystals

Hagler, A. T.; Huler, E.; Lifson, Shneior

doi:10.1021/ja00824a004

Cited by 700 publications

(383 citation statements)

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“…For instance, Hagler et al (1974) optimized force-®eld parameters to agree with crystal dimensions, vaporization energies, etc. for a variety of small molecules with H-bonded amide groups, reaching the conclusion that van der Waals terms from the polar H atoms do not make a signi®cant contribution beyond what can be ®t with only electrostatic terms and van der Waals interactions for the heavy atoms.…”

Section: Adding H Atomsmentioning

confidence: 99%

“…'' In order to decide the best polar H radius for use in calculating contact dots, we have analyzed the spacings actually seen for non-polar-to-amide contacts and then compared the proposed radii to the shape of electrondensity distributions calculated by quantum mechanics. Figure 9(a) shows calculated electron density contours for an NH group (Bader et al, 1967), the nearly round shape of which has been used to argue for a negligible effect of the polar H van der Waals terms (Hagler et al, 1974). However, equivalent contours lie about 0.5 A Ê farther out in the H direction than elsewhere, a difference that can be quite crucial in tightly packed regions.…”

Section: Adding H Atomsmentioning

confidence: 99%

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Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation 1 1Edited by J. Thornton

Word

Lovell

Richardson

et al. 1999

Journal of Molecular Biology

1,310

1,150

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Section: Adding H Atomsmentioning

confidence: 99%

Section: Adding H Atomsmentioning

confidence: 99%

Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation 1 1Edited by J. Thornton

Word

Lovell

Richardson

et al. 1999

Journal of Molecular Biology

1,310

1,150

View full text Add to dashboard Cite

“…The calculations were performed on Silicon Graphics workstations. Several molecular dynamics (MD) trajectories were calculated with the DISCOVER software using different parametrizations: CVFF (Consistent Valence Force Field) (11,12) and the AMBER program (Assisted Model Building with Energy Refinement) (13,14). In addition, other programs with different force fields, e.g.…”

Section: Preparation Of the Ligand A Mixture Of 1-o-[3ј-(trifluoroacmentioning

confidence: 99%

NMR-Based, Molecular Dynamics- and Random Walk Molecular Mechanics-Supported Study of Conformational Aspects of a Carbohydrate Ligand (Galβ1-2Galβ1-R) for an Animal Galectin in the Free and in the Bound State

Siebert

Gilleron

Kaltner

et al. 1996

Biochemical and Biophysical Research Communications

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The binding of a carbohydrate to a lectin may affect the conformation of the ligand. To address this question for the galectin from chicken liver, the conformation of Gal␤1-2Gal␤1-R was analyzed in the free and in the galectin-bound state with 2D-ROESY-and 1D-as well as 2D-transferred NOE-experiments. A computerassisted analysis of spatial parameters of the ligand by molecular dynamics (MD) and random walk molecular mechanics (RAMM) calculations, taking different dielectric constants from ⑀ ‫ס‬ 1 to ⑀ ‫ס‬ 80 and various force fields into account, were instrumental to define the energetic minima of the free state. NMR-derived interresidual distance constraints enabled a conformational mapping. The two overlapping interresidual distance constraints obtained from transferred-NOE experiments of the galectin-ligand complex clearly support the notion that the conformation of the disaccharide in the bound state is at least very close to its global energy minimum state in solution. © 1996 Academic Press, Inc.Protein-carbohydrate interactions can guide crucial physiological reactions such as cell adhesion, inter-and intracellular glycoprotein routing and regulation of various cellular functions (1, 2). Their evident importance prompts to analyze in detail the molecular characteristics of this type of recognition in solution. The combination of computer-assisted calculations of the conformation and NMR-based experiments for the free ligand and lectin-saccharide complex provides a suitable tool to address this question. It enables us to compare spatial parameters of a certain ligand before and after association with members of a lectin family with similar binding specificity, e.g. to galactosides. Agglutinins of this class mediate cell-matrix interactions and enhance immune functions (3-5). Due to the remarkable affinity of Gal␤1-2Gal␤1-R to the immunomodulatory Viscum album agglutinin, reported previously (6, 7), we have chosen to map conformational aspects of this high-affinity ligand for galactoside-binding lectins of organisms from different branches of the evolutionary tree. Herein, we report the first study in this area for an animal galectin. Transferred nuclear Overhauser effect (TRNOE)-based experiments in combination with conformational distance mapping, random walk molecular mechanics (RAMM) and molecular dynamics (MD) calculations indicate that the actual conformations of this disaccharide in the complex and in the free form are at least very similar.

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“…Therefore, right-and left-handed forms were minimized in the presence of 200 water molecules using the potential of Hagler et al (1974). The final energy values for the minimized cyu-and a,-helices are 10 and 1.7 X lo3 kcal/mol, respectively.…”

Section: Molecular Modelingmentioning

confidence: 99%

Structure of synthetic peptide analogues of an eggshell protein of Schistosoma mansoni

et al. 1993

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The peptide (Gly-L-Tyr-L-Asp-L-Lys-L-Tyr),, referred to as F4-6, was synthesized as a model for a schistosome eggshell protein in which the Gly-Tyr-Asp-Lys-Tyr consensus sequence is repeated over 40 times. Analysis by CD, Fourier transform infrared spectroscopy, potentiometric and spectrophotometric titrations, NMR, and molecular modeling suggests that F4-6 forms some type of left-handed structure. A likely possibility appears to be a lefthanded a-helix stabilized by Lysj-Aspj+, salt bridges and possibly Aspj-Tyrj+, hydrogen bonding and Tyr-Tyr interactions. Spectroscopic studies of a number of F4-6 analogues support this conclusion. For example, substitution of D-Ala for Gly produces a peptide with enhanced left-handed helical spectral characteristics, whereas an L-Ala substitution results in a peptide with minimal structure. These studies suggest that the F4 protein from Schistosoma mansoni may be the first example of a naturally occurring protein devoid of proline and carbohydrate that forms a left-handed helix composed of L-amino acids, although alternative forms of other left-handed structures have yet to be rigorously excluded.Keywords: F4-6 peptide; Schistosoma mansoni; schistosome eggshell protein The pathology of schistosomiasis is due to the inflammatory response to the eggs of the parasitic trematode, Schistosoma mansoni (or other closely related schistosomes) lodged in the hosts' body tissues. Granulomas form around the eggs in response to soluble carbohydrate and protein antigens secreted by the eggs. When an egg is deposited by the female schistosome, it contains a fertilized ovum and 30-40 vitelline cells. Development of the miracidium larva occurs inside the eggshell lodged in the host tissues. The eggshell is formed shortly before egg laying from protein precursors secreted by the vitelline cells that subsequently become surrounded by the eggshell. These vitelline cells serve as a food supply for the developing miracidium and disappear before hatching. The secreted

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Energy functions for peptides and proteins. I. Derivation of a consistent force field including the hydrogen bond from amide crystals

Cited by 700 publications

References 2 publications

Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation 1 1Edited by J. Thornton

Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation 1 1Edited by J. Thornton

NMR-Based, Molecular Dynamics- and Random Walk Molecular Mechanics-Supported Study of Conformational Aspects of a Carbohydrate Ligand (Galβ1-2Galβ1-R) for an Animal Galectin in the Free and in the Bound State

Structure of synthetic peptide analogues of an eggshell protein of Schistosoma mansoni

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