Hydrogen bonding in MM2

Allinger, Norman L.; Kok, Randall A.; Imam, Mita R.

doi:10.1002/jcc.540090602

Cited by 123 publications

(45 citation statements)

References 17 publications

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“…Parametrization of this force field allows the investigation of hydrogen bonding by reducing the van der Waals radius of hydrogen atoms attached to electronegative atoms to 0.05 nm when such a hydrogen interacts with a hydrogen acceptor atom; the well depth is increased to 1.0 kcal/mol. These parameters guarantee similar potential functions as those used lie Estelberger et al /FEBS Letters 357 (1995) [37][38][39][40] in the well-known MM2 force field [15]. Moreover, comparison with ab initio quantum chemical calculations has shown that the molecular mechanical technique described yields results which are excellently comparable with those of the much more sophisticated ab initio approach (Reibnegger et al, submitted).…”

Section: Systematic Generation Of Reasonable Geometries Jorsupporting

confidence: 63%

The conformational flexibility of 5,6,7,8‐tetrahydrobiopterin and 5,6,7,8‐tetrahydroneopterin: a molecular dynamical simulation

1995

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Section: Systematic Generation Of Reasonable Geometries Jorsupporting

confidence: 63%

The conformational flexibility of 5,6,7,8‐tetrahydrobiopterin and 5,6,7,8‐tetrahydroneopterin: a molecular dynamical simulation

1995

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“…The RAMM program is especially suitable to detect local minima of higher energy than those which are normally adopted in a molecular dynamics run (19). The force field and energy functions used in RAMM correspond to the Allinger molecular mechanics method MM2-87 (20,21).…”

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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“…We have made a comparison of calculated conformational properties employing four different molecular mechanics methods, MM2(85), [4][5][6][7][8] fluoro subsituted test compounds. Optimization was done by using the ChemX default optimizer algorithm and the convergence criterion for the minimization was set to 0.0001 kcal/mol.…”

Section: Introductionmentioning

confidence: 99%

A comparison of conformational energies calculated by molecular mechanics (MM2(85), Sybyl 5.1, Sybyl 5.21, and ChemX) and semiempirical (AM1 and PM3) methods

et al. 1991

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Conformational energies of different conformers have been calculated for a series of molecules using various molecular mechanics and semiempirical methods. The quality of the force fields has also been tested by calculating barriers to rotation about carbon-carbon bonds. The molecular mechanics force fields used are MM2(85), Syby15.1, Sybyl5.21, and ChemX, ver. Jan 89. The semiempirical methods used are AM1 and PM3. Molecules with different functional groups, for which good experimental data exist, have been selected. The semiempirical methods generally calculate barriers to rotation which are lower than the experimentally determined. The conformational energies for hydrocarbons are reasonably well reproduced by all tested methods although MMZ(85) gives the quantitatively best agreement with experiments. For compounds containing oxygen, nitrogen and halogens MMZ(85) gives results which are in best agreement with the experimentally determined values.

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Hydrogen bonding in MM2

Cited by 123 publications

References 17 publications

The conformational flexibility of 5,6,7,8‐tetrahydrobiopterin and 5,6,7,8‐tetrahydroneopterin: a molecular dynamical simulation

The conformational flexibility of 5,6,7,8‐tetrahydrobiopterin and 5,6,7,8‐tetrahydroneopterin: a molecular dynamical simulation

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

A comparison of conformational energies calculated by molecular mechanics (MM2(85), Sybyl 5.1, Sybyl 5.21, and ChemX) and semiempirical (AM1 and PM3) methods

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