Theoretical studies of molecular conformation. Derivation of an additive procedure for the computation of intramolecular interaction energies. Comparison withab initio SCF computations

Gresh, Nohad; Claverie, P.; Pullman, Alberte

doi:10.1007/bf00577135

Cited by 140 publications

(100 citation statements)

References 24 publications

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“…However, even considering a single static configuration, our results cannot be considered as quantitative ones because our methodological approach does not include inter-fragment polarization effects (only a local correction is introduced by the OME reassociation method in the important peptide junction region). A methodology that incorporates inter-fragment polarization effects 69,[81][82][83] and a correction for the charge penetration effect 84 is under development. These improvements are especially important to avoid significant errors when evaluating the internal ion pair energy and also when evaluating the ion pair interaction with the surrounding protein residues and water molecules.…”

Section: Discussionmentioning

confidence: 99%

“…The first library is used by another program 46 that performs all the steps of the OME procedure necessary to generate the final library of fragment multicentered multipolar expansions. This final library is used by an adapted version of the SIBFA program 69 to calculate the electrostatic potential and the electric field PM contribution in a set of predefined points. Only points with a distance Ն2.0 Å from any multipolar expansion center are considered to guarantee the electrostatic calculations accuracy and avoid important errors due to electron cloud penetration effects.…”

Section: Electrostatics In the Papain Catalytic Sitementioning

confidence: 99%

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Electrostatic properties in the catalytic site of papain: A possible regulatory mechanism for the reactivity of the ion pair

et al. 2003

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We present an analysis of the electrostatic properties in the catalytic site of papain (EC 3.4.22.2), an archetype enzyme of the C1 cysteine proteinase family, and we investigate their possible role in the formation, stabilization and regulation of the Cys25 (؊) …His159 (؉) catalytic ion pair. The electrostatic properties were computed using a reassociation method based in multicentered multipolar expansions obtained from ab initio quantum calculations of overlapping protein fragments. Solvent effects were introduced by coupling the use of multicentered multipolar expansions to two continuum boundary element methods to solve the Poisson and the linearized Poisson-Boltzmann equations. The electrostatic profile found in the proton transfer region of papain showed that this enzyme has a well-defined electrostatic environment to favor the formation and stabilization of the catalytic ion pair. The papain catalytic site electrostatic profile can be considered as an electrostatic fingerprint of the papain family with the following characteristics: (i) the presence of a net electric field highly aligned in the (Cys25)-SG3(His159)-ND1 direction; (ii) the electrostatic profile has a saddlepoint character; (iii) it is basically a local environmental effect. Furthermore, our analysis describes a possible regulatory mechanism (the E SG3 ND1 attenuation effect) controlling the ion pair reactivity and permits to infer the Asp57 acidic residue as the most probable candidate to act as the electrostatic modulator. Proteins 2003;52:236 -253.

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Section: Discussionmentioning

confidence: 99%

Section: Electrostatics In the Papain Catalytic Sitementioning

confidence: 99%

Electrostatic properties in the catalytic site of papain: A possible regulatory mechanism for the reactivity of the ion pair

et al. 2003

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“…The specificity of interaction of mitoxantrone has been already investigated by us [ 251 by the SIBFA method, elaborated in our laboratory [ 29,301, which allows for the flexibility of the drug but maintains rigid the skeleton of the receptor model oligonucleotide. The computations related in the present article have been camed out by the JUMNA method ([ 3 1,321, for a summary, see, e.g., [ 193) also elaborated in our laboratory, which allows for the flexibility of both the drug and the receptor.…”

Section: Methodsmentioning

confidence: 99%

Effect of side chains on the groove-binding specificity of anthraquinone intercalators

Hui

Gresh

Pullman

1991

Int. J. Quantum Chem.

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Anthraquinone intercalators possessing two side chains offer potentially the three possibilities of having these chains located ( 1 ) both in the major groove, (2) both in the minor groove, and ( 3 ) one in the major and the other in the minor groove ("threading" mode of intercalation). Computations camed out on two related doubly substituted anthraquinones, mitoxantrone (I) and bisglycylglycylanthraquinone (II), indicate that while I should intercalate with its two side chains located both in the major groove, I1 should adopt the threading arrangement. This result is interpreted in terms of the importance of ligand-DNA mutual adaptation. The results of the computations are in agreement with very recent experimental findings of Palumbo and Gatto at

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“…Also along these lines, the sum of interactions between fragments computed ab initio (SIBFA) method, developed by Gresh et al (1984), is not strictly a classical method, in that it incorporated more than just polarization into the classical model, including, for example, an electrostatic term based upon ab initio calculations on fragments of the molecules of a system. However, it can be broadly fitted into this category, in that it makes use of point dipoles to model polarization.…”

Section: Equation (38) Is Solved By Rearranging Into the Formmentioning

confidence: 99%

Many-body effects and simulations of potassium channels

Illingworth

Domene

2009

Proc. R. Soc. A.

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The electronic polarizability of an ion or a molecule is a measure of the relative tendency of its electron cloud to be distorted from its normal shape by an electric field. On the molecular scale, in a condensed phase, any species sits in an electric field due to its neighbours, and the resulting polarization is an important contribution to the total interaction energy. Electrostatic interactions are crucial for determining the majority of chemical-physical properties of the system and electronic polarization is a fundamental component of these interactions. Thus, polarization effects should be taken into account if accurate descriptions are desired. In classical computer simulations, the forces required to drive the system are typically based on interatomic interaction potentials derived in part from electronic structure calculations or from experimental data. Owing to the difficulties in including polarization effects in classical force fields, most of them are based just on pairwise additive interaction potentials. At present, major efforts are underway to develop polarizable interaction potentials for biomolecular simulations. In this review, various ways of introducing explicit polarizability into biomolecular models and force fields are reviewed, and the progress that might be achieved in applying such methods to study potassium channels is described.

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Theoretical studies of molecular conformation. Derivation of an additive procedure for the computation of intramolecular interaction energies. Comparison withab initio SCF computations

Cited by 140 publications

References 24 publications

Electrostatic properties in the catalytic site of papain: A possible regulatory mechanism for the reactivity of the ion pair

Electrostatic properties in the catalytic site of papain: A possible regulatory mechanism for the reactivity of the ion pair

Effect of side chains on the groove-binding specificity of anthraquinone intercalators

Many-body effects and simulations of potassium channels

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