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Special Issue "Proceedings of the Workshop on Modeling Interaction in Biomolecules"

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry, Molecular Biology and Biophysics".

Deadline for manuscript submissions: closed (31 March 2004)

Special Issue Editors

Guest Editor
Dr. Jaroslav V. Burda

- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Prag
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Guest Editor
Prof. W. Andrzej Sokalski

Molecular Modeling Laboratory, Institute of Physical and Theoretical Chemistry Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw
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Published Papers (8 papers)

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Editorial

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Open AccessEditorial Preface
Int. J. Mol. Sci. 2004, 5(4), 129; doi:10.3390/i5040129
Received: 22 May 2004 / Published: 28 May 2004
Cited by 3 | PDF Full-text (78 KB) | HTML Full-text | XML Full-text
(This article belongs to the Special Issue Proceedings of the Workshop on Modeling Interaction in Biomolecules)

Research

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Open AccessArticle Visualization of the Differential Transition State Stabilization within the Active Site Environment
Int. J. Mol. Sci. 2004, 5(4), 186-195; doi:10.3390/i5040186
Received: 15 December 2003 / Published: 31 May 2004
Cited by 1 | PDF Full-text (634 KB) | HTML Full-text | XML Full-text
Abstract
Increasing interest in the enzymatic reaction mechanisms and in the nature of catalytic effects in enzymes causes the need of appropriate visualization methods. A new interactive method to investigate catalytic effects using differential transition state stabilization approach (DTSS) [1, 2] is presented. The
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Increasing interest in the enzymatic reaction mechanisms and in the nature of catalytic effects in enzymes causes the need of appropriate visualization methods. A new interactive method to investigate catalytic effects using differential transition state stabilization approach (DTSS) [1, 2] is presented. The catalytic properties of the active site of cytidine deaminase (E.C. 3.5.4.5) is visualized in the form of differential electrostatic properties. The visualization was implemented using scripting interface of VMD [3]. Cumulative Atomic Multipole Moments (CAMM) [4,5,6] were utilized for efficient yet accurate evaluation of the electrostatic properties. The implementation is efficient enough for interactive presentation of catalytic effects in the active site of the enzyme due to transition state or substrate movement. This system of visualization of DTTS approach can be potentially used to validate hypotheses regarding the catalytic mechanism or to study binding properties of transition state analogues. Full article
(This article belongs to the Special Issue Proceedings of the Workshop on Modeling Interaction in Biomolecules)
Open AccessArticle Estimation of Electron Spectra Transitions of Free-Based Porphin and Mg-Porphin Using Various Quantum Chemical Approaches
Int. J. Mol. Sci. 2004, 5(4), 196-213; doi:10.3390/i5040196
Received: 15 December 2003 / Accepted: 14 April 2004 / Published: 31 May 2004
Cited by 3 | PDF Full-text (751 KB) | HTML Full-text | XML Full-text
Abstract
For optimized molecules of free-base porphin and magnesium-porphin (at Hartree-Fock level and 6-31G* basis set) excitation spectra were determined using several ab initio methods: CIS, RPA, CASSCF, and TDDFT. Obtained values were compared with semiempirical ZINDO method, other calculations found recently in literature
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For optimized molecules of free-base porphin and magnesium-porphin (at Hartree-Fock level and 6-31G* basis set) excitation spectra were determined using several ab initio methods: CIS, RPA, CASSCF, and TDDFT. Obtained values were compared with semiempirical ZINDO method, other calculations found recently in literature and experimental data. It was demonstrated that for qualitatively correct spectra description the AO basis must include both the polarization and diffuse functions. The later play an important role in formation of Rydberg MOs. Estimated energies of the spectra transitions using the CIS method remain relatively far from the measured values. RPA method can be already considered as a quantitatively accurate method when sufficiently large basis set is used. For CASSCF approach, it was shown that even the lowest energy transitions are insufficiently described in CAS formalism and much larger active space or inclusion of more inactive orbitals in correlation treatment would be necessary for obtaining sufficient accuracy. It can be stated that without sufficiently large correlation contributions, the determined spectra are not able to reach quantitative agreement with experimental data. From the methods treated in this study, only TDDFT can be considered as a useful tool for spectra prediction, at least for calculations of lower excited states. It is relatively fast and feasible for calculation of middle-size molecules. ZINDO approximation is also relatively successful for such large systems. Acceptable predictions of experimentally observed energy transitions in the range of Q and B bands were obtained. Until higher (UV) part of spectra is examined where the excitations to Rydberg orbital will happen, it can be considered as a good candidate for electron spectra calculations. Full article
(This article belongs to the Special Issue Proceedings of the Workshop on Modeling Interaction in Biomolecules)
Open AccessArticle Interactions between Physics and Biodisciplines within the Framework of Molecular Sciences
Int. J. Mol. Sci. 2004, 5(4), 214-223; doi:10.3390/i5040214
Received: 15 March 2004 / Accepted: 23 April 2004 / Published: 31 May 2004
PDF Full-text (160 KB) | HTML Full-text | XML Full-text
Abstract
In order to be able to study interactions within, between, and among biomolecules, it is highly desirable to use tools of experimental and theoretical physics, or preferably a combination thereof. Very brief comments are presented which concern biochemical reactivity, enzymatic catalysis, origin of
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In order to be able to study interactions within, between, and among biomolecules, it is highly desirable to use tools of experimental and theoretical physics, or preferably a combination thereof. Very brief comments are presented which concern biochemical reactivity, enzymatic catalysis, origin of life, experimental tools for structure elucidation and quantum chemistry methods. Additional remarks are related to ultrafast processes, experiments with individual molecules, and to symmetry considerations. Full article
(This article belongs to the Special Issue Proceedings of the Workshop on Modeling Interaction in Biomolecules)
Open AccessArticle Electronic Density Approaches to the Energetics of Noncovalent Interactions
Int. J. Mol. Sci. 2004, 5(4), 130-140; doi:10.3390/i5040130
Received: 15 December 2003 / Accepted: 11 March 2004 / Published: 1 April 2004
Cited by 1 | PDF Full-text (213 KB) | HTML Full-text | XML Full-text
Abstract
We present an overview of procedures that have been developed to compute several energetic quantities associated with noncovalent interactions. These formulations involve numerical integration over appropriate electronic densities. Our focus is upon the electrostatic interaction between two unperturbed molecules, the effect of the
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We present an overview of procedures that have been developed to compute several energetic quantities associated with noncovalent interactions. These formulations involve numerical integration over appropriate electronic densities. Our focus is upon the electrostatic interaction between two unperturbed molecules, the effect of the polarization of each charge distribution by the other, and the total energy of interaction. The expression for the latter is based upon the Hellmann-Feynman theorem. Applications to a number of systems are discussed; among them are dimers of uracil and interacting pairs of molecules in the crystal lattice of the energetic compound RDX. Full article
(This article belongs to the Special Issue Proceedings of the Workshop on Modeling Interaction in Biomolecules)
Open AccessArticle The Mechanism of Phosphoryl Transfer Reaction and the Role of Active Site Residues on the Basis of Ribokinase-Like Kinases
Int. J. Mol. Sci. 2004, 5(4), 141-153; doi:10.3390/i5040141
Received: 15 December 2003 / Accepted: 11 March 2004 / Published: 1 April 2004
Cited by 8 | PDF Full-text (924 KB) | HTML Full-text | XML Full-text
Abstract
The role of ribokinase-like carbohydrate kinases consists in ATP dependent phosphorylation of small molecules containing hydroxymethyl group. Although they differ substantially in structural terms and exhibit a broad substrate specificity, some family-wide conserved features can be distinguished suggesting the common mode of action.
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The role of ribokinase-like carbohydrate kinases consists in ATP dependent phosphorylation of small molecules containing hydroxymethyl group. Although they differ substantially in structural terms and exhibit a broad substrate specificity, some family-wide conserved features can be distinguished suggesting the common mode of action. 4-methyl-5-β-hydroxyethylthiazole kinase (Thz kinase) was chosen as a representative model and the mechanism proposed in X-ray crystal structure paper provided the basis for calculations. In particular, the possible role of several active site residues (Arg121 and Cys198 among others) and of the two magnesium ions was examined. Static and dynamic catalytic fields for the reaction were generated revealing the most favourable environment for the preferential transition state stabilization. An attempt to model the phosphoryl transfer reaction as well as to investigate the influence of the cysteine residue on the reaction course at the semiempirical PM3 level of theory was undertaken. Full article
(This article belongs to the Special Issue Proceedings of the Workshop on Modeling Interaction in Biomolecules)
Open AccessArticle Complexity and Convergence of Electrostatic and van der Waals Energies within PME and Cutoff Methods
Int. J. Mol. Sci. 2004, 5(4), 154-173; doi:10.3390/i5040154
Received: 15 December 2003 / Accepted: 11 March 2004 / Published: 1 April 2004
Cited by 3 | PDF Full-text (357 KB) | HTML Full-text | XML Full-text
Abstract
In this paper, we report a detailed comparison between the popularly used cutoff and Particle Mesh Ewald (PME) methods in terms of the time complexity and the energy convergence of the long-range electrostatic and van der Waals interaction calculations. For the comparison, we
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In this paper, we report a detailed comparison between the popularly used cutoff and Particle Mesh Ewald (PME) methods in terms of the time complexity and the energy convergence of the long-range electrostatic and van der Waals interaction calculations. For the comparison, we performed various calculations on various representative biological molecules, including seven peptides and proteins, eleven oligonucleotides, and three conformations of a nucleotide-sugar. The results provide useful insights into the appropriate choice of the methods (i.e. the cutoff or PME) and that of the cutoff values for the calculations on different kinds of molecules. It has also been demonstrated that for some cases using different cutoff values for calculating the electrostatic and van der Waals interaction energies will be computationally more efficient. Full article
(This article belongs to the Special Issue Proceedings of the Workshop on Modeling Interaction in Biomolecules)
Open AccessArticle Intramolecular C−H···π Interactions in Metal-Porphyrin Complexes
Int. J. Mol. Sci. 2004, 5(4), 174-185; doi:10.3390/i5040174
Received: 15 December 2003 / Accepted: 11 March 2004 / Published: 1 April 2004
Cited by 10 | PDF Full-text (339 KB) | HTML Full-text | XML Full-text
Abstract
Cambridge Structural Database (CSD) was screened in order to find intramolecular C−H···π interactions with a chelate ring of coordinated porphyrin. It was found 154 crystal structures with 244 intramolecular C−H···π interactions in transition metal complexes with derivatives of porphyrin. Comparison of interacting distances
[...] Read more.
Cambridge Structural Database (CSD) was screened in order to find intramolecular C−H···π interactions with a chelate ring of coordinated porphyrin. It was found 154 crystal structures with 244 intramolecular C−H···π interactions in transition metal complexes with derivatives of porphyrin. Comparison of interacting distances indicates that interactions of hydrogen atoms in positions 2 and 6 of axially coordinated pyridine are more favorable with ruffled than with planar porphyrin. Full article
(This article belongs to the Special Issue Proceedings of the Workshop on Modeling Interaction in Biomolecules)

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