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Nakagawa S, Kimura A, Okamoto Y. Polarizable Molecular Block Model: Toward the Development of an Induced Dipole Force Field for DNA. J Phys Chem B 2022; 126:10646-10661. [PMID: 36512703 DOI: 10.1021/acs.jpcb.2c06227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
For flexible and highly ionized macromolecules such as DNA, it is important to correctly evaluate the intramolecular polarization in an induced dipole force field. In a proposed polarizable molecular block (PMB) model, a large molecule is divided into several molecular blocks. The atomic charges of the blocks are optimized by using the respective electrostatic potentials (ESPs) on the molecular surface. By using the capped hydrogen removal operation, the total charge of the blocks is controlled exactly to have an integer charge. The atomic polarizabilities of the blocks are optimized by using the respective polarized one-electron potentials that are the differences between ESPs with and without an external test charge. Induced dipole-charge interactions between the blocks are all included, but those interactions within the blocks are strictly excluded. All dipole-dipole interactions are included, but the damping functions are applied to the close dipole-dipole pairs. Several types of damping (simple scaling, exponential, linear, and Gaussian) are evaluated. The validity of the PMB model was verified by using trinucleotide duplexes which have A-, B-, and Z-DNA forms. The reference energies of trinucleotide duplexes including counterions (GGT3Na-ACC3Na, GAC3Na-GTC3Na, and GCG3Na-CGC3Na) are calculated using ωB97XD/aug-cc-pVDZ. All damping types reproduced well the reference interaction energies, dipole moments, and ESPs. Among them, the simple scaling with strong attenuation to 1-2 atomic pairs showed the highest stability against the polarization catastrophe. This study shows that it is possible to develop a high-quality polarizable force field by treating the intramolecular polarization on a block-by-block basis.
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Affiliation(s)
- Setsuko Nakagawa
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi464-8602, Japan.,Kinjo Gakuin University, Nagoya, Aichi463-8521, Japan
| | - Akihiro Kimura
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi464-8602, Japan
| | - Yuko Okamoto
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi464-8602, Japan.,High Performance Computing Division, Information Technology Center, Nagoya University, Nagoya, Aichi464-8601, Japan.,Global Engagement Center, International Affairs, Nagoya University, Nagoya, Aichi464-8601, Japan
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Nottoli M, Cupellini L, Lipparini F, Granucci G, Mennucci B. Multiscale Models for Light-Driven Processes. Annu Rev Phys Chem 2021; 72:489-513. [PMID: 33561359 DOI: 10.1146/annurev-physchem-090419-104031] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Multiscale models combining quantum mechanical and classical descriptions are a very popular strategy to simulate properties and processes of complex systems. Many alternative formulations have been developed, and they are now available in all of the most widely used quantum chemistry packages. Their application to the study of light-driven processes, however, is more recent, and some methodological and numerical problems have yet to be solved. This is especially the case for the polarizable formulation of these models, the recent advances in which we review here. Specifically, we identify and describe the most important specificities that the polarizable formulation introduces into both the simulation of excited-state dynamics and the modeling of excitation energy and electron transfer processes.
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Affiliation(s)
- Michele Nottoli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, 56124 Pisa, Italy;
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, 56124 Pisa, Italy;
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, 56124 Pisa, Italy;
| | - Giovanni Granucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, 56124 Pisa, Italy;
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, 56124 Pisa, Italy;
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Jeong KJ, McDaniel JG, Yethiraj A. A Transferable Polarizable Force Field for Urea Crystals and Aqueous Solutions. J Phys Chem B 2020; 124:7475-7483. [DOI: 10.1021/acs.jpcb.0c05814] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Kyeong-jun Jeong
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Jesse G. McDaniel
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332, United States
| | - Arun Yethiraj
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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Tiwari A, Honingh C, Ensing B. Accurate calculation of zero point energy from molecular dynamics simulations of liquids and their mixtures. J Chem Phys 2019; 151:244124. [PMID: 31893925 DOI: 10.1063/1.5131145] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The two-phase thermodynamic (2PT) method is used to compute the zero point energy (ZPE) of several liquids and their mixtures. The 2PT method uses the density of states (DoS), which is computed from the velocity autocorrelation (VAC) function obtained from a short classical molecular dynamics trajectory. By partitioning the VAC and the DoS of a fluid into solid and gaslike components, quantum mechanical corrections to thermodynamical properties can be computed. The ZPE is obtained by combining the partition function of the quantum harmonic oscillator with the vibrational part of the solidlike DoS. The resulting ZPE is found to be in excellent agreement with both experimental and ab initio results. Solvent effects such as hydrogen bonding and polarization can be included by the utilization of ab initio density functional theory based molecular dynamics simulations. It is found that these effects significantly influence the DoS of water molecules. The obtained results demonstrate that the 2PT model is a powerful method for efficient ZPE calculations, in particular, to account for solvent effects and polarization.
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Affiliation(s)
- A Tiwari
- Van't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - C Honingh
- Van't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - B Ensing
- Van't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
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Puratchikody A, Umamaheswari A, Irfan N, Sriram D. Molecular Dynamics Studies on COX-2 Protein-tyrosine Analogue Complex and Ligand-based Computational Analysis of Halo-substituted Tyrosine Analogues. LETT DRUG DES DISCOV 2019. [DOI: 10.2174/1570180815666180627123445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
The quest for new drug entities and novel structural fragments with
applications in therapeutic areas is always at the core of medicinal chemistry.
Methods:
As part of our efforts to develop novel selective cyclooxygenase-2 (COX-2) inhibitors
containing tyrosine scaffold. The objective of this study was to identify potent COX-2 inhibitors by
dynamic simulation, pharmacophore and 3D-QSAR methodologies. Dynamics simulation was performed
for COX-2/tyrosine derivatives complex to characterise structure validation and binding
stability. Certainly, Arg120 and Tyr355 residue of COX-2 protein formed a constant interaction
with tyrosine inhibitor throughout the dynamic simulation phase. A four-point pharmacophore with
one hydrogen bond acceptor, two hydrophobic and one aromatic ring was developed using the
HypoGen algorithm. The generated, statistically significant pharmacophore model, Hypo 1 with a
correlation coefficient of r2, 0.941, root mean square deviation, 1.15 and total cost value of 96.85.
Results:
The QSAR results exhibited good internal (r2, 0.992) and external predictions (r2pred,
0.814). The results of this study concluded the COX-2 docked complex was stable and interactive
like experimental protein structure. Also, it offered vital chemical features with geometric constraints
responsible for the inhibition of the selective COX-2 enzyme by tyrosine derivatives.
Conclusion:
In principle, this work offers significant structural understandings to design and develop
novel COX-2 inhibitors.
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Affiliation(s)
- Ayarivan Puratchikody
- Drug Discovery and Development Research Group, Department of Pharmaceutical Technology, Bharathidasan Institute of Technology, Anna University, Tiruchirappalli 620024, Tamilnadu, India
| | - Appavoo Umamaheswari
- Drug Discovery and Development Research Group, Department of Pharmaceutical Technology, Bharathidasan Institute of Technology, Anna University, Tiruchirappalli 620024, Tamilnadu, India
| | - Navabshan Irfan
- Drug Discovery and Development Research Group, Department of Pharmaceutical Technology, Bharathidasan Institute of Technology, Anna University, Tiruchirappalli 620024, Tamilnadu, India
| | - Dharmarajan Sriram
- Pharmacy Group, Birla Institute of Technology and Sciences-Pilani, Hyderabad Campus, Jawahar Nagar, Hyderabad 560078, India
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Varsano D, Caprasecca S, Coccia E. Theoretical description of protein field effects on electronic excitations of biological chromophores. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:013002. [PMID: 27830666 DOI: 10.1088/0953-8984/29/1/013002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Photoinitiated phenomena play a crucial role in many living organisms. Plants, algae, and bacteria absorb sunlight to perform photosynthesis, and convert water and carbon dioxide into molecular oxygen and carbohydrates, thus forming the basis for life on Earth. The vision of vertebrates is accomplished in the eye by a protein called rhodopsin, which upon photon absorption performs an ultrafast isomerisation of the retinal chromophore, triggering the signal cascade. Many other biological functions start with the photoexcitation of a protein-embedded pigment, followed by complex processes comprising, for example, electron or excitation energy transfer in photosynthetic complexes. The optical properties of chromophores in living systems are strongly dependent on the interaction with the surrounding environment (nearby protein residues, membrane, water), and the complexity of such interplay is, in most cases, at the origin of the functional diversity of the photoactive proteins. The specific interactions with the environment often lead to a significant shift of the chromophore excitation energies, compared with their absorption in solution or gas phase. The investigation of the optical response of chromophores is generally not straightforward, from both experimental and theoretical standpoints; this is due to the difficulty in understanding diverse behaviours and effects, occurring at different scales, with a single technique. In particular, the role played by ab initio calculations in assisting and guiding experiments, as well as in understanding the physics of photoactive proteins, is fundamental. At the same time, owing to the large size of the systems, more approximate strategies which take into account the environmental effects on the absorption spectra are also of paramount importance. Here we review the recent advances in the first-principle description of electronic and optical properties of biological chromophores embedded in a protein environment. We show their applications on paradigmatic systems, such as the light-harvesting complexes, rhodopsin and green fluorescent protein, emphasising the theoretical frameworks which are of common use in solid state physics, and emerging as promising tools for biomolecular systems.
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Affiliation(s)
- Daniele Varsano
- S3 Center, CNR Institute of Nanoscience, Via Campi 213/A, 41125 Modena, Italy
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Sousa SF, Ribeiro AJM, Neves RPP, Brás NF, Cerqueira NMFSA, Fernandes PA, Ramos MJ. Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2016. [DOI: 10.1002/wcms.1281] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Sérgio Filipe Sousa
- Departamento de Química e Bioquímica, Faculdade de Ciências UCIBIO, REQUIMTE, Universidade do Porto Porto Portugal
| | - António J. M. Ribeiro
- Departamento de Química e Bioquímica, Faculdade de Ciências UCIBIO, REQUIMTE, Universidade do Porto Porto Portugal
| | - Rui P. P. Neves
- Departamento de Química e Bioquímica, Faculdade de Ciências UCIBIO, REQUIMTE, Universidade do Porto Porto Portugal
| | - Natércia F. Brás
- Departamento de Química e Bioquímica, Faculdade de Ciências UCIBIO, REQUIMTE, Universidade do Porto Porto Portugal
| | - Nuno M. F. S. A. Cerqueira
- Departamento de Química e Bioquímica, Faculdade de Ciências UCIBIO, REQUIMTE, Universidade do Porto Porto Portugal
| | - Pedro A. Fernandes
- Departamento de Química e Bioquímica, Faculdade de Ciências UCIBIO, REQUIMTE, Universidade do Porto Porto Portugal
| | - Maria João Ramos
- Departamento de Química e Bioquímica, Faculdade de Ciências UCIBIO, REQUIMTE, Universidade do Porto Porto Portugal
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Dans PD, Walther J, Gómez H, Orozco M. Multiscale simulation of DNA. Curr Opin Struct Biol 2016; 37:29-45. [DOI: 10.1016/j.sbi.2015.11.011] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/23/2015] [Accepted: 11/25/2015] [Indexed: 01/05/2023]
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Mennucci B, Caprasecca S, Guido C. Computational Studies of Environmental Effects and Their Interplay With Experiment. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2016. [DOI: 10.1016/bs.apoc.2016.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Qiu L, Lin J, Bertaccini EJ. Insights into the Nature of Anesthetic-Protein Interactions: An ONIOM Study. J Phys Chem B 2015; 119:12771-82. [PMID: 26388288 DOI: 10.1021/acs.jpcb.5b05897] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Anesthetics have been employed widely to relieve surgical suffering, but their mechanism of action is not yet clear. For over a century, the mechanism of anesthesia was previously thought to be via lipid bilayer interactions. In the present work, a rigorous three-layer ONIOM(M06-2X/6-31+G*:PM6:AMBER) method was utilized to investigate the nature of interactions between several anesthetics and actual protein binding sites. According to the calculated structural features, interaction energies, atomic charges, and electrostatic potential surfaces, the amphiphilic nature of anesthetic-protein interactions was demonstrated for both inhalational and injectable anesthetics. The existence of hydrogen and halogen bonding interactions between anesthetics and proteins was clearly identified, and these interactions served to assist ligand recognition and binding by the protein. Within all complexes of inhalational or injectable anesthetics, the polarization effects play a dominant role over the steric effects and induce a significant asymmetry in the otherwise symmetric atomic charge distributions of the free ligands in vacuo. This study provides new insight into the mechanism of action of general anesthetics in a more rigorous way than previously described. Future rational design of safer anesthetics for an aging and more physiologically vulnerable population will be predicated on this greater understanding of such specific interactions.
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Affiliation(s)
- Ling Qiu
- Key Laboratory of Nuclear Medicine, Ministry of Health & Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine , Wuxi 214063, P. R. China.,Department of Anesthesia, Stanford University School of Medicine, Palo Alto VA Health Care System , 112A, PAVAHCS, 3801 Miranda Avenue, Palo Alto, California 94304, United States
| | - Jianguo Lin
- Key Laboratory of Nuclear Medicine, Ministry of Health & Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine , Wuxi 214063, P. R. China
| | - Edward J Bertaccini
- Department of Anesthesia, Stanford University School of Medicine, Palo Alto VA Health Care System , 112A, PAVAHCS, 3801 Miranda Avenue, Palo Alto, California 94304, United States
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Zgarbová M, Rosnik AM, Luque FJ, Curutchet C, Jurečka P. Transferability and additivity of dihedral parameters in polarizable and nonpolarizable empirical force fields. J Comput Chem 2015. [DOI: 10.1002/jcc.24012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Marie Zgarbová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science; Palacky University; 17. listopadu 12 Olomouc 77146 Czech Republic
| | - Andreana M. Rosnik
- Department de Fisicoquímica; Facultat de Farmàcia, Universitat de Barcelona; Av. Joan XXIII s/n Barcelona 08028 Spain
| | - F. Javier Luque
- Department de Fisicoquímica and Institut de Biomedicina (IBUB); Facultat de Farmàcia, Universitat de Barcelona; Avgda Prat de la Riba 171, Santa Coloma de Gramenet 08921 Spain
| | - Carles Curutchet
- Department de Fisicoquímica; Facultat de Farmàcia, Universitat de Barcelona; Av. Joan XXIII s/n Barcelona 08028 Spain
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science; Palacky University; 17. listopadu 12 Olomouc 77146 Czech Republic
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Vanommeslaeghe K, MacKerell AD. CHARMM additive and polarizable force fields for biophysics and computer-aided drug design. BIOCHIMICA ET BIOPHYSICA ACTA 2015; 1850:861-871. [PMID: 25149274 PMCID: PMC4334745 DOI: 10.1016/j.bbagen.2014.08.004] [Citation(s) in RCA: 178] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 08/10/2014] [Accepted: 08/12/2014] [Indexed: 11/29/2022]
Abstract
BACKGROUND Molecular Mechanics (MM) is the method of choice for computational studies of biomolecular systems owing to its modest computational cost, which makes it possible to routinely perform molecular dynamics (MD) simulations on chemical systems of biophysical and biomedical relevance. SCOPE OF REVIEW As one of the main factors limiting the accuracy of MD results is the empirical force field used, the present paper offers a review of recent developments in the CHARMM additive force field, one of the most popular biomolecular force fields. Additionally, we present a detailed discussion of the CHARMM Drude polarizable force field, anticipating a growth in the importance and utilization of polarizable force fields in the near future. Throughout the discussion emphasis is placed on the force fields' parametrization philosophy and methodology. MAJOR CONCLUSIONS Recent improvements in the CHARMM additive force field are mostly related to newly found weaknesses in the previous generation of additive force fields. Beyond the additive approximation is the newly available CHARMM Drude polarizable force field, which allows for MD simulations of up to 1μs on proteins, DNA, lipids and carbohydrates. GENERAL SIGNIFICANCE Addressing the limitations ensures the reliability of the new CHARMM36 additive force field for the types of calculations that are presently coming into routine computational reach while the availability of the Drude polarizable force fields offers an inherently more accurate model of the underlying physical forces driving macromolecular structures and dynamics. This article is part of a Special Issue entitled "Recent developments of molecular dynamics".
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Affiliation(s)
- K Vanommeslaeghe
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
| | - A D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA.
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Lin Z, Bachmann SJ, van Gunsteren WF. GROMOS polarizable charge-on-spring models for liquid urea: COS/U and COS/U2. J Chem Phys 2015; 142:094117. [DOI: 10.1063/1.4913955] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Zhixiong Lin
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zürich, Switzerland
| | - Stephan J. Bachmann
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zürich, Switzerland
| | - Wilfred F. van Gunsteren
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zürich, Switzerland
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Abstract
Proteins are fascinating supramolecular structures, which are able to recognize ligands transforming binding information into chemical signals. They can transfer information across the cell, can catalyse complex chemical reactions, and are able to transform energy into work with much more efficiency than any human engine. The unique abilities of proteins are tightly coupled with their dynamic properties, which are coded in a complex way in the sequence and carefully refined by evolution. Despite its importance, our experimental knowledge of protein dynamics is still rather limited, and mostly derived from theoretical calculations. I will review here, in a systematic way, the current state-of-the-art theoretical approaches to the study of protein dynamics, emphasizing the most recent advances, examples of use and the expected lines of development in the near future.
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Affiliation(s)
- Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri i Reixac 8, Barcelona 08028, Spain.
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17
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Marenich AV, Cramer CJ, Truhlar DG. Reduced and quenched polarizabilities of interior atoms in molecules. Chem Sci 2013. [DOI: 10.1039/c3sc50242b] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Šponer J, Mládek A, Šponer JE, Svozil D, Zgarbová M, Banáš P, Jurečka P, Otyepka M. The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies. Phys Chem Chem Phys 2012; 14:15257-77. [PMID: 23072945 DOI: 10.1039/c2cp41987d] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Knowledge of geometrical and physico-chemical properties of the sugar-phosphate backbone substantially contributes to the comprehension of the structural dynamics, function and evolution of nucleic acids. We provide a side by side overview of structural biology/bioinformatics, quantum chemical and molecular mechanical/simulation studies of the nucleic acids backbone. We highlight main features, advantages and limitations of these techniques, with a special emphasis given to their synergy. The present status of the research is then illustrated by selected examples which include classification of DNA and RNA backbone families, benchmark structure-energy quantum chemical calculations, parameterization of the dihedral space of simulation force fields, incorporation of arsenate into DNA, sugar-phosphate backbone self-cleavage in small RNA enzymes, and intricate geometries of the backbone in recurrent RNA building blocks. Although not apparent from the current literature showing limited overlaps between the QM, simulation and bioinformatics studies of the nucleic acids backbone, there in fact should be a major cooperative interaction between these three approaches in studies of the sugar-phosphate backbone.
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Affiliation(s)
- Jiří Šponer
- Institute of Biophysics, Academy Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic.
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In Silico Strategies Toward Enzyme Function and Dynamics. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2012. [DOI: 10.1016/b978-0-12-398312-1.00009-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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Molecular simulation methods in drug discovery: a prospective outlook. J Comput Aided Mol Des 2011; 26:81-6. [DOI: 10.1007/s10822-011-9506-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Accepted: 11/30/2011] [Indexed: 11/27/2022]
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Suárez D, Rayón VM, Díaz N, Valdés H. Ab Initio Benchmark Calculations on Ca(II) Complexes and Assessment of Density Functional Theory Methodologies. J Phys Chem A 2011; 115:11331-43. [DOI: 10.1021/jp205101z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Dimas Suárez
- Departamento de Química Física y Analítica, Facultad de Química Universidad de Oviedo, 33007 Oviedo, Spain
| | - Víctor M. Rayón
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias Universidad de Valladolid, 47005 Valladolid, Spain
| | - Natalia Díaz
- Departamento de Química Física y Analítica, Facultad de Química Universidad de Oviedo, 33007 Oviedo, Spain
| | - Haydée Valdés
- Departamento de Química Física y Analítica, Facultad de Química Universidad de Oviedo, 33007 Oviedo, Spain
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