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Pradhan R, Panigrahi S, Sahu PK. Conformational Search for the Building Block of Proteins Based on the Gradient Gravitational Search Algorithm (ConfGGS) Using Force Fields: CHARMM, AMBER, and OPLS-AA. J Chem Inf Model 2023; 63:670-690. [PMID: 36625780 DOI: 10.1021/acs.jcim.2c01398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Proteins are linear polymers built from a repertoire of 20 different amino acids, which are considered building blocks of proteins. The diversity and versatility of these 20 building blocks with regard to their conformations are key to adopting three-dimensional structures that facilitate proteins to undergo important mechanistic biological processes in living systems. The present investigation reports a conformational search of 20 different amino acids, building blocks of proteins, using three different force fields, CHARMM, AMBER, and OPLS-AA, implemented in the gradient gravitational search algorithm. The search technique (ConfGGS) includes the contribution from both bonded and nonbonded terms using Cartesian coordinates. The efficiency of such conformational searches has also been compared with other optimization algorithms: DE/Best, DE/Rand, and PSO algorithms with respect to computational time and accuracy based on the minimum number of iteration steps and computed lowest mean absolute error (MAE) and mean standard deviation (MSD) values for dihedral angles of respective near-optimal structures. Moreover, the ConfGGS technique has also been extended to an ordered protein fragment (PQITL) extracted from HIV-1 protease (PDB ID: 1YTH), an intrinsically disordered protein fragment, i.e., an amyloid-forming segment (AVVTGVTAV), from the NAC domain of Parkinson's disease protein α-synuclein, residues 69-77 (PDB ID: 4RIK), the experimental NMR atomic-resolution structure of α-synuclein fibrils (PDB ID: 2N0A), and a disulfide bond-containing protein fragment sequence (PCYGWPVCY), residues 59-67 (PDB ID: 6Y4F) toward structure prediction as a close homologue compared with experimental accuracy, using the CHARMM force field. The MolProbity validation results for the protein fragment (PQITL) obtained by ConfGGS/CHARMM are in better agreement with the native protein fragment structure of HIV-1 protease (PDB ID: 1YTH). Furthermore, the computed results have also been compared with the coordinates obtained from the AlphaFold network.
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Affiliation(s)
- Rojalin Pradhan
- Computational Modeling Research Laboratory, School of Chemistry (Autonomous), Sambalpur University, Jyoti Vihar, Burla768019, India
| | - Sibarama Panigrahi
- Computational Modeling Research Laboratory, School of Chemistry (Autonomous), Sambalpur University, Jyoti Vihar, Burla768019, India
- Department of Computer Science and Engineering, Sambalpur University Institute of Information Technology, Jyoti Vihar, Burla768019, India
| | - Prabhat K Sahu
- Computational Modeling Research Laboratory, School of Chemistry (Autonomous), Sambalpur University, Jyoti Vihar, Burla768019, India
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Failali A, Acher E, Guillaumont D, Vallet V, Réal F. Structural and thermodynamics properties of pure phase alkanes, monoamides and alkane/monoamide mixtures with an ab initio based force-field model. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Edr A, Wrobel D, Krupková A, Šťastná LČ, Cuřínová P, Novák A, Malý J, Kalasová J, Malý J, Malý M, Strašák T. Adaptive Synthesis of Functional Amphiphilic Dendrons as a Novel Approach to Artificial Supramolecular Objects. Int J Mol Sci 2022; 23:ijms23042114. [PMID: 35216229 PMCID: PMC8877797 DOI: 10.3390/ijms23042114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/04/2022] [Accepted: 02/09/2022] [Indexed: 11/16/2022] Open
Abstract
Supramolecular structures, such as micelles, liposomes, polymerosomes or dendrimerosomes, are widely studied and used as drug delivery systems. The behavior of amphiphilic building blocks strongly depends on their spatial distribution and shape of polar and nonpolar component. This report is focused on the development of new versatile synthetic protocols for amphiphilic carbosilane dendrons (amp-CS-DDNs) capable of self-assembly to regular micelles and other supramolecular objects. The presented strategy enables the fine modification of amphiphilic structure in several ways and also enables the facile connection of a desired functionality. DLS experiments demonstrated correlations between structural parameters of amp-CS-DDNs and the size of formed nanoparticles. For detailed information about the organization and spatial distribution of amp-CS-DDNs assemblies, computer simulation models were studied by using molecular dynamics in explicit water.
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Affiliation(s)
- Antonín Edr
- Institute of Chemical Process Fundamentals of the CAS, v.v.i., Rozvojová 135, 16502 Prague, Czech Republic; (A.E.); (A.K.); (L.Č.Š.); (P.C.)
- Faculty of Science, J.E. Purkyně University in Ústí nad Labem, Pasteurova 15, 40096 Ústí nad Labem, Czech Republic; (D.W.); (A.N.); (J.M.)
| | - Dominika Wrobel
- Faculty of Science, J.E. Purkyně University in Ústí nad Labem, Pasteurova 15, 40096 Ústí nad Labem, Czech Republic; (D.W.); (A.N.); (J.M.)
| | - Alena Krupková
- Institute of Chemical Process Fundamentals of the CAS, v.v.i., Rozvojová 135, 16502 Prague, Czech Republic; (A.E.); (A.K.); (L.Č.Š.); (P.C.)
- Faculty of Science, J.E. Purkyně University in Ústí nad Labem, Pasteurova 15, 40096 Ústí nad Labem, Czech Republic; (D.W.); (A.N.); (J.M.)
| | - Lucie Červenková Šťastná
- Institute of Chemical Process Fundamentals of the CAS, v.v.i., Rozvojová 135, 16502 Prague, Czech Republic; (A.E.); (A.K.); (L.Č.Š.); (P.C.)
- Faculty of Science, J.E. Purkyně University in Ústí nad Labem, Pasteurova 15, 40096 Ústí nad Labem, Czech Republic; (D.W.); (A.N.); (J.M.)
| | - Petra Cuřínová
- Institute of Chemical Process Fundamentals of the CAS, v.v.i., Rozvojová 135, 16502 Prague, Czech Republic; (A.E.); (A.K.); (L.Č.Š.); (P.C.)
- Faculty of Science, J.E. Purkyně University in Ústí nad Labem, Pasteurova 15, 40096 Ústí nad Labem, Czech Republic; (D.W.); (A.N.); (J.M.)
| | - Aleš Novák
- Faculty of Science, J.E. Purkyně University in Ústí nad Labem, Pasteurova 15, 40096 Ústí nad Labem, Czech Republic; (D.W.); (A.N.); (J.M.)
| | - Jan Malý
- Faculty of Chemical Technology, University of Chemistry and Technology Prague, Technická 5, 16828 Prague 6, Czech Republic; (J.M.); (J.K.)
| | - Jitka Kalasová
- Faculty of Chemical Technology, University of Chemistry and Technology Prague, Technická 5, 16828 Prague 6, Czech Republic; (J.M.); (J.K.)
| | - Jan Malý
- Faculty of Science, J.E. Purkyně University in Ústí nad Labem, Pasteurova 15, 40096 Ústí nad Labem, Czech Republic; (D.W.); (A.N.); (J.M.)
| | - Marek Malý
- Faculty of Science, J.E. Purkyně University in Ústí nad Labem, Pasteurova 15, 40096 Ústí nad Labem, Czech Republic; (D.W.); (A.N.); (J.M.)
- Correspondence: (M.M.); (T.S.)
| | - Tomáš Strašák
- Institute of Chemical Process Fundamentals of the CAS, v.v.i., Rozvojová 135, 16502 Prague, Czech Republic; (A.E.); (A.K.); (L.Č.Š.); (P.C.)
- Faculty of Science, J.E. Purkyně University in Ústí nad Labem, Pasteurova 15, 40096 Ústí nad Labem, Czech Republic; (D.W.); (A.N.); (J.M.)
- Correspondence: (M.M.); (T.S.)
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Müllerová M, Maciel D, Nunes N, Wrobel D, Stofik M, Červenková Št Astná L, Krupková A, Cuřínová P, Nováková K, Božík M, Malý M, Malý J, Rodrigues J, Strašák T. Carbosilane Glycodendrimers for Anticancer Drug Delivery: Synthetic Route, Characterization, and Biological Effect of Glycodendrimer-Doxorubicin Complexes. Biomacromolecules 2022; 23:276-290. [PMID: 34928129 DOI: 10.1021/acs.biomac.1c01264] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The complexity of drug delivery mechanisms calls for the development of new transport system designs. Here, we report a robust synthetic procedure toward stable glycodendrimer (glyco-DDM) series bearing glucose, galactose, and oligo(ethylene glycol)-modified galactose peripheral units. In vitro cytotoxicity assays showed exceptional biocompatibility of the glyco-DDMs. To demonstrate applicability in drug delivery, the anticancer agent doxorubicin (DOX) was encapsulated in the glyco-DDM structure. The anticancer activity of the resulting glyco-DDM/DOX complexes was evaluated on the noncancerous (BJ) and cancerous (MCF-7 and A2780) cell lines, revealing their promising generation- and concentration-dependent effect. The glyco-DDM/DOX complexes show gradual and pH-dependent DOX release profiles. Fluorescence spectra elucidated the encapsulation process. Confocal fluorescence microscopy demonstrated preferential cancer cell internalization of the glyco-DDM/DOX complexes. The conclusions were supported by computer modeling. Overall, our results are consistent with the assumption that novel glyco-DDMs and their drug complexes are very promising in drug delivery and related applications.
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Affiliation(s)
- Monika Müllerová
- The Czech Academy of Sciences, Institute of Chemical Process Fundamentals, Rozvojová 135, 165 02 Prague, Czech Republic
- Faculty of Science, University of Jan Evangelista Purkyně in Ústí nad Labem, Pasteurova 1, 400 96 Ústí nad Labem, Czech Republic
| | - Dina Maciel
- CQM-Centro de Química da Madeira, Universidade da Madeira Campus Universitário da Penteada, 9020-105 Funchal, Portugal
| | - Nádia Nunes
- CQM-Centro de Química da Madeira, Universidade da Madeira Campus Universitário da Penteada, 9020-105 Funchal, Portugal
| | - Dominika Wrobel
- Faculty of Science, University of Jan Evangelista Purkyně in Ústí nad Labem, Pasteurova 1, 400 96 Ústí nad Labem, Czech Republic
| | - Marcel Stofik
- Faculty of Science, University of Jan Evangelista Purkyně in Ústí nad Labem, Pasteurova 1, 400 96 Ústí nad Labem, Czech Republic
| | - Lucie Červenková Št Astná
- The Czech Academy of Sciences, Institute of Chemical Process Fundamentals, Rozvojová 135, 165 02 Prague, Czech Republic
- Faculty of Science, University of Jan Evangelista Purkyně in Ústí nad Labem, Pasteurova 1, 400 96 Ústí nad Labem, Czech Republic
| | - Alena Krupková
- The Czech Academy of Sciences, Institute of Chemical Process Fundamentals, Rozvojová 135, 165 02 Prague, Czech Republic
- Faculty of Science, University of Jan Evangelista Purkyně in Ústí nad Labem, Pasteurova 1, 400 96 Ústí nad Labem, Czech Republic
| | - Petra Cuřínová
- The Czech Academy of Sciences, Institute of Chemical Process Fundamentals, Rozvojová 135, 165 02 Prague, Czech Republic
- Faculty of Science, University of Jan Evangelista Purkyně in Ústí nad Labem, Pasteurova 1, 400 96 Ústí nad Labem, Czech Republic
| | - Kateřina Nováková
- The Czech Academy of Sciences, Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Matěj Božík
- Department of Food Science, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 16500 Praha-Suchdol, Czech Republic
| | - Marek Malý
- Faculty of Science, University of Jan Evangelista Purkyně in Ústí nad Labem, Pasteurova 1, 400 96 Ústí nad Labem, Czech Republic
| | - Jan Malý
- Faculty of Science, University of Jan Evangelista Purkyně in Ústí nad Labem, Pasteurova 1, 400 96 Ústí nad Labem, Czech Republic
| | - João Rodrigues
- CQM-Centro de Química da Madeira, Universidade da Madeira Campus Universitário da Penteada, 9020-105 Funchal, Portugal
| | - Tomáš Strašák
- The Czech Academy of Sciences, Institute of Chemical Process Fundamentals, Rozvojová 135, 165 02 Prague, Czech Republic
- Faculty of Science, University of Jan Evangelista Purkyně in Ústí nad Labem, Pasteurova 1, 400 96 Ústí nad Labem, Czech Republic
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Müllerová M, Maciel D, Nunes N, Wrobel D, Stofik M, Červenková Št́astná L, Krupková A, Cuřínová P, Nováková K, Božík M, Malý M, Malý J, Rodrigues J, Strašák T. Carbosilane Glycodendrimers for Anticancer Drug Delivery: Synthetic Route, Characterization, and Biological Effect of Glycodendrimer–Doxorubicin Complexes. Biomacromolecules 2022. [DOI: https:/doi.org/10.1021/acs.biomac.1c01264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
Affiliation(s)
- Monika Müllerová
- The Czech Academy of Sciences, Institute of Chemical Process Fundamentals, Rozvojová 135, 165 02 Prague, Czech Republic
- Faculty of Science, University of Jan Evangelista Purkyně in Ústí nad Labem, Pasteurova 1, 400 96 Ústí nad Labem, Czech Republic
| | - Dina Maciel
- CQM-Centro de Química da Madeira, Universidade da Madeira Campus Universitário da Penteada, 9020-105 Funchal, Portugal
| | - Nádia Nunes
- CQM-Centro de Química da Madeira, Universidade da Madeira Campus Universitário da Penteada, 9020-105 Funchal, Portugal
| | - Dominika Wrobel
- Faculty of Science, University of Jan Evangelista Purkyně in Ústí nad Labem, Pasteurova 1, 400 96 Ústí nad Labem, Czech Republic
| | - Marcel Stofik
- Faculty of Science, University of Jan Evangelista Purkyně in Ústí nad Labem, Pasteurova 1, 400 96 Ústí nad Labem, Czech Republic
| | - Lucie Červenková Št́astná
- The Czech Academy of Sciences, Institute of Chemical Process Fundamentals, Rozvojová 135, 165 02 Prague, Czech Republic
- Faculty of Science, University of Jan Evangelista Purkyně in Ústí nad Labem, Pasteurova 1, 400 96 Ústí nad Labem, Czech Republic
| | - Alena Krupková
- The Czech Academy of Sciences, Institute of Chemical Process Fundamentals, Rozvojová 135, 165 02 Prague, Czech Republic
- Faculty of Science, University of Jan Evangelista Purkyně in Ústí nad Labem, Pasteurova 1, 400 96 Ústí nad Labem, Czech Republic
| | - Petra Cuřínová
- The Czech Academy of Sciences, Institute of Chemical Process Fundamentals, Rozvojová 135, 165 02 Prague, Czech Republic
- Faculty of Science, University of Jan Evangelista Purkyně in Ústí nad Labem, Pasteurova 1, 400 96 Ústí nad Labem, Czech Republic
| | - Kateřina Nováková
- The Czech Academy of Sciences, Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Matěj Božík
- Department of Food Science, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 16500 Praha-Suchdol, Czech Republic
| | - Marek Malý
- Faculty of Science, University of Jan Evangelista Purkyně in Ústí nad Labem, Pasteurova 1, 400 96 Ústí nad Labem, Czech Republic
| | - Jan Malý
- Faculty of Science, University of Jan Evangelista Purkyně in Ústí nad Labem, Pasteurova 1, 400 96 Ústí nad Labem, Czech Republic
| | - João Rodrigues
- CQM-Centro de Química da Madeira, Universidade da Madeira Campus Universitário da Penteada, 9020-105 Funchal, Portugal
| | - Tomáš Strašák
- The Czech Academy of Sciences, Institute of Chemical Process Fundamentals, Rozvojová 135, 165 02 Prague, Czech Republic
- Faculty of Science, University of Jan Evangelista Purkyně in Ústí nad Labem, Pasteurova 1, 400 96 Ústí nad Labem, Czech Republic
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Müllerová M, Maciel D, Nunes N, Wrobel D, Stofik M, Červenková Št́astná L, Krupková A, Cuřínová P, Nováková K, Božík M, Malý M, Malý J, Rodrigues J, Strašák T. Carbosilane Glycodendrimers for Anticancer Drug Delivery: Synthetic Route, Characterization, and Biological Effect of Glycodendrimer–Doxorubicin Complexes. Biomacromolecules 2021. [DOI: https://doi.org/10.1021/acs.biomac.1c01264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Monika Müllerová
- The Czech Academy of Sciences, Institute of Chemical Process Fundamentals, Rozvojová 135, 165 02 Prague, Czech Republic
- Faculty of Science, University of Jan Evangelista Purkyně in Ústí nad Labem, Pasteurova 1, 400 96 Ústí nad Labem, Czech Republic
| | - Dina Maciel
- CQM-Centro de Química da Madeira, Universidade da Madeira Campus Universitário da Penteada, 9020-105 Funchal, Portugal
| | - Nádia Nunes
- CQM-Centro de Química da Madeira, Universidade da Madeira Campus Universitário da Penteada, 9020-105 Funchal, Portugal
| | - Dominika Wrobel
- Faculty of Science, University of Jan Evangelista Purkyně in Ústí nad Labem, Pasteurova 1, 400 96 Ústí nad Labem, Czech Republic
| | - Marcel Stofik
- Faculty of Science, University of Jan Evangelista Purkyně in Ústí nad Labem, Pasteurova 1, 400 96 Ústí nad Labem, Czech Republic
| | - Lucie Červenková Št́astná
- The Czech Academy of Sciences, Institute of Chemical Process Fundamentals, Rozvojová 135, 165 02 Prague, Czech Republic
- Faculty of Science, University of Jan Evangelista Purkyně in Ústí nad Labem, Pasteurova 1, 400 96 Ústí nad Labem, Czech Republic
| | - Alena Krupková
- The Czech Academy of Sciences, Institute of Chemical Process Fundamentals, Rozvojová 135, 165 02 Prague, Czech Republic
- Faculty of Science, University of Jan Evangelista Purkyně in Ústí nad Labem, Pasteurova 1, 400 96 Ústí nad Labem, Czech Republic
| | - Petra Cuřínová
- The Czech Academy of Sciences, Institute of Chemical Process Fundamentals, Rozvojová 135, 165 02 Prague, Czech Republic
- Faculty of Science, University of Jan Evangelista Purkyně in Ústí nad Labem, Pasteurova 1, 400 96 Ústí nad Labem, Czech Republic
| | - Kateřina Nováková
- The Czech Academy of Sciences, Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Matěj Božík
- Department of Food Science, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 16500 Praha-Suchdol, Czech Republic
| | - Marek Malý
- Faculty of Science, University of Jan Evangelista Purkyně in Ústí nad Labem, Pasteurova 1, 400 96 Ústí nad Labem, Czech Republic
| | - Jan Malý
- Faculty of Science, University of Jan Evangelista Purkyně in Ústí nad Labem, Pasteurova 1, 400 96 Ústí nad Labem, Czech Republic
| | - João Rodrigues
- CQM-Centro de Química da Madeira, Universidade da Madeira Campus Universitário da Penteada, 9020-105 Funchal, Portugal
| | - Tomáš Strašák
- The Czech Academy of Sciences, Institute of Chemical Process Fundamentals, Rozvojová 135, 165 02 Prague, Czech Republic
- Faculty of Science, University of Jan Evangelista Purkyně in Ústí nad Labem, Pasteurova 1, 400 96 Ústí nad Labem, Czech Republic
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Burley LG, Srivastava AK, Rudić S, Saines PJ. Spectroscopic Identification of Disordered Molecular Cations in Defect Perovskite‐Like A
Ln
(HCO
2
)(C
2
O
4
)
1.5
(
Ln
=Tb‐Er) Phases. Eur J Inorg Chem 2021. [DOI: 10.1002/ejic.202100591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Lydia G. Burley
- School of Physical Sciences University of Kent Canterbury CT2 7NH UK
| | - Anant Kumar Srivastava
- School of Physical Sciences University of Kent Canterbury CT2 7NH UK
- Department of Materials Engineering Indian Institute of Science (IISc) Bangalore-560012 Karnataka India
| | - Svemir Rudić
- ISIS Neutron and Muon Source STFC Rutherford Appleton Laboratory Chilton, Didcot OX11 0QX UK
| | - Paul J. Saines
- School of Physical Sciences University of Kent Canterbury CT2 7NH UK
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Ohno T, Kubicki JD. Adsorption of Organic Acids and Phosphate to an Iron (Oxyhydr)oxide Mineral: A Combined Experimental and Density Functional Theory Study. J Phys Chem A 2020; 124:3249-3260. [PMID: 32227955 DOI: 10.1021/acs.jpca.9b12044] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The interaction of soil organic matter with mineral surfaces is a critical reaction involved in many ecosystem services, including stabilization of organic matter in the terrestrial carbon pool and bioavailability of plant nutrients. Using model organic acids typically present in soil solutions, this study couples laboratory adsorption studies with density functional theory (DFT) to provide physical insights into the nature of the chemical bonding between carboxylate functional groups and a model FeOOH cluster. Topological determination of electron density at bond critical points using quantum theory of atoms in molecules (QTAIM) analysis revealed that the presence of multiple bonding paths between the organic acid and the FeOOH cluster is essential in determining the competitive adsorption of organic acids and phosphate for FeOOH surface adsorption sites. The electron density and Laplacian parameter values from QTAIM indicated that the primary carboxylate-FeOOH bond was more ionic than covalent in nature. The experimental and computational results provide molecular-level evidence of the important role of electrostatic forces in the bonding between carboxylic acids and Fe-hydroxides. This knowledge may assist in the formulation of management studies to meet the challenges of maintaining ecosystems services in the face of a changing climate.
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Affiliation(s)
- Tsutomu Ohno
- School of Food and Agriculture, University of Maine, Orono, Maine 04469, United States
| | - James D Kubicki
- Department of Geological Sciences, The University of Texas at El Paso, El Paso, Texas 79968, United States
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De Sousa J, Autreto P, Galvão D. Hydrogenation Dynamics Process of Single-Wall Carbon Nanotube Twisted. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2019.136960] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Gutierrez-Ulloa CE, Sepúlveda-Crespo D, García-Broncano P, Malý M, Muñoz-Fernández MA, de la Mata FJ, Gómez R. Synthesis of bow-tie carbosilane dendrimers and their HIV antiviral capacity: A comparison of the dendritic topology on the biological process. Eur Polym J 2019. [DOI: 10.1016/j.eurpolymj.2019.07.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Dubbeldam D, Walton KS, Vlugt TJH, Calero S. Design, Parameterization, and Implementation of Atomic Force Fields for Adsorption in Nanoporous Materials. ADVANCED THEORY AND SIMULATIONS 2019. [DOI: 10.1002/adts.201900135] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- David Dubbeldam
- Van 't Hoff Institute for Molecular SciencesUniversity of AmsterdamScience Park 904 1098XH Amsterdam The Netherlands
| | - Krista S. Walton
- School of Chemical & Biomolecular EngineeringGeorgia Institute of Technology311 Ferst Dr. NW Atlanta GA 30332‐0100 USA
| | - Thijs J. H. Vlugt
- Delft University of TechnologyProcess & Energy DepartmentLeeghwaterstraat 39 2628CB Delft The Netherlands
| | - Sofia Calero
- Department of PhysicalChemical and Natural SystemsUniversity Pablo de OlavideSevilla 41013 Spain
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Bertolani SJ, Siegel JB. A new benchmark illustrates that integration of geometric constraints inferred from enzyme reaction chemistry can increase enzyme active site modeling accuracy. PLoS One 2019; 14:e0214126. [PMID: 30947258 PMCID: PMC6448891 DOI: 10.1371/journal.pone.0214126] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 03/07/2019] [Indexed: 01/06/2023] Open
Abstract
Enzymes play a critical role in a wide array of industrial, medical, and research applications and with the recent explosion of genomic sequencing, we now have sequences for millions of enzymes for which there is no known structure. In order to utilize modern computational design tools for constructing inhibitors or engineering novel catalysts, the ability to accurately model enzymes is critical. A popular approach for modeling enzymes are comparative modeling techniques which can often accurately predict the global structural features. However, achieving atomic accuracy of an active site remains a challenge and is an issue when trying to utilize the molecular details for designing inhibitors or enhanced catalysts. Here we explore integrating knowledge about the required geometric orientation of conserved catalytic residues into the comparative modeling process in order to improve modeling accuracy. In order to investigate the utility of adding this information, we first carefully construct a benchmark set of reference structures to use. Consistent with previous findings, our benchmark demonstrates that the geometry between catalytic residues across an enzyme family is conserved and does not tend to deviate by more than 0.5Å. We then find that by integrating these geometric constraints during modeling, we can double the number of atomic level accuracy models (<1Å RMSD to the crystal structure ligand) within our benchmarking dataset, even for targets with templates as low as 20-30% sequence identity. Catalytic residues within an enzyme family are highly conserved and can often be readily identified through comparative sequence analysis to a known structure within the enzyme family. Therefore utilizing this readily available information has the potential to significantly improve drug design and enzyme engineering efforts for which there is no known structure for the enzyme of interest.
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Affiliation(s)
- Steve J. Bertolani
- Department of Chemistry, University of California Davis, Davis, California, United States of America
| | - Justin B. Siegel
- Department of Chemistry, University of California Davis, Davis, California, United States of America
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, California, United States of America
- Genome Center, University of California Davis, Davis, California, United States of America
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Shannon RJ, Hornung B, Tew DP, Glowacki DR. Anharmonic Molecular Mechanics: Ab Initio Based Morse Parametrizations for the Popular MM3 Force Field. J Phys Chem A 2019; 123:2991-2999. [PMID: 30793911 DOI: 10.1021/acs.jpca.8b12006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Methodologies for creating reactive potential energy surfaces from molecular mechanics force-fields are becoming increasingly popular. To date, molecular mechanics force-fields in biochemistry and small molecule organic chemistry tend to use harmonic expressions to treat bonding stretches, which is a poor approximation in reactive and nonequilibirum molecular dynamics simulations since bonds are often displaced significantly from their equilibrium positions. For such applications there is need for a better treatment of anharmonicity. In this contribution, Morse bonding potentials have been extensively parametrized for the atom types in the MM3 force field of Allinger and co-workers using high level CCSD(T)(F12*) energies. To our knowledge this is among the first instances of a comprehensive parametrization of Morse potentials in a popular organic chemistry force field. In the context of molecular dynamics simulations, these data will: (1) facilitate the fitting of reactive potential energy surfaces using empirical valence bond approaches and (2) enable more accurate treatments of energy transfer.
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Affiliation(s)
- R J Shannon
- School of Chemistry, Cantock's Close , University of Bristol , Bristol BS8 1TS , U.K.,Department of Mechanical Engineering , Stanford University , 452 Escondido Mall , Stanford , California 94305 , United States
| | - B Hornung
- School of Chemistry, Cantock's Close , University of Bristol , Bristol BS8 1TS , U.K
| | - D P Tew
- School of Chemistry, Cantock's Close , University of Bristol , Bristol BS8 1TS , U.K
| | - D R Glowacki
- School of Chemistry, Cantock's Close , University of Bristol , Bristol BS8 1TS , U.K.,Department of Computer Science , University of Bristol , Bristol BS8 1UB , U.K
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15
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Anticancer Activity of Dendriplexes against Advanced Prostate Cancer from Protumoral Peptides and Cationic Carbosilane Dendrimers. Biomacromolecules 2019; 20:1224-1234. [PMID: 30669830 DOI: 10.1021/acs.biomac.8b01632] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The interaction of neuropeptides, vasoactive intestinal peptide (VIP), or growth hormone-releasing hormone (GHRH), with a cationic carbosilane dendrimer forms dendriplexes with antitumoral behavior in advanced prostate cancer cells PC3. At the concentrations used for dendriplexes formation, the free peptides were protumoral and prometastatic in advanced prostate cancer, while dendrimer only showed low cytotoxicity, but did not avoid the metastatic behavior of PC3 cells. However, these nanoplexes favored also cell adhesion and avoided cell migration. Also, the dendriplexes were not toxic for no tumoral prostate cells (RPWE-1) or fibroblasts. The use of labeled GHRH peptide (rhodamine labeled) and a dendrimer (fluorescein labeled) allowed us to observe that both systems reach the intracellular milieu after dendriplex formation. The treatment of PC3 cells with the nanoplexes reduced expression of vascular endothelial growth factor (VEGF) and cyclic adenosine monophosphate (cAMP). Molecular modeling analysis highlights the important contribution of the carbosilane framework in the stabilization of the dendriplex, since dendrimer interacts with a peptide region where hydrophobic amino acids are presented.
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16
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Hagler AT. Force field development phase II: Relaxation of physics-based criteria… or inclusion of more rigorous physics into the representation of molecular energetics. J Comput Aided Mol Des 2018; 33:205-264. [DOI: 10.1007/s10822-018-0134-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 07/18/2018] [Indexed: 01/04/2023]
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17
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Biomolecular force fields: where have we been, where are we now, where do we need to go and how do we get there? J Comput Aided Mol Des 2018; 33:133-203. [DOI: 10.1007/s10822-018-0111-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 03/09/2018] [Indexed: 10/27/2022]
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18
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Rackers JA, Wang Z, Lu C, Laury ML, Lagardère L, Schnieders MJ, Piquemal JP, Ren P, Ponder JW. Tinker 8: Software Tools for Molecular Design. J Chem Theory Comput 2018; 14:5273-5289. [PMID: 30176213 PMCID: PMC6335969 DOI: 10.1021/acs.jctc.8b00529] [Citation(s) in RCA: 280] [Impact Index Per Article: 46.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Tinker software, currently released as version 8, is a modular molecular mechanics and dynamics package written primarily in a standard, easily portable dialect of Fortran 95 with OpenMP extensions. It supports a wide variety of force fields, including polarizable models such as the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field. The package runs on Linux, macOS, and Windows systems. In addition to canonical Tinker, there are branches, Tinker-HP and Tinker-OpenMM, designed for use on message passing interface (MPI) parallel distributed memory supercomputers and state-of-the-art graphical processing units (GPUs), respectively. The Tinker suite also includes a tightly integrated Java-based graphical user interface called Force Field Explorer (FFE), which provides molecular visualization capabilities as well as the ability to launch and control Tinker calculations.
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Affiliation(s)
- Joshua A. Rackers
- Program in Computational & Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri 63110, United States
| | - Zhi Wang
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, United States
| | - Chao Lu
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, United States
| | - Marie L. Laury
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, United States
| | - Louis Lagardère
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC Paris 06, UMR 7616, case courrier 137, 4 place Jussieu, F-75005, Paris, France
| | - Michael J. Schnieders
- Department of Biomedical Engineering, The University of Iowa, Iowa City, IA 52242, United States
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC Paris 06, UMR 7616, case courrier 137, 4 place Jussieu, F-75005, Paris, France
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jay W. Ponder
- Program in Computational & Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri 63110, United States
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, United States
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19
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Liegertová M, Wrobel D, Herma R, Müllerová M, Šťastná LČ, Cuřínová P, Strašák T, Malý M, Čermák J, Smejkal J, Štofik M, Maly J. Evaluation of toxicological and teratogenic effects of carbosilane glucose glycodendrimers in zebrafish embryos and model rodent cell lines. Nanotoxicology 2018; 12:797-818. [DOI: 10.1080/17435390.2018.1475582] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Michaela Liegertová
- Faculty of Science, Jan Evangelista Purkyne University, Usti nad Labem, Czech Republic
| | - Dominika Wrobel
- Faculty of Science, Jan Evangelista Purkyne University, Usti nad Labem, Czech Republic
| | - Regina Herma
- Faculty of Science, Jan Evangelista Purkyne University, Usti nad Labem, Czech Republic
| | - Monika Müllerová
- Institute of Chemical Process Fundamentals of the CAS, Prague, Czech Republic
| | | | - Petra Cuřínová
- Institute of Chemical Process Fundamentals of the CAS, Prague, Czech Republic
| | - Tomáš Strašák
- Institute of Chemical Process Fundamentals of the CAS, Prague, Czech Republic
| | - Marek Malý
- Faculty of Science, Jan Evangelista Purkyne University, Usti nad Labem, Czech Republic
| | - Jan Čermák
- Faculty of Science, Jan Evangelista Purkyne University, Usti nad Labem, Czech Republic
- Institute of Chemical Process Fundamentals of the CAS, Prague, Czech Republic
| | - Jiří Smejkal
- Faculty of Science, Jan Evangelista Purkyne University, Usti nad Labem, Czech Republic
| | - Marcel Štofik
- Faculty of Science, Jan Evangelista Purkyne University, Usti nad Labem, Czech Republic
| | - Jan Maly
- Faculty of Science, Jan Evangelista Purkyne University, Usti nad Labem, Czech Republic
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20
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Heredero-Bermejo I, Hernández-Ros JM, Sánchez-García L, Maly M, Verdú-Expósito C, Soliveri J, Javier de la Mata F, Copa-Patiño JL, Pérez-Serrano J, Sánchez-Nieves J, Gómez R. Ammonium and guanidine carbosilane dendrimers and dendrons as microbicides. Eur Polym J 2018. [DOI: 10.1016/j.eurpolymj.2018.02.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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21
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Xu P, Guidez EB, Bertoni C, Gordon MS. Perspective:Ab initioforce field methods derived from quantum mechanics. J Chem Phys 2018. [DOI: 10.1063/1.5009551] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Peng Xu
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Emilie B. Guidez
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80217, USA
| | - Colleen Bertoni
- Argonne Leadership Computing Facility, Argonne, Illinois 60439, USA
| | - Mark S. Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
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22
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Cramer JT, Führing JI, Baruch P, Brütting C, Knölker HJ, Gerardy-Schahn R, Fedorov R. Decoding Allosteric Networks in Biocatalysts: Rational Approach to Therapies and Biotechnologies. ACS Catal 2018. [DOI: 10.1021/acscatal.7b03714] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Johannes T. Cramer
- Institute of Clinical Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
- Institute for Biophysical Chemistry/Research Division for Structural Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Jana I. Führing
- Institute of Clinical Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Petra Baruch
- Institute for Biophysical Chemistry/Research Division for Structural Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Christian Brütting
- Department of Chemistry, Technische Universität Dresden, Bergstrasse 66, 01069 Dresden, Germany
| | - Hans-Joachim Knölker
- Department of Chemistry, Technische Universität Dresden, Bergstrasse 66, 01069 Dresden, Germany
| | - Rita Gerardy-Schahn
- Institute of Clinical Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Roman Fedorov
- Institute for Biophysical Chemistry/Research Division for Structural Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
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23
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Study of non-covalent interactions on dendriplex formation: Influence of hydrophobic, electrostatic and hydrogen bonds interactions. Colloids Surf B Biointerfaces 2018; 162:380-388. [DOI: 10.1016/j.colsurfb.2017.12.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 11/10/2017] [Accepted: 12/07/2017] [Indexed: 11/20/2022]
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24
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Klyne J, Bouchet A, Ishiuchi SI, Fujii M, Schneider M, Baldauf C, Dopfer O. Probing chirality recognition of protonated glutamic acid dimers by gas-phase vibrational spectroscopy and first-principles simulations. Phys Chem Chem Phys 2018; 20:28452-28464. [DOI: 10.1039/c8cp05855e] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We characterize stereospecific aspects of homochiral and heterochiral dimers of glutamic acid by infrared spectroscopy and first-principles molecular dynamics simulations.
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Affiliation(s)
- Johanna Klyne
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- 10623 Berlin
- Germany
| | - Aude Bouchet
- Laboratory for Chemistry and Life Science
- Institute of Innovation Research
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Shun-ichi Ishiuchi
- Laboratory for Chemistry and Life Science
- Institute of Innovation Research
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science
- Institute of Innovation Research
- Tokyo Institute of Technology
- Yokohama
- Japan
| | | | - Carsten Baldauf
- Fritz-Haber-Institut der MPG
- 14195 Berlin
- Germany
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie
- Universität Leipzig
| | - Otto Dopfer
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- 10623 Berlin
- Germany
- Tokyo Tech World Research Hub Initiative (WRHI)
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25
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Verma A, Parashar A, Packirisamy M. Atomistic modeling of graphene/hexagonal boron nitride polymer nanocomposites: a review. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1346] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Akarsh Verma
- Department of Mechanical and Industrial Engineering Indian Institute of Technology Roorkee India
| | - Avinash Parashar
- Department of Mechanical and Industrial Engineering Indian Institute of Technology Roorkee India
| | - M. Packirisamy
- Department of Mechanical and Industrial Engineering Concordia University Montreal Canada
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26
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Pirrotta A, De Vico L, Solomon GC, Franco I. Single-molecule force-conductance spectroscopy of hydrogen-bonded complexes. J Chem Phys 2017. [DOI: 10.1063/1.4976626] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Alessandro Pirrotta
- Nano-Science Center and Department of Chemistry, University of Copenhagen, 2100 Copenhagen Ø, Denmark
| | - Luca De Vico
- Department of Chemistry, University of Copenhagen, 2100 Copenhagen Ø, Denmark
| | - Gemma C. Solomon
- Nano-Science Center and Department of Chemistry, University of Copenhagen, 2100 Copenhagen Ø, Denmark
| | - Ignacio Franco
- Departments of Chemistry and Physics, University of Rochester, Rochester, New York 14627-0216, USA
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27
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Abstract
Metal ions play significant roles in numerous fields including chemistry, geochemistry, biochemistry, and materials science. With computational tools increasingly becoming important in chemical research, methods have emerged to effectively face the challenge of modeling metal ions in the gas, aqueous, and solid phases. Herein, we review both quantum and classical modeling strategies for metal ion-containing systems that have been developed over the past few decades. This Review focuses on classical metal ion modeling based on unpolarized models (including the nonbonded, bonded, cationic dummy atom, and combined models), polarizable models (e.g., the fluctuating charge, Drude oscillator, and the induced dipole models), the angular overlap model, and valence bond-based models. Quantum mechanical studies of metal ion-containing systems at the semiempirical, ab initio, and density functional levels of theory are reviewed as well with a particular focus on how these methods inform classical modeling efforts. Finally, conclusions and future prospects and directions are offered that will further enhance the classical modeling of metal ion-containing systems.
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Affiliation(s)
| | - Kenneth M. Merz
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute of Cyber-Enabled Research, Michigan State University, East Lansing, Michigan 48824, United States
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28
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Strašák T, Malý J, Wróbel D, Malý M, Herma R, Čermák J, Müllerová M, Št′astná LČ, Cuřínová P. Phosphonium carbosilane dendrimers for biomedical applications – synthesis, characterization and cytotoxicity evaluation. RSC Adv 2017. [DOI: 10.1039/c7ra01845b] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Phosphonium carbosilane dendrimers could represent an alternative to ammonium ones in gene therapy applications with high potential of mitochondrial targeting.
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Affiliation(s)
- Tomáš Strašák
- Institute of Chemical Process Fundamentals of the CAS
- CZ-165 02 Prague 6 - Suchdol
- Czech Republic
| | - Jan Malý
- Department of Biology
- J.E. Purkyně University
- 40096 Usti nad Labem
- Czech Republic
| | - Dominika Wróbel
- Department of Biology
- J.E. Purkyně University
- 40096 Usti nad Labem
- Czech Republic
| | - Marek Malý
- Department of Physics
- J. E. Purkyně University
- 40096 Usti nad Labem
- Czech Republic
| | - Regina Herma
- Department of Biology
- J.E. Purkyně University
- 40096 Usti nad Labem
- Czech Republic
| | - Jan Čermák
- Institute of Chemical Process Fundamentals of the CAS
- CZ-165 02 Prague 6 - Suchdol
- Czech Republic
- Department of Chemistry
- J.E. Purkyně University
| | - Monika Müllerová
- Institute of Chemical Process Fundamentals of the CAS
- CZ-165 02 Prague 6 - Suchdol
- Czech Republic
| | | | - Petra Cuřínová
- Institute of Chemical Process Fundamentals of the CAS
- CZ-165 02 Prague 6 - Suchdol
- Czech Republic
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29
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Huang IS, Li JJ, Tsai MK. Solvation Dynamics of CO₂(g) by Monoethanolamine at the Gas-Liquid Interface: A Molecular Mechanics Approach. Molecules 2016; 22:molecules22010008. [PMID: 28025552 PMCID: PMC6155642 DOI: 10.3390/molecules22010008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 12/14/2016] [Accepted: 12/19/2016] [Indexed: 11/25/2022] Open
Abstract
A classical force field approach was used to characterize the solvation dynamics of high-density CO2(g) by monoethanolamine (MEA) at the air–liquid interface. Intra- and intermolecular CO2 and MEA potentials were parameterized according to the energetics calculated at the MP2 and BLYP-D2 levels of theory. The thermodynamic properties of CO2 and MEA, such as heat capacity and melting point, were consistently predicted using this classical potential. An approximate interfacial simulation for CO2(g)/MEA(l) was performed to monitor the depletion of the CO2(g) phase, which was influenced by amino and hydroxyl groups of MEA. There are more intramolecular hydrogen bond interactions notably identified in the interfacial simulation than the case of bulk MEA(l) simulation. The hydroxyl group of MEA was found to more actively approach CO2 and overpower the amino group to interact with CO2 at the air–liquid interface. With artificially reducing the dipole moment of the hydroxyl group, CO2–amino group interaction was enhanced and suppressed CO2(g) depletion. The hydroxyl group of MEA was concluded to play dual but contradictory roles for CO2 capture.
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Affiliation(s)
- I-Shou Huang
- Department of Chemistry, National Taiwan Normal University, Taipei 11677, Taiwan.
| | - Jia-Jen Li
- Department of Chemistry, National Taiwan Normal University, Taipei 11677, Taiwan.
| | - Ming-Kang Tsai
- Department of Chemistry, National Taiwan Normal University, Taipei 11677, Taiwan.
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30
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Evaluations of AMBER force field parameters by MINA approach for copper-based nucleases. Struct Chem 2016. [DOI: 10.1007/s11224-016-0764-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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31
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Kaminský J, Jensen F. Conformational Interconversions of Amino Acid Derivatives. J Chem Theory Comput 2016; 12:694-705. [PMID: 26691979 DOI: 10.1021/acs.jctc.5b00911] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Exhaustive conformational interconversions including transition structure analyses of N-acetyl-l-glycine-N-methylamide as well as its alanine, serine, and cysteine analogues have been investigated at the MP2/6-31G** level, yielding a total of 142 transition states. Improved estimates of relative energies were obtained by separately extrapolating the Hartree-Fock and MP2 energies to the basis set limit and adding the difference between CCSD(T) and MP2 results with the cc-pVDZ basis set to the extrapolated MP2 results. The performance of eight empirical force fields (AMBER94, AMBER14SB, MM2, MM3, MMFFs, CHARMM22_CMAP, OPLS_2005, and AMOEBAPRO13) in reproducing ab initio energies of transition states was tested. Our results indicate that commonly used class I force fields employing a fixed partial charge model for the electrostatic interaction provide mean errors in the ∼10 kJ/mol range for energies of conformational transition states for amino acid conformers. Modern reparametrized versions, such as CHARMM22_CMAP, and polarizable force fields, such as AMOEBAPRO13, have slightly lower mean errors, but maximal errors are still in the 35 kJ/mol range. There are differences between the force fields in their ability for reproducing conformational transitions classified according to backbone/side-chain or regions in the Ramachandran angles, but the data set is likely too small to draw any general conclusions. Errors in conformational interconversion barriers by ∼10 kJ/mol suggest that the commonly used force field may bias certain types of transitions by several orders of magnitude in rate and thus lead to incorrect dynamics in simulations. It is therefore suggested that information for conformational transition states should be included in parametrizations of new force fields.
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Affiliation(s)
- Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Frank Jensen
- Department of Chemistry, Aarhus University , Langelandsgade 140, DK-8000 Aarhus C, Denmark
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32
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Sarkar A, Drouillard S, Rivet A, Perez S. Databases of Conformations and NMR Structures of Glycan Determinants. Glycobiology 2015; 25:1480-90. [PMID: 26240168 DOI: 10.1093/glycob/cwv054] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 07/15/2015] [Indexed: 11/13/2022] Open
Abstract
The present study reports a comprehensive nuclear magnetic resonance (NMR) characterization and a systematic conformational sampling of the conformational preferences of 170 glycan moieties of glycosphingolipids as produced in large-scale quantities by bacterial fermentation. These glycans span across a variety of families including the blood group antigens (A, B and O), core structures (Types 1, 2 and 4), fucosylated oligosaccharides (core and lacto-series), sialylated oligosaccharides (Types 1 and 2), Lewis antigens, GPI-anchors and globosides. A complementary set of about 100 glycan determinants occurring in glycoproteins and glycosaminoglycans has also been structurally characterized using molecular mechanics-based computation. The experimental and computational data generated are organized in two relational databases that can be queried by the user through a user-friendly search engine. The NMR ((1)H and (13)C, COSY, TOCSY, HMQC, HMBC correlation) spectra and 3D structures are available for visualization and download in commonly used structure formats. Emphasis has been given to the use of a common nomenclature for the structural encoding of the carbohydrates and each glycan molecule is described by four different types of representations in order to cope with the different usages in chemistry and biology. These web-based databases were developed with non-proprietary software and are open access for the scientific community available at http://glyco3d.cermav.cnrs.fr.
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Affiliation(s)
- Anita Sarkar
- Centre de Recherches sur les Macromolécules Végétales, UPR5301 CNRS-Université Grenoble Alpes, BP53, 38041 Grenoble cédex 09, France
| | - Sophie Drouillard
- Centre de Recherches sur les Macromolécules Végétales, UPR5301 CNRS-Université Grenoble Alpes, BP53, 38041 Grenoble cédex 09, France
| | - Alain Rivet
- Centre de Recherches sur les Macromolécules Végétales, UPR5301 CNRS-Université Grenoble Alpes, BP53, 38041 Grenoble cédex 09, France
| | - Serge Perez
- Centre de Recherches sur les Macromolécules Végétales, UPR5301 CNRS-Université Grenoble Alpes, BP53, 38041 Grenoble cédex 09, France Département de Pharmacochimie Moléculaire, UMR5063 CNRS-Université Grenoble Alpes, BP53, 38041 Grenoble cédex 09, France
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Abstract
The article reviews the significant contributions to, and the present status of, applications of computational methods for the characterization and prediction of protein-carbohydrate interactions. After a presentation of the specific features of carbohydrate modeling, along with a brief description of the experimental data and general features of carbohydrate-protein interactions, the survey provides a thorough coverage of the available computational methods and tools. At the quantum-mechanical level, the use of both molecular orbitals and density-functional theory is critically assessed. These are followed by a presentation and critical evaluation of the applications of semiempirical and empirical methods: QM/MM, molecular dynamics, free-energy calculations, metadynamics, molecular robotics, and others. The usefulness of molecular docking in structural glycobiology is evaluated by considering recent docking- validation studies on a range of protein targets. The range of applications of these theoretical methods provides insights into the structural, energetic, and mechanistic facets that occur in the course of the recognition processes. Selected examples are provided to exemplify the usefulness and the present limitations of these computational methods in their ability to assist in elucidation of the structural basis underlying the diverse function and biological roles of carbohydrates in their dialogue with proteins. These test cases cover the field of both carbohydrate biosynthesis and glycosyltransferases, as well as glycoside hydrolases. The phenomenon of (macro)molecular recognition is illustrated for the interactions of carbohydrates with such proteins as lectins, monoclonal antibodies, GAG-binding proteins, porins, and viruses.
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Affiliation(s)
- Serge Pérez
- Department of Molecular Pharmacochemistry, CNRS, University Grenoble-Alpes, Grenoble, France.
| | - Igor Tvaroška
- Department of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic; Department of Chemistry, Faculty of Natural Sciences, Constantine The Philosopher University, Nitra, Slovak Republic.
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34
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Costa PRR, Sansano JM, Cossío U, Barcellos JCF, Dias AG, Nájera C, Arrieta A, de Cózar A, Cossío FP. Synthesis of Chromen[4,3-b]pyrrolidines by Intramolecular 1,3-Dipolar Cycloadditions of Azomethine Ylides: An Experimental and Computational Assessment of the Origin of Stereocontrol. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500434] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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35
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Marson D, Laurini E, Posocco P, Fermeglia M, Pricl S. Cationic carbosilane dendrimers and oligonucleotide binding: an energetic affair. NANOSCALE 2015; 7:3876-3887. [PMID: 25340619 DOI: 10.1039/c4nr04510f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Generation 2 cationic carbosilane dendrimers hold great promise as internalizing agents for gene therapy as they present low toxicity and retain and internalize the genetic material as an oligonucleotide or siRNA. In this work we carried out complete in silico structural and energetical characterization of the interactions of a set of G2 carbosilane dendrimers, showing different affinity towards two single strand oligonucleotide (ODN) sequences in vitro. Our simulations predict that these four dendrimers and the relevant ODN complexes are characterized by similar size and shape, and that the molecule-specific ODN binding ability can be rationalized only by considering a critical molecular design parameter: the normalized effective binding energy ΔG(bind,eff)/N(eff), i.e. the performance of each active individual dendrimer branch directly involved in a binding interaction.
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Affiliation(s)
- D Marson
- Molecular Simulation Engineering (MOSE) Laboratory, DEA, University of Trieste, Piazzale Europa 1, 34127 Trieste, Italy.
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MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FT, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiórkiewicz-Kuczera J, Yin D, Karplus M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 2014; 102:3586-616. [PMID: 24889800 DOI: 10.1021/jp973084f] [Citation(s) in RCA: 10819] [Impact Index Per Article: 1081.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
New protein parameters are reported for the all-atom empirical energy function in the CHARMM program. The parameter evaluation was based on a self-consistent approach designed to achieve a balance between the internal (bonding) and interaction (nonbonding) terms of the force field and among the solvent-solvent, solvent-solute, and solute-solute interactions. Optimization of the internal parameters used experimental gas-phase geometries, vibrational spectra, and torsional energy surfaces supplemented with ab initio results. The peptide backbone bonding parameters were optimized with respect to data for N-methylacetamide and the alanine dipeptide. The interaction parameters, particularly the atomic charges, were determined by fitting ab initio interaction energies and geometries of complexes between water and model compounds that represented the backbone and the various side chains. In addition, dipole moments, experimental heats and free energies of vaporization, solvation and sublimation, molecular volumes, and crystal pressures and structures were used in the optimization. The resulting protein parameters were tested by applying them to noncyclic tripeptide crystals, cyclic peptide crystals, and the proteins crambin, bovine pancreatic trypsin inhibitor, and carbonmonoxy myoglobin in vacuo and in crystals. A detailed analysis of the relationship between the alanine dipeptide potential energy surface and calculated protein φ, χ angles was made and used in optimizing the peptide group torsional parameters. The results demonstrate that use of ab initio structural and energetic data by themselves are not sufficient to obtain an adequate backbone representation for peptides and proteins in solution and in crystals. Extensive comparisons between molecular dynamics simulations and experimental data for polypeptides and proteins were performed for both structural and dynamic properties. Energy minimization and dynamics simulations for crystals demonstrate that the latter are needed to obtain meaningful comparisons with experimental crystal structures. The presented parameters, in combination with the previously published CHARMM all-atom parameters for nucleic acids and lipids, provide a consistent set for condensed-phase simulations of a wide variety of molecules of biological interest.
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Affiliation(s)
- A D MacKerell
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, Baltimore, Maryland 21201, and Laboratoire de Chimie Biophysique, ISIS, Institut Le Bel, Université Louis Pasteur, 67000 Strasbourg, France
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Vlachakis D, Bencurova E, Papangelopoulos N, Kossida S. Current state-of-the-art molecular dynamics methods and applications. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 94:269-313. [PMID: 24629189 DOI: 10.1016/b978-0-12-800168-4.00007-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Molecular dynamics simulations are used to describe the patterns, strength, and properties of protein behavior, drug-receptor interactions, the solvation of molecules, the conformational changes that a protein or molecule may undergo under various conditions, and other events that require the systematic evaluation of molecular properties in dynamic molecular systems. Only few years ago proteins were considered to be rigid body structures with very limited conformational flexibility. However, it is now clear that proteins are highly dynamic structures, the internal organization of which is the key to their 3D spatial arrangement and hence biological function. The study of protein dynamics in the lab is a very complicated, expensive, and time-consuming process. Therefore, a lot of effort and hope lies with the computers and the in silico study of protein structure and molecular dynamics. Herein, an effort has been made to describe the ever-evolving field of molecular dynamics, the different algorithms, and force fields that are being used as well as to provide some insight on what the near future holds for this auspicious field of computational structural biology.
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Affiliation(s)
- Dimitrios Vlachakis
- Bioinformatics & Medical Informatics Team, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Elena Bencurova
- Bioinformatics & Medical Informatics Team, Biomedical Research Foundation, Academy of Athens, Athens, Greece; Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, Kosice, Slovakia
| | - Nikitas Papangelopoulos
- Bioinformatics & Medical Informatics Team, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Sophia Kossida
- Bioinformatics & Medical Informatics Team, Biomedical Research Foundation, Academy of Athens, Athens, Greece.
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38
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Galán M, Sánchez Rodríguez J, Jiménez JL, Relloso M, Maly M, de la Mata FJ, Muñoz-Fernández MA, Gómez R. Synthesis of new anionic carbosilane dendrimers via thiol–ene chemistry and their antiviral behaviour. Org Biomol Chem 2014; 12:3222-37. [DOI: 10.1039/c4ob00162a] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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Dubbeldam D, Torres-Knoop A, Walton KS. On the inner workings of Monte Carlo codes. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2013.819102] [Citation(s) in RCA: 202] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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40
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Li J, Wang F, Cheng X, Li X. Reactive Molecular Dynamics Simulation on Thermal Decomposition of n‐Heptane. CHINESE J CHEM PHYS 2013. [DOI: 10.1063/1674-0068/26/02/211-219] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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41
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Rasines B, Sánchez-Nieves J, Maiolo M, Maly M, Chonco L, Jiménez JL, Muñoz-Fernández MÁ, de la Mata FJ, Gómez R. Synthesis, structure and molecular modelling of anionic carbosilane dendrimers. Dalton Trans 2013; 41:12733-48. [PMID: 22968584 DOI: 10.1039/c2dt31099f] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Anionic carbosilane dendrimers of generations 1-3 have been synthesized containing carboxylate G(n)X(C(2)H(4)CO(2)Na)(m) and sulfonate G(n)X(C(2)H(4)SO(3)Na)(m) peripheral groups and derived from two different cores, 1,3,5-(HO)(3)C(6)H(3) (X = O(3)) and Si(C(3)H(5))(4) (X = Si). The peripheral anionic groups make these dendrimers water soluble, despite their highly hydrophobic framework. These dendrimers present a net negative charge in water, which was influenced by the pH of the medium. This characteristic was studied by pH titration. Also molecular modeling calculations have been performed to study differences in an aqueous medium between carboxylate and sulfonate dendrimers of different cores. The results obtained were also compared with those obtained from DOSY NMR experiments and zeta-potential measurements.
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Affiliation(s)
- Beatriz Rasines
- Dpto. de Química Inorgánica, Universidad de Alcalá, Campus Universitario, E-28871 Alcalá de Henares (Madrid), Spain
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43
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Tolosa S, Hidalgo A, Sansón JA. Amino Acid Tautomerization Reactions in Aqueous Solution via Concerted and Assisted Mechanisms Using Free Energy Curves from MD Simulation. J Phys Chem B 2012; 116:13033-44. [DOI: 10.1021/jp307391s] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Santiago Tolosa
- Departamento de Ingeniería Química y
Química Física, Universidad de Extremadura, 06071-Badajoz, Spain
| | - Antonio Hidalgo
- Departamento de Ingeniería Química y
Química Física, Universidad de Extremadura, 06071-Badajoz, Spain
| | - Jorge A. Sansón
- Departamento de Ingeniería Química y
Química Física, Universidad de Extremadura, 06071-Badajoz, Spain
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44
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Taha HA, Richards MR, Lowary TL. Conformational Analysis of Furanoside-Containing Mono- and Oligosaccharides. Chem Rev 2012; 113:1851-76. [DOI: 10.1021/cr300249c] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Hashem A. Taha
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Michele R. Richards
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Todd L. Lowary
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
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45
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Drummond ML, Wilson AK, Cundari TR. Nature of protein-CO2 interactions as elucidated via molecular dynamics. J Phys Chem B 2012; 116:11578-93. [PMID: 22882078 DOI: 10.1021/jp304770h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Rising global temperatures require innovative measures to reduce atmospheric concentrations of CO(2). The most successful carbon capture technology on Earth is the enzymatic capture of CO(2) and its sequestration in the form of glucose. Efforts to improve upon or mimic this naturally occurring process will require a rich understanding of protein-CO(2) interactions. Toward that end, extensive all-atom molecular dynamics (MD) simulations were performed on the CO(2)-utilizing enzyme phosphoenolpyruvate carboxykinase (PEPCK). Preliminary simulations were performed using implicit and explicit solvent models, which yielded similar results: arginine, lysine, tyrosine, and asparagine enhance the ability of a protein to bind carbon dioxide. Extensive explicit solvent simulations were performed for both wild-type PEPCK and five single-point PEPCK mutants, revealing three prevalent channels by which CO(2) enters (or exits) the active site cleft, as well as a fourth channel (observed only once), the existence of which can be rationalized in terms of the position of a key Arg residue. The strongest CO(2) binding sites in these simulations consist of appropriately positioned hydrogen bond donors and acceptors. Interactions between CO(2) and both Mn(2+) and Mg(2+) present in PEPCK are minimal due to the stable protein- and solvent-based coordination environments of these cations. His 232, suggested by X-ray crystallography as being a potential important CO(2) binding site, is indeed found to be particularly "CO(2)-philic" in these simulations. Finally, a recent mechanism, proposed on the basis of X-ray crystallography, for PEPCK active site lid closure is discussed in light of the MD trajectories. Overall, the results of this work will prove useful not only to scientists investigating PEPCK, but also to groups seeking to develop an environmentally benign, protein-based carbon capture, sequestration, and utilization system.
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Affiliation(s)
- Michael L Drummond
- Department of Chemistry, Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, Denton, Texas 76201, USA.
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46
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Chonco L, Pion M, Vacas E, Rasines B, Maly M, Serramía M, López-Fernández L, De la Mata J, Alvarez S, Gómez R, Muñoz-Fernández M. Carbosilane dendrimer nanotechnology outlines of the broad HIV blocker profile. J Control Release 2012; 161:949-58. [DOI: 10.1016/j.jconrel.2012.04.050] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2012] [Accepted: 04/26/2012] [Indexed: 12/27/2022]
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Abstract
The (H2SO4)2, H2SO4-DMF, and (H2SO4)2-DMF complexes have been investigated, using the B3LYP functional with cc-pVQZ basis set. The characteristics of structure and energetics for binary complexes of sulfuric acid with dimethylformamide (DMF) have been obtained for the first time. The H-bond formation both between molecules of sulfuric acid as well as sulfuric acid-DMF were studied, on the basis of Weinhold’s natural bond orbital (NBO) analysis. It was shown that the H-bond formation between sulfuric acid and DMF molecules is stronger than ones for the acids dimer. The value of charge transfer from lone pair (LP) orbitals of DMF oxygen to the antibonding orbital of acid OH-bond significantly exceeds the criterion of H-bond existance (0.01 e). As follows from energy, among the complexes under investigation the most preferable one was found to be (H2SO4)2-DMF in which sulfuric acid molecules are linked with each other by three H-bonds.
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48
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Nazarski RB, Pasternak B, Leśniak S. Three-component conformational equilibria of some flexible pyrrolidin-2-(thi)ones in solution by NMR data (δC, δH, and nJHH) and their DFT predictions: a confrontation of different approaches. Tetrahedron 2011. [DOI: 10.1016/j.tet.2011.06.095] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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49
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Eriksen JJ, Olsen JMH, Aidas K, Ågren H, Mikkelsen KV, Kongsted J. Computational protocols for prediction of solute NMR relative chemical shifts. A case study of
L
‐tryptophan in aqueous solution. J Comput Chem 2011; 32:2853-64. [DOI: 10.1002/jcc.21867] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Revised: 05/16/2011] [Accepted: 05/17/2011] [Indexed: 01/19/2023]
Affiliation(s)
- Janus J. Eriksen
- Department of Chemistry, Center for Computational Molecular Sciences, H. C. Ørsted Institute, University of Copenhagen, Copenhagen Ø DK‐2100, Denmark
| | - Jógvan Magnus H. Olsen
- Department of Physics and Chemistry, University of Southern Denmark, Odense M DK‐5230, Denmark
| | - Kȩstutis Aidas
- Department of Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology, Stockholm SE‐106 91, Sweden
| | - Hans Ågren
- Department of Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology, Stockholm SE‐106 91, Sweden
| | - Kurt V. Mikkelsen
- Department of Chemistry, Center for Computational Molecular Sciences, H. C. Ørsted Institute, University of Copenhagen, Copenhagen Ø DK‐2100, Denmark
| | - Jacob Kongsted
- Department of Physics and Chemistry, University of Southern Denmark, Odense M DK‐5230, Denmark
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50
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Burggraf F, Koslowski T. The simulation of interquinone charge transfer in a bacterial photoreaction center highlights the central role of a hydrogen-bonded non-heme iron complex. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:53-8. [DOI: 10.1016/j.bbabio.2010.08.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Revised: 08/02/2010] [Accepted: 08/05/2010] [Indexed: 11/30/2022]
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