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Munro TA. Reanalysis of a μ opioid receptor crystal structure reveals a covalent adduct with BU72. BMC Biol 2023; 21:213. [PMID: 37817141 PMCID: PMC10566028 DOI: 10.1186/s12915-023-01689-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 08/25/2023] [Indexed: 10/12/2023] Open
Abstract
BACKGROUND The first crystal structure of the active μ opioid receptor (μOR) exhibited several unexplained features. The ligand BU72 exhibited many extreme deviations from ideal geometry, along with unexplained electron density. I previously showed that inverting the benzylic configuration resolved these problems, establishing revised stereochemistry of BU72 and its analog BU74. However, another problem remains unresolved: additional unexplained electron density contacts both BU72 and a histidine residue in the N-terminus, revealing the presence of an as-yet unidentified atom. RESULTS These short contacts and uninterrupted density are inconsistent with non-covalent interactions. Therefore, BU72 and μOR form a covalent adduct, rather than representing two separate entities as in the original model. A subsequently proposed magnesium complex is inconsistent with multiple lines of evidence. However, oxygen fits the unexplained density well. While the structure I propose is tentative, similar adducts have been reported previously in the presence of reactive oxygen species. Moreover, known sources of reactive oxygen species were present: HEPES buffer, nickel ions, and a sequence motif that forms redox-active nickel complexes. This motif contacts the unexplained density. The adduct exhibits severe strain, and the tethered N-terminus forms contacts with adjacent residues. These forces, along with the nanobody used as a G protein substitute, would be expected to influence the receptor conformation. Consistent with this, the intracellular end of the structure differs markedly from subsequent structures of active μOR bound to Gi protein. CONCLUSIONS Later Gi-bound structures are likely to be more accurate templates for ligand docking and modelling of active G protein-bound μOR. The possibility of reactions like this should be considered in the choice of protein truncation sites and purification conditions, and in the interpretation of excess or unexplained density.
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Affiliation(s)
- Thomas A Munro
- School of Life and Environmental Sciences, Deakin University, Burwood, VIC, 3125, Australia.
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2
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Villot C, Lao KU. Electronic structure theory on modeling short-range noncovalent interactions between amino acids. J Chem Phys 2023; 158:094301. [PMID: 36889981 DOI: 10.1063/5.0138032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
While short-range noncovalent interactions (NCIs) are proving to be of importance in many chemical and biological systems, these atypical bindings happen within the so-called van der Waals envelope and pose an enormous challenge for current computational methods. We introduce SNCIAA, a database of 723 benchmark interaction energies of short-range noncovalent interactions between neutral/charged amino acids originated from protein x-ray crystal structures at the "gold standard" coupled-cluster with singles, doubles, and perturbative triples/complete basis set [CCSD(T)/CBS] level of theory with a mean absolute binding uncertainty less than 0.1 kcal/mol. Subsequently, a systematic assessment of commonly used computational methods, such as the second-order Møller-Plesset theory (MP2), density functional theory (DFT), symmetry-adapted perturbation theory (SAPT), composite electronic-structure methods, semiempirical approaches, and the physical-based potentials with machine learning (IPML) on SNCIAA is carried out. It is shown that the inclusion of dispersion corrections is essential even though these dimers are dominated by electrostatics, such as hydrogen bondings and salt bridges. Overall, MP2, ωB97M-V, and B3LYP+D4 turned out to be the most reliable methods for the description of short-range NCIs even in strongly attractive/repulsive complexes. SAPT is also recommended in describing short-range NCIs only if the δMP2 correction has been included. The good performance of IPML for dimers at close-equilibrium and long-range conditions is not transferable to the short-range. We expect that SNCIAA will assist the development/improvement/validation of computational methods, such as DFT, force-fields, and ML models, in describing NCIs across entire potential energy surfaces (short-, intermediate-, and long-range NCIs) on the same footing.
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Affiliation(s)
- Corentin Villot
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, USA
| | - Ka Un Lao
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, USA
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3
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Mráziková K, Kruse H, Mlýnský V, Auffinger P, Šponer J. Multiscale Modeling of Phosphate···π Contacts in RNA U-Turns Exposes Differences between Quantum-Chemical and AMBER Force Field Descriptions. J Chem Inf Model 2022; 62:6182-6200. [PMID: 36454943 DOI: 10.1021/acs.jcim.2c01064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Phosphate···π, also called anion···π, contacts occur between nucleobases and anionic phosphate oxygens (OP2) in r(GNRA) and r(UNNN) U-turn motifs (N = A,G,C,U; R = A,G). These contacts were investigated using state-of-the-art quantum-chemical methods (QM) to characterize their physicochemical properties and to serve as a reference to evaluate AMBER force field (AFF) performance. We found that phosphate···π interaction energies calculated with the AFF for dimethyl phosphate···nucleobase model systems are less stabilizing in comparison with double-hybrid DFT and that minimum contact distances are larger for all nucleobases. These distance stretches are also observed in large-scale AFF vs QM/MM computations and classical molecular dynamics (MD) simulations on several r(gcGNRAgc) tetraloop hairpins when compared to experimental data extracted from X-ray/cryo-EM structures (res. ≤ 2.5 Å) using the WebFR3D bioinformatic tool. MD simulations further revealed shifted OP2/nucleobase positions. We propose that discrepancies between the QM and AFF result from a combination of missing polarization in the AFF combined with too large AFF Lennard-Jones (LJ) radii of nucleobase carbon atoms in addition to an exaggerated short-range repulsion of the r-12 LJ repulsive term. We compared these results with earlier data gathered on lone pair···π contacts in CpG Z-steps occurring in r(UNCG) tetraloops. In both instances, charge transfer calculations do not support any significant n → π* donation effects. We also investigated thiophosphate···π contacts that showed reduced stabilizing interaction energies when compared to phosphate···π contacts. Thus, we challenge suggestions that the experimentally observed enhanced thermodynamic stability of phosphorothioated r(GNRA) tetraloops can be explained by larger London dispersion.
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Affiliation(s)
- Klaudia Mráziková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00Brno, Czech Republic
| | - Holger Kruse
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65Brno, Czech Republic
| | - Vojtěch Mlýnský
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65Brno, Czech Republic
| | - Pascal Auffinger
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg67084, France
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65Brno, Czech Republic
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4
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Chawla M, Kalra K, Cao Z, Cavallo L, Oliva R. Occurrence and stability of anion-π interactions between phosphate and nucleobases in functional RNA molecules. Nucleic Acids Res 2022; 50:11455-11469. [PMID: 36416268 PMCID: PMC9723503 DOI: 10.1093/nar/gkac1081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 10/19/2022] [Accepted: 10/26/2022] [Indexed: 11/24/2022] Open
Abstract
We present a systematic structural and energetic characterization of phosphate(OP)-nucleobase anion…π stacking interactions in RNAs. We observed OP-nucleobase stacking contacts in a variety of structural motifs other than regular helices and spanning broadly diverse sequence distances. Apart from the stacking between a phosphate and a guanine or a uracil two-residue upstream in specific U-turns, such interactions in RNA have been scarcely characterized to date. Our QM calculations showed an energy minimum at a distance between the OP atom and the nucleobase plane centroid slightly below 3 Å for all the nucleobases. By sliding the OP atom over the nucleobase plane we localized the optimal mutual positioning of the stacked moieties, corresponding to an energy minimum below -6 kcal•mol-1, for all the nucleobases, consistently with the projections of the OP atoms over the different π-rings we observed in experimental occurrences. We also found that the strength of the interaction clearly correlates with its electrostatic component, pointing to it as the most relevant contribution. Finally, as OP-uracil and OP-guanine interactions represent together 86% of the instances we detected, we also proved their stability under dynamic conditions in model systems simulated by state-of-the art DFT-MD calculations.
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Affiliation(s)
- Mohit Chawla
- Correspondence may also be addressed to Mohit Chawla. ;
| | - Kanav Kalra
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad 121002, Haryana, India
| | - Zhen Cao
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
| | - Luigi Cavallo
- Correspondence may also be addressed to Luigi Cavallo. Tel: +966 02 8027566; Fax: +966 02 8021347;
| | - Romina Oliva
- To whom correspondence should be addressed. Tel: +39 081 5476541; Fax: +39 081 5476514;
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5
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Zirbel CL, Auffinger P. Lone Pair…π Contacts and Structure Signatures of r(UNCG) Tetraloops, Z-Turns, and Z-Steps: A WebFR3D Survey. Molecules 2022; 27:molecules27144365. [PMID: 35889236 PMCID: PMC9323530 DOI: 10.3390/molecules27144365] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 06/29/2022] [Accepted: 07/04/2022] [Indexed: 02/04/2023] Open
Abstract
Z-DNA and Z-RNA have long appeared as oddities to nucleic acid scientists. However, their Z-step constituents are recurrently observed in all types of nucleic acid systems including ribosomes. Z-steps are NpN steps that are isostructural to Z-DNA CpG steps. Among their structural features, Z-steps are characterized by the presence of a lone pair…π contact that involves the stacking of the ribose O4′ atom of the first nucleotide with the 3′-face of the second nucleotide. Recently, it has been documented that the CpG step of the ubiquitous r(UNCG) tetraloops is a Z-step. Accordingly, such r(UNCG) conformations were called Z-turns. It has also been recognized that an r(GAAA) tetraloop in appropriate conditions can shapeshift to an unusual Z-turn conformation embedding an ApA Z-step. In this report, we explore the multiplicity of RNA motifs based on Z-steps by using the WebFR3D tool to which we added functionalities to be able to retrieve motifs containing lone pair…π contacts. Many examples that underscore the diversity and universality of these motifs are provided as well as tutorial guidance on using WebFR3D. In addition, this study provides an extensive survey of crystallographic, cryo-EM, NMR, and molecular dynamics studies on r(UNCG) tetraloops with a critical view on how to conduct database searches and exploit their results.
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Affiliation(s)
- Craig L. Zirbel
- Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, OH 43403, USA;
| | - Pascal Auffinger
- Architecture et Réactivité de l’ARN, UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, 67084 Strasbourg, France
- Correspondence: ; Tel.: +33-3-8841-7049; Fax: +33-3-8860-2218
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6
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Zhang Z, Vögele J, Mráziková K, Kruse H, Cang X, Wöhnert J, Krepl M, Šponer J. Phosphorothioate Substitutions in RNA Structure Studied by Molecular Dynamics Simulations, QM/MM Calculations, and NMR Experiments. J Phys Chem B 2021; 125:825-840. [PMID: 33467852 DOI: 10.1021/acs.jpcb.0c10192] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Phosphorothioates (PTs) are important chemical modifications of the RNA backbone where a single nonbridging oxygen of the phosphate is replaced with a sulfur atom. PT can stabilize RNAs by protecting them from hydrolysis and is commonly used as a tool to explore their function. It is, however, unclear what basic physical effects PT has on RNA stability and electronic structure. Here, we present molecular dynamics (MD) simulations, quantum mechanical (QM) calculations, and NMR spectroscopy measurements, exploring the effects of PT modifications in the structural context of the neomycin-sensing riboswitch (NSR). The NSR is the smallest biologically functional riboswitch with a well-defined structure stabilized by a U-turn motif. Three of the signature interactions of the U-turn: an H-bond, an anion-π interaction, and a potassium binding site; are formed by RNA phosphates, making the NSR an ideal model for studying how PT affects RNA structure and dynamics. By comparing with high-level QM calculations, we reveal the distinct physical properties of the individual interactions facilitated by the PT. The sulfur substitution, besides weakening the direct H-bond interaction, reduces the directionality of H-bonding while increasing its dispersion and induction components. It also reduces the induction and increases the dispersion component of the anion-π stacking. The sulfur force-field parameters commonly employed in the literature do not reflect these distinctions, leading to the unsatisfactory description of PT in simulations of the NSR. We show that it is not possible to accurately describe the PT interactions using one universal set of van der Waals sulfur parameters and provide suggestions for improving the force-field performance.
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Affiliation(s)
- Zhengyue Zhang
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.,Faculty of Science, Masaryk University, Kotlarska 2, 602 00 Brno, Czech Republic
| | - Jennifer Vögele
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
| | - Klaudia Mráziková
- Faculty of Science, Masaryk University, Kotlarska 2, 602 00 Brno, Czech Republic.,Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Holger Kruse
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Xiaohui Cang
- Institute of Genetics, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jens Wöhnert
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Jiří Šponer
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.,Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
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7
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Auffinger P, Ennifar E, D'Ascenzo L. Deflating the RNA Mg 2+ bubble. Stereochemistry to the rescue! RNA (NEW YORK, N.Y.) 2020; 27:rna.076067.120. [PMID: 33268500 PMCID: PMC7901845 DOI: 10.1261/rna.076067.120] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 11/20/2020] [Indexed: 05/03/2023]
Abstract
Proper evaluation of the ionic structure of biomolecular systems through X ray and cryo-EM techniques remains challenging but is essential for advancing our understanding of the underlying structure/activity/solvent relationships. However, numerous studies overestimate the number of Mg2+ in deposited structures due to assignment errors finding their origin in improper consideration of stereochemical rules. Herein, to tackle such issues, we re-evaluate the PDBid 6QNR and 6SJ6 models of the ribosome ionic structure. We establish that stereochemical principles need to be carefully pondered when evaluating ion binding features, even when K+ anomalous signals are available as it is the case for the 6QNR PDB entry. For ribosomes, assignment errors can result in misleading conceptions of their solvent structure. For instance, present stereochemical analysis result in a significant decrease of the number of assigned Mg2+ in 6QNR, suggesting that K+ and not Mg2+ is the prevalent ion in the ribosome 1st solvation shell. We stress that the use of proper stereochemical guidelines in combination or not with other identification techniques, such as those pertaining to the detection of transition metals, of some anions and of K+ anomalous signals, is critical for deflating the current Mg2+ bubble witnessed in many ribosome and other RNA structures. We also stress that for the identification of lighter ions such as Mg2+, Na+, …, for which no anomalous signals can be detected, stereochemistry coupled with high resolution structures (<2.4 Å) remain the best currently available option.
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Kruse H, Mrazikova K, D'Ascenzo L, Sponer J, Auffinger P. Short but Weak: The Z‐DNA Lone‐Pair⋅⋅⋅π Conundrum Challenges Standard Carbon Van der Waals Radii. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004201] [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)
- Holger Kruse
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61265 Brno Czech Republic
| | - Klaudia Mrazikova
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61265 Brno Czech Republic
- National Centre for Biomolecular ResearchFaculty of ScienceMasaryk University Kamenice 5 62500 Brno Czech Republic
| | - Luigi D'Ascenzo
- Department of Integrative Structural and Computational BiologyThe Scripps Research Institute La Jolla CA 92037 USA
| | - Jiri Sponer
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61265 Brno Czech Republic
- Regional Centre of Advanced Technologies and MaterialsFaculty of SciencePalacký University Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Pascal Auffinger
- Université de StrasbourgCNRS, Architecture et Réactivité de l'ARN, UPR9002 F-67000 Strasbourg France
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9
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Kruse H, Mrazikova K, D'Ascenzo L, Sponer J, Auffinger P. Short but Weak: The Z‐DNA Lone‐Pair⋅⋅⋅π Conundrum Challenges Standard Carbon Van der Waals Radii. Angew Chem Int Ed Engl 2020; 59:16553-16560. [DOI: 10.1002/anie.202004201] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Indexed: 12/31/2022]
Affiliation(s)
- Holger Kruse
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61265 Brno Czech Republic
| | - Klaudia Mrazikova
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61265 Brno Czech Republic
- National Centre for Biomolecular Research Faculty of Science Masaryk University Kamenice 5 62500 Brno Czech Republic
| | - Luigi D'Ascenzo
- Department of Integrative Structural and Computational Biology The Scripps Research Institute La Jolla CA 92037 USA
| | - Jiri Sponer
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61265 Brno Czech Republic
- Regional Centre of Advanced Technologies and Materials Faculty of Science Palacký University Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Pascal Auffinger
- Université de Strasbourg CNRS, Architecture et Réactivité de l'ARN, UPR9002 F-67000 Strasbourg France
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10
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Kruse H, Šponer J. Revisiting the Potential Energy Surface of the Stacked Cytosine Dimer: FNO-CCSD(T) Interaction Energies, SAPT Decompositions, and Benchmarking. J Phys Chem A 2019; 123:9209-9222. [PMID: 31560201 DOI: 10.1021/acs.jpca.9b05940] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nucleobase stacking interactions are crucial for the stability of nucleic acids. This study investigates base stacking energies of the cytosine homodimer in different configurations, including intermolecular separation plots, detailed twist dependence, and displaced structures. Highly accurate ab initio quantum chemical single point energies using an energy function based on MP2 complete basis set extrapolation ([6 → 7]ZaPa-NR) and a CCSD(T)/cc-pVTZ-F12 high-level correction are presented as new reference data, providing the most accurate stacking energies of nucleobase dimers currently available. Accurate SAPT2+(3)δMP2 energy decomposition is used to obtain detailed insights into the nature of base stacking interactions at varying vertical distances and twist values. The ab initio symmetry adapted perturbation theory (SAPT) energy decomposition suggests that the base stacking originates from an intricate interplay between dispersion attraction, short-range exchange-repulsion, and Coulomb interaction. The interpretation of the SAPT data is a complex issue as key energy terms vary substantially in the region of optimal (low energy) base stacking geometries. Thus, attempts to highlight one leading stabilizing SAPT base stacking term may be misleading and the outcome strongly depends on the used geometries within the range of geometries sampled in nucleic acids upon thermal fluctuations. Modern dispersion-corrected density functional theory (among them DSD-BLYP-D3, ωB97M-V, and ωB97M-D3BJ) is benchmarked and often reaches up to spectroscopic accuracy (below 1 kJ/mol). The classical AMBER force field is benchmarked with multiple different sets of point-charges (e.g. HF, DFT, and MP2-based) and is found to produce reasonable agreement with the benchmark data.
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Affiliation(s)
- Holger Kruse
- Institute of Biophysics of the Czech Academy of Sciences , Královopolská 135 , CZ-61265 Brno , Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences , Královopolská 135 , CZ-61265 Brno , Czech Republic.,Central European Institute of Technology , Masaryk University , Kamenice 753/5 , 62500 Brno , Czech Republic
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11
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Qi HW, Kulik HJ. Reply to "Comment on 'Evaluating Unexpectedly Short Non-covalent Distances in X-ray Crystal Structures of Proteins with Electronic Structure Analysis'". J Chem Inf Model 2019; 59:3609-3610. [PMID: 31424928 DOI: 10.1021/acs.jcim.9b00606] [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]
Affiliation(s)
- Helena W Qi
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States.,Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Heather J Kulik
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
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