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Fanfrlík J, Brynda J, Rezác J, Hobza P, Lepsík M. Interpretation of protein/ligand crystal structure using QM/MM calculations: case of HIV-1 protease/metallacarborane complex. J Phys Chem B 2009; 112:15094-102. [PMID: 18975888 DOI: 10.1021/jp803528w] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Deltahedral metallacarborane compounds have recently been discovered as potent, specific, stable, and nontoxic inhibitors of HIV-1 protease (PR), the major target for AIDS therapy. The 2.15 A-resolution X-ray structure has exhibited a nonsymmetrical binding of the parental compound [Co(3+)-(C2B9H11)2](-) (GB-18) into PR dimer and a symmetrical arrangement in the crystal of two PR dimer complexes into a tetramer. In order to explore structural and energetic details of the inhibitor binding, quantum mechanics coupled with molecular mechanics approach was utilized. Realizing the close positioning of anionic inhibitors in the active site cavity, the possibility of an exchange of structural water molecules Wat50 and Wat128 by Na+ counterions was studied. The energy profiles for the rotation of the GB-18 molecules along their longitudinal axes in complex with PR were calculated. The results show that two Na+ counterions are present in the active site cavity and provide energetically favorable and unfavorable positions for carbon atoms within the carborane cages. Eighty-one rotamer combinations of four molecules of GB-18 bound to PR out of 4 x 10(5) are predicted to be highly populated. These results lay ground for further calculations of interaction energies between GB-18 and amino acids of PR active site and will make it possible to interpret computationally the binding of similar metallacarborane molecules to PR as well as to resistant PR variants. Moreover, this computational tool will allow the design of new, more potent metallacarborane-based HIV-1 protease inhibitors.
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202
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Pitonák M, Neogrády P, Cerný J, Grimme S, Hobza P. Scaled MP3 non-covalent interaction energies agree closely with accurate CCSD(T) benchmark data. Chemphyschem 2009; 10:282-9. [PMID: 19115327 DOI: 10.1002/cphc.200800718] [Citation(s) in RCA: 207] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Scaled MP3 interaction energies calculated as a sum of MP2/CBS (complete basis set limit) interaction energies and scaled third-order energy contributions obtained in small or medium size basis sets agree very closely with the estimated CCSD(T)/CBS interaction energies for the 22 H-bonded, dispersion-controlled and mixed non-covalent complexes from the S22 data set. Performance of this so-called MP2.5 (third-order scaling factor of 0.5) method has also been tested for 33 nucleic acid base pairs and two stacked conformers of porphine dimer. In all the test cases, performance of the MP2.5 method was shown to be superior to the scaled spin-component MP2 based methods, e.g. SCS-MP2, SCSN-MP2 and SCS(MI)-MP2. In particular, a very balanced treatment of hydrogen-bonded compared to stacked complexes is achieved with MP2.5. The main advantage of the approach is that it employs only a single empirical parameter and is thus biased by two rigorously defined, asymptotically correct ab-initio methods, MP2 and MP3. The method is proposed as an accurate but computationally feasible alternative to CCSD(T) for the computation of the properties of various kinds of non-covalently bound systems.
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203
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Zelený T, Hobza P, Kabelác M. Microhydration of guanine...cytosine base pairs, a theoretical Study on the role of water in stability, structure and tautomeric equilibrium. Phys Chem Chem Phys 2009; 11:3430-5. [PMID: 19421545 DOI: 10.1039/b819350a] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The potential energy surfaces of guanine...cytosine complexes and microhydrated guanine...cytosine (one and two water molecules) were investigated by the molecular dynamics/quenching method (MD/Q), using the empirical potential Parm94 force field, implemented in the Amber program package. The calculations were conducted for all the possible combinations of the four most stable tautomers of guanine and three of cytosine (covering the canonical forms in both cases). The obtained structures were sorted by their structural motifs into three main groups: planar hydrogen-bonded; stacked; and T-shaped structures. The most stable structures found at the empirical potential energy surfaces were fully reoptimised at the second-order Møller-Plesset perturbation theory as well as using the density functional method with an empirical dispersion term (DFT-D). A combination of the canonical form of guanine and cytosine and canonical cytosine with a guanine tautomer where the hydrogen is switched from position N9 to N7 are energetically preferred in microsolvated systems as well as those without the presence of a solvent. The rising number of water molecules leads to smaller differences between the stability of the various combinations of the tautomers of bases in the base pairs. For some of the tautomer combinations (mainly the enol-enol combination), two water molecules are sufficient for the preference of stacked structures over the H-bonded ones. The interaction energies and geometries obtained by the second-order Møller-Plesset perturbation theory method and the much less computationally demanding DFT-D method are comparable, except for stacked complexes, where the interaction energies are overestimated on average by 3 kcal mol(-1) at the MP2 level.
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204
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Šponer J, Zgarbová M, Jurečka P, Riley KE, Šponer JE, Hobza P. Reference Quantum Chemical Calculations on RNA Base Pairs Directly Involving the 2′-OH Group of Ribose. J Chem Theory Comput 2009; 5:1166-79. [DOI: 10.1021/ct800547k] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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205
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Berka K, Hobza P, Vondrášek J. Analysis of Energy Stabilization inside the Hydrophobic Core of Rubredoxin. Chemphyschem 2009; 10:543-8. [DOI: 10.1002/cphc.200800401] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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206
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Maity S, Sedlak R, Hobza P, Patwari GN. Infrared–optical double resonance spectroscopic measurements and high level ab initio calculations on a binary complex between phenylacetylene and borane-trimethylamine. Understanding the role of C–H⋯π interactions. Phys Chem Chem Phys 2009; 11:9738-43. [DOI: 10.1039/b911926d] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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207
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Kabeláč M, Hobza P, Špirko V. The structure and vibrational dynamics of the pyrrole dimer. Phys Chem Chem Phys 2009; 11:3885-91. [DOI: 10.1039/b822764k] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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208
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Riley KE, Murray JS, Politzer P, Concha MC, Hobza P. Br···O Complexes as Probes of Factors Affecting Halogen Bonding: Interactions of Bromobenzenes and Bromopyrimidines with Acetone. J Chem Theory Comput 2008; 5:155-63. [PMID: 26609829 DOI: 10.1021/ct8004134] [Citation(s) in RCA: 292] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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209
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Zierkiewicz W, Komorowski L, Michalska D, Cerny J, Hobza P. The Amino Group in Adenine: MP2 and CCSD(T) Complete Basis Set Limit Calculations of the Planarization Barrier and DFT/B3LYP Study of the Anharmonic Frequencies of Adenine. J Phys Chem B 2008; 112:16734-40. [DOI: 10.1021/jp8058118] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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210
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Pluháčková K, Grimme S, Hobza P. On the Importance of Electron Correlation Effects for the Intramolecular Stacking Geometry of a Bis-Thiophene Derivative. J Phys Chem A 2008; 112:12469-74. [DOI: 10.1021/jp8051664] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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211
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Černý J, Kabeláč M, Hobza P. Double-Helical → Ladder Structural Transition in the B-DNA is Induced by a Loss of Dispersion Energy. J Am Chem Soc 2008; 130:16055-9. [DOI: 10.1021/ja805428q] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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212
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Řezáč J, Hobza P. Benzene Dimer: Dynamic Structure and Thermodynamics Derived from On-the-Fly ab initio DFT-D Molecular Dynamic Simulations. J Chem Theory Comput 2008; 4:1835-40. [DOI: 10.1021/ct8002282] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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213
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Biedermannova L, E Riley K, Berka K, Hobza P, Vondrasek J. Another role of proline: stabilization interactions in proteins and protein complexes concerning proline and tryptophane. Phys Chem Chem Phys 2008; 10:6350-9. [PMID: 18972023 DOI: 10.1039/b805087b] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Proline-tryptophan complexes derived from experimental structures are investigated by quantum chemical procedures known to properly describe the London dispersion energy. We study two geometrical arrangements: the "L-shaped", stabilized by an H-bond, and the "stacked-like", where the two residues are in parallel orientation without any H-bond. Interestingly, the interaction energies in both cases are comparable and very large ( approximately 7 kcal mol(-1)). The strength of stabilization in the stacked arrangement is rather surprising considering the fact that only one partner has an aromatic character. The interaction energy decomposition using the SAPT method further demonstrates the very important role of dispersion energy in such arrangement. To elucidate the structural features responsible for this unexpectedly large stabilization we examined the role of the nitrogen heteroatom and the importance of the cyclicity of the proline residue. We show that the electrostatic interaction due to the presence of the dipole, caused by the nitrogen heteroatom, contributes largely to the strength of the interaction. Nevertheless, the cyclic arrangement of proline, which allows for the largest amount of dispersive contact with the aromatic partner, also has a notable-effect. Geometry optimizations carried out for the "stacked-like" complexes show that the arrangements derived from protein structure are close to their gas phase optimum geometry, suggesting that the environment has only a minor effect on the geometry of the interaction. We conclude that the strength of proline non-covalent interactions, combined with this residue's rigidity, might be the explanation for its prominent role in protein stabilization and recognition processes.
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214
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Pitoňák M, Riley KE, Neogrády P, Hobza P. Highly Accurate CCSD(T) and DFT-SAPT Stabilization Energies of H-Bonded and Stacked Structures of the Uracil Dimer. Chemphyschem 2008; 9:1636-44. [DOI: 10.1002/cphc.200800286] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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215
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Bendová-Biedermannová L, Hobza P, Vondrásek J. Identifying stabilizing key residues in proteins using interresidue interaction energy matrix. Proteins 2008; 72:402-13. [PMID: 18214960 DOI: 10.1002/prot.21938] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We are proposing an interresidue interaction energy map (IEM)--a new tool for protein structure analysis and protein bioinformatics. This approach employs the sum of pair-wise interaction energies of a particular residue as a measure of its structural importance. We will show that the IEM can serve as a means for identifying key residues responsible for the stability of a protein. Our method can be compared with the interresidue contact map but has the advantage of weighting the contacts by the stabilization energy content which they bring to the protein structure. For the theoretical adjustment of the proposed method, we chose the Trp-cage mini protein as a model system to compare a spectrum of computational methods ranging from the ab initio MP2 level through the DFT method to empirical force-field methods. The IEM method correctly identifies Tryptophane 6 as the key residue in the Trp-cage. The other residues with the highest stabilizing contributions correspond to the structurally important positions in the protein. We have further tested our method on the Trp2Cage miniprotein--a P12W mutant of the Trp-cage and on two proteins from the rubredoxin family that differ in their thermostability. Our method correctly identified the thermodynamically more stable variants in both cases and therefore can also be used as a tool for the relative measurement of protein stability. Finally, we will point out the important role played by dispersion energy, which contributes significantly to the total stabilization energy and whose role in aromatic pairs is clearly dominant. Surprisingly, the dispersion energy plays an even more important role in the interaction of prolines with aromatic systems.
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216
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Valdes H, Spiwok V, Rezac J, Reha D, Abo-Riziq A, de Vries M, Hobza P. Potential-Energy and Free-Energy Surfaces of Glycyl-Phenylalanyl-Alanine (GFA) Tripeptide: Experiment and Theory. Chemistry 2008; 14:4886-98. [DOI: 10.1002/chem.200800085] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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217
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Wang W, Hobza P. Theoretical study on the complexes of benzene with isoelectronic nitrogen-containing heterocycles. Chemphyschem 2008; 9:1003-9. [PMID: 18389512 PMCID: PMC2970914 DOI: 10.1002/cphc.200700587] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2007] [Revised: 02/29/2008] [Indexed: 11/10/2022]
Abstract
The pi-pi interactions between benzene and the aromatic nitrogen heterocycles pyridine, pyrimidine, 1,3,5-triazine, 1,2,3-triazine, 1,2,4,5-tetrazine, and 1,2,3,4,5-pentazine are systematically investigated. The T-shaped structures of all complexes studied exhibit a contraction of the C--H bond accompanied by a rather large blue shift (40-52 cm(-1)) of its stretching frequency, and they are almost isoenergetic with the corresponding displaced-parallel structures at reliable levels of theory. With increasing number of nitrogen atoms in the heterocycle, the geometries, frequencies, energies, percentage of s character at C, and the electron density in the C--H sigma antibonding orbital of the complexes all increase or decrease systematically. Decomposition analysis of the total binding energy showed that for all the complexes, the dispersion energy is the dominant attractive contribution, and a rather large attraction originating from electrostatic contribution is compensated by its exchange counterpart.
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218
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Vácha R, Cwiklik L, Řezáč J, Hobza P, Jungwirth P, Valsaraj K, Bahr S, Kempter V. Adsorption of Aromatic Hydrocarbons and Ozone at Environmental Aqueous Surfaces. J Phys Chem A 2008; 112:4942-50. [DOI: 10.1021/jp711813p] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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219
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Sponer J, Riley KE, Hobza P. Nature and magnitude of aromatic stacking of nucleic acid bases. Phys Chem Chem Phys 2008; 10:2595-610. [PMID: 18464974 DOI: 10.1039/b719370j] [Citation(s) in RCA: 267] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
This review summarises recent advances in quantum chemical calculations of base-stacking forces in nucleic acids. We explain in detail the very complex relationship between the gas-phase base-stacking energies, as revealed by quantum chemical (QM) calculations, and the highly variable roles of these interactions in nucleic acids. This issue is rarely discussed in quantum chemical and physical chemistry literature. We further extensively discuss methods that are available for base-stacking studies, complexity of comparison of stacking calculations with gas phase experiments, balance of forces in stacked complexes of nucleic acid bases, and the relation between QM and force field descriptions. We also review all recent calculations on base-stacking systems, including details analysis of the B-DNA stacking. Specific attention is paid to the highest accuracy QM calculations, to the decomposition of the interactions, and development of dispersion-balanced DFT methods. Future prospects of computational studies of base stacking are discussed.
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220
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Černý J, Tong X, Hobza P, Müller-Dethlefs K. State of the art theoretical study and comparison to experiment for the phenol⋯argon complex. J Chem Phys 2008; 128:114319. [DOI: 10.1063/1.2838185] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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221
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Wang W, Hobza P. Origin of the X−Hal (Hal = Cl, Br) Bond-Length Change in the Halogen-Bonded Complexes. J Phys Chem A 2008; 112:4114-9. [PMID: 18345653 DOI: 10.1021/jp710992h] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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222
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Riley KE, Hobza P. A DFT−D Investigation of the Mechanisms for Activation of the Wild-Type and S810L Mutated Mineralocorticoid Receptor by Steroid Hormones. J Phys Chem B 2008; 112:3157-63. [DOI: 10.1021/jp076362b] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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223
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Nachtigallová D, Hobza P, Špirko V. Assigning the NH Stretches of the Guanine Tautomers Using Adiabatic Separation: CCSD(T) Benchmark Calculations. J Phys Chem A 2008; 112:1854-6. [DOI: 10.1021/jp711151a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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224
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Vondrásek J, Kubar T, Jenney FE, Adams MWW, Kozísek M, Cerný J, Sklenár V, Hobza P. Dispersion interactions govern the strong thermal stability of a protein. Chemistry 2008; 13:9022-7. [PMID: 17696186 DOI: 10.1002/chem.200700428] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Rubredoxin from the hyperthermophile Pyrococcus furiosus (Pf Rd) is an extremely thermostable protein, which makes it an attractive subject of protein folding and stability studies. A fundamental question arises as to what the reason for such extreme stability is and how it can be elucidated from a complex set of interatomic interactions. We addressed this issue first theoretically through a computational analysis of the hydrophobic core of the protein and its mutants, including the interactions taking place inside the core. Here we show that a single mutation of one of phenylalanine's residues inside the protein's hydrophobic core results in a dramatic decrease in its thermal stability. The calculated unfolding Gibbs energy as well as the stabilization energy differences between a few core residues follows the same trend as the melting temperature of protein variants determined experimentally by microcalorimetry measurements. NMR spectroscopy experiments have shown that the only part of the protein affected by mutation is the reasonably rearranged hydrophobic core. It is hence concluded that stabilization energies, which are dominated by London dispersion, represent the main source of stability of this protein.
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225
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Nachtigallová D, Hobza P, Ritze HH. Electronic splitting in the excited states of DNA base homodimers and -trimers: an evaluation of short-range and Coulombic interactions. Phys Chem Chem Phys 2008; 10:5689-97. [DOI: 10.1039/b806323k] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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