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Pandey RB, Farmer BL. Conformation of a coarse-grained protein chain (an aspartic acid protease) model in effective solvent by a bond-fluctuating Monte Carlo simulation. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2008; 77:031902. [PMID: 18517417 DOI: 10.1103/physreve.77.031902] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2007] [Indexed: 05/26/2023]
Abstract
In a coarse-grained description of a protein chain, all of the 20 amino acid residues can be broadly divided into three groups: Hydrophobic (H) , polar (P) , and electrostatic (E) . A protein can be described by nodes tethered in a chain with a node representing an amino acid group. Aspartic acid protease consists of 99 residues in a well-defined sequence of H , P , and E nodes tethered together by fluctuating bonds. The protein chain is placed on a cubic lattice where empty lattice sites constitute an effective solvent medium. The amino groups (nodes) interact with the solvent (S) sites with appropriate attractive (PS) and repulsive (HS) interactions with the solvent and execute their stochastic movement with the Metropolis algorithm. Variations of the root mean square displacements of the center of mass and that of its center node of the protease chain and its gyration radius with the time steps are examined for different solvent strength. The structure of the protease swells on increasing the solvent interaction strength which tends to enhance the relaxation time to reach the diffusive behavior of the chain. Equilibrium radius of gyration increases linearly on increasing the solvent strength: A slow rate of increase in weak solvent regime is followed by a faster swelling in stronger solvent. Variation of the gyration radius with the time steps suggests that the protein chain moves via contraction and expansion in a somewhat quasiperiodic pattern particularly in strong solvent.
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Affiliation(s)
- R B Pandey
- Department of Physics and Astronomy, University of Southern Mississippi, Hattiesburg, Mississippi 39406-5046, USA
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52
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Hu H, Yang W. Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods. Annu Rev Phys Chem 2008; 59:573-601. [PMID: 18393679 PMCID: PMC3727228 DOI: 10.1146/annurev.physchem.59.032607.093618] [Citation(s) in RCA: 349] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Combined quantum mechanics/molecular mechanics (QM/MM) methods provide an accurate and efficient energetic description of complex chemical and biological systems, leading to significant advances in the understanding of chemical reactions in solution and in enzymes. Here we review progress in QM/MM methodology and applications, focusing on ab initio QM-based approaches. Ab initio QM/MM methods capitalize on the accuracy and reliability of the associated quantum-mechanical approaches, however, at a much higher computational cost compared with semiempirical quantum-mechanical approaches. Thus reaction-path and activation free-energy calculations based on ab initio QM/MM methods encounter unique challenges in simulation timescales and phase-space sampling. This review features recent developments overcoming these challenges and enabling accurate free-energy determination for reaction processes in solution and in enzymes, along with applications.
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Affiliation(s)
- Hao Hu
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA.
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53
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Neri M, Baaden M, Carnevale V, Anselmi C, Maritan A, Carloni P. Microseconds dynamics simulations of the outer-membrane protease T. Biophys J 2008; 94:71-8. [PMID: 17827219 PMCID: PMC2134885 DOI: 10.1529/biophysj.107.116301] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2007] [Accepted: 08/24/2007] [Indexed: 11/18/2022] Open
Abstract
Conformational fluctuations of enzymes may play an important role for substrate recognition and/or catalysis, as it has been suggested in the case of the protease enzymatic superfamily. Unfortunately, theoretically addressing this issue is a problem of formidable complexity, as the number of the involved degrees of freedom is enormous: indeed, the biological function of a protein depends, in principle, on all its atoms and on the surrounding water molecules. Here we investigated a membrane protease enzyme, the OmpT from Escherichia coli, by a hybrid molecular mechanics/coarse-grained approach, in which the active site is treated with the GROMOS force field, whereas the protein scaffold is described with a Go-model. The method has been previously tested against results obtained with all-atom simulations. Our results show that the large-scale motions and fluctuations of the electric field in the microsecond timescale may impact on the biological function and suggest that OmpT employs the same catalytic strategy as aspartic proteases. Such a conclusion cannot be drawn within the 10- to 100-ns timescale typical of current molecular dynamics simulations. In addition, our studies provide a structural explanation for the drop in the catalytic activity of two known mutants (S99A and H212A), suggesting that the coarse-grained approach is a fast and reliable tool for providing structure/function relationships for both wild-type OmpT and mutants.
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Affiliation(s)
- Marilisa Neri
- International School for Advanced Studies and CNR National Institute for the Physics of Matter, National Simulation Center, Trieste, Italy
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54
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Dechancie J, Clemente FR, Smith AJT, Gunaydin H, Zhao YL, Zhang X, Houk KN. How similar are enzyme active site geometries derived from quantum mechanical theozymes to crystal structures of enzyme-inhibitor complexes? Implications for enzyme design. Protein Sci 2007; 16:1851-66. [PMID: 17766382 PMCID: PMC2206971 DOI: 10.1110/ps.072963707] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Quantum mechanical optimizations of theoretical enzymes (theozymes), which are predicted catalytic arrays of biological functionalities stabilizing a transition state, have been carried out for a set of nine diverse enzyme active sites. For each enzyme, the theozyme for the rate-determining transition state plus the catalytic groups modeled by side-chain mimics was optimized using B3LYP/6-31G(d) or, in one case, HF/3-21G(d) quantum mechanical calculations. To determine if the theozyme can reproduce the natural evolutionary catalytic geometry, the positions of optimized catalytic atoms, i.e., covalent, partial covalent, or stabilizing interactions with transition state atoms, are compared to the positions of the atoms in the X-ray crystal structure with a bound inhibitor. These structure comparisons are contrasted to computed substrate-active site structures surrounded by the same theozyme residues. The theozyme/transition structure is shown to predict geometries of active sites with an average RMSD of 0.64 A from the crystal structure, while the RMSD for the bound intermediate complexes are significantly higher at 1.42 A. The implications for computational enzyme design are discussed.
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Affiliation(s)
- Jason Dechancie
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, USA
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55
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Carnevale V, Raugei S, Micheletti C, Carloni P. Large-Scale Motions and Electrostatic Properties of Furin and HIV-1 Protease. J Phys Chem A 2007; 111:12327-32. [DOI: 10.1021/jp0751716] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- V. Carnevale
- International School for Advanced Studies and CNR-INFM Democritos, Via Beirut 2-4, I-34014 Trieste, Italy
| | - S. Raugei
- International School for Advanced Studies and CNR-INFM Democritos, Via Beirut 2-4, I-34014 Trieste, Italy
| | - C. Micheletti
- International School for Advanced Studies and CNR-INFM Democritos, Via Beirut 2-4, I-34014 Trieste, Italy
| | - P. Carloni
- International School for Advanced Studies and CNR-INFM Democritos, Via Beirut 2-4, I-34014 Trieste, Italy
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56
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Capozzi F, Luchinat C, Micheletti C, Pontiggia F. Essential Dynamics of Helices Provide a Functional Classification of EF-Hand Proteins. J Proteome Res 2007; 6:4245-55. [DOI: 10.1021/pr070314m] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Francesco Capozzi
- Department of Food Science, University of Bologna, Piazza Goidanich, 60, 47023 Cesena, Italy, Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi, 6, 50019 Sesto Fiorentino, Italy, Department of Agricultural Biotechnology, Via F. Maragliano, 75-77, 50144 Florence, Italy, and International School for Advanced Studies (SISSA), INFM-Democritos and Italian Institute of Technology, Via Beirut 2-4, 34014 Trieste, Italy
| | - Claudio Luchinat
- Department of Food Science, University of Bologna, Piazza Goidanich, 60, 47023 Cesena, Italy, Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi, 6, 50019 Sesto Fiorentino, Italy, Department of Agricultural Biotechnology, Via F. Maragliano, 75-77, 50144 Florence, Italy, and International School for Advanced Studies (SISSA), INFM-Democritos and Italian Institute of Technology, Via Beirut 2-4, 34014 Trieste, Italy
| | - Cristian Micheletti
- Department of Food Science, University of Bologna, Piazza Goidanich, 60, 47023 Cesena, Italy, Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi, 6, 50019 Sesto Fiorentino, Italy, Department of Agricultural Biotechnology, Via F. Maragliano, 75-77, 50144 Florence, Italy, and International School for Advanced Studies (SISSA), INFM-Democritos and Italian Institute of Technology, Via Beirut 2-4, 34014 Trieste, Italy
| | - Francesco Pontiggia
- Department of Food Science, University of Bologna, Piazza Goidanich, 60, 47023 Cesena, Italy, Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi, 6, 50019 Sesto Fiorentino, Italy, Department of Agricultural Biotechnology, Via F. Maragliano, 75-77, 50144 Florence, Italy, and International School for Advanced Studies (SISSA), INFM-Democritos and Italian Institute of Technology, Via Beirut 2-4, 34014 Trieste, Italy
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57
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Dal Peraro M, Ruggerone P, Raugei S, Gervasio FL, Carloni P. Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations. Curr Opin Struct Biol 2007; 17:149-56. [PMID: 17419051 DOI: 10.1016/j.sbi.2007.03.018] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2006] [Revised: 01/11/2007] [Accepted: 03/20/2007] [Indexed: 11/25/2022]
Abstract
Density functional theory (DFT)-based Car-Parrinello molecular dynamics (CPMD) simulations describe the time evolution of molecular systems without resorting to a predefined potential energy surface. CPMD and hybrid molecular mechanics/CPMD schemes have recently enabled the calculation of redox properties of electron transfer proteins in their complex biological environment. They provided structural and spectroscopic information on novel platinum-based anticancer drugs that target DNA, also setting the basis for the construction of force fields for the metal lesion. Molecular mechanics/CPMD also lead to mechanistic hypotheses for a variety of metalloenzymes. Recent advances that increase the accuracy of DFT and the efficiency of investigating rare events are further expanding the domain of CPMD applications to biomolecules.
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Affiliation(s)
- Matteo Dal Peraro
- Center for Molecular Modeling, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
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58
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Understanding the structure–function role of specific catalytic residues in a model food related enzyme: Pepsin. Enzyme Microb Technol 2007. [DOI: 10.1016/j.enzmictec.2006.08.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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59
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Cavalli A, Carloni P, Recanatini M. Target-Related Applications of First Principles Quantum Chemical Methods in Drug Design. Chem Rev 2006; 106:3497-519. [PMID: 16967914 DOI: 10.1021/cr050579p] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Andrea Cavalli
- Department of Pharmaceutical Sciences, University of Bologna, Via Belmeloro 6, I-40126 Bologna, Italy
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60
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Carnevale V, Raugei S, Micheletti C, Carloni P. Convergent Dynamics in the Protease Enzymatic Superfamily. J Am Chem Soc 2006; 128:9766-72. [PMID: 16866533 DOI: 10.1021/ja060896t] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proteases regulate various aspects of the life cycle in all organisms by cleaving specific peptide bonds. Their action is so central for biochemical processes that at least 2% of any known genome encodes for proteolytic enzymes. Here we show that selected proteases pairs, despite differences in oligomeric state, catalytic residues, and fold, share a common structural organization of functionally relevant regions which are further shown to undergo similar concerted movements. The structural and dynamical similarities found pervasively across evolutionarily distant clans point to common mechanisms for peptide hydrolysis.
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Affiliation(s)
- Vincenzo Carnevale
- International School for Advanced Studies (SISSA) and INFM Democritos, Via Beirut 2-4, I-34014 Trieste, Italy
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61
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Bjelic S, Aqvist J. Catalysis and Linear Free Energy Relationships in Aspartic Proteases. Biochemistry 2006; 45:7709-23. [PMID: 16784222 DOI: 10.1021/bi060131y] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aspartic proteases are receiving considerable attention as potential drug targets in several serious diseases, such as AIDS, malaria, and Alzheimer's disease. These enzymes cleave polypeptide chains, often between specific amino acid residues, but despite the common reaction mechanism, they exhibit large structural differences. Here, the catalytic mechanism of aspartic proteases plasmepsin II, cathepsin D, and HIV-1 protease is examined by computer simulations utilizing the empirical valence bond approach in combination with molecular dynamics and free energy perturbation calculations. Free energy profiles are established for four different substrates, each six amino acids long and containing hydrophobic side chains in the P1 and P1' positions. Our simulations reproduce the catalytic effect of these enzymes, which accelerate the reaction rate by a factor of approximately 10(10) compared to that of the corresponding uncatalyzed reaction in water. The calculations elucidate the origin of the catalytic effect and allow a rationalization of the fact that, despite large structural differences between plasmepsin II/cathepsin D and HIV-1 protease, the magnitude of their rate enhancement is very similar. Amino acid residues surrounding the active site together with structurally conserved water molecules are found to play an important role in catalysis, mainly through dipolar (electrostatic) stabilization. A linear free energy relationship for the reactions in the different enzymes is established that also demonstrates the reduced reorganization energy in the enzymes compared to that in the uncatalyzed water reaction.
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Affiliation(s)
- Sinisa Bjelic
- Department of Cell and Molecular Biology, Uppsala University Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
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62
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Andreeva NS, Gurskaya GV. Interdomain interactions in aspartic proteases of higher organisms and their analogs in retroviral enzymes. Mol Biol 2006. [DOI: 10.1134/s0026893306030095] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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63
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Spiegel K, Magistrato A. Modeling anticancer drug–DNA interactions via mixed QM/MM molecular dynamics simulations. Org Biomol Chem 2006; 4:2507-17. [PMID: 16791311 DOI: 10.1039/b604263p] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The development of anticancer drugs started over four decades ago, with the serendipitous discovery of the antitumor activity of cisplatin and its successful use in the treatment of various cancer types. Despite the efforts made in unraveling the mechanism of the action of cisplatin, as well as in the rational design of new anticancer compounds, in many cases detailed structural and mechanistic information is still lacking. Many of these drugs exert their anticancer activity by covalently binding to DNA inducing a distortion or simply impeding replication, thus triggering a cellular response, which eventually leads to cell death. A detailed understanding of the structural and electronic properties of drug-DNA complexes and their mechanism of binding is the key step in elucidating the principles of their anticancer activity. At the theoretical level, the description of covalent drug-DNA complexes requires the use of state-of-the-art computer simulation techniques such as hybrid quantum/classical molecular dynamics simulations. In this review we provide a general overview on: drugs which covalently bind to DNA duplexes, the basic concepts of quantum mechanics/molecular mechanics (QM/MM), molecular dynamics methods and a list of selected applications of these simulations to the study of drug-DNA adducts. Finally, the potential and the limitations of this approach to the study of such systems are critically evaluated.
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Affiliation(s)
- Katrin Spiegel
- University of Pennsylvania, Department of Chemistry, Philadelphia, PA, USA
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64
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Vidossich P, Carloni P. Binding of Phosphinate and Phosphonate Inhibitors to Aspartic Proteases: A First-Principles Study. J Phys Chem B 2005; 110:1437-42. [PMID: 16471695 DOI: 10.1021/jp0544639] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phosphinate and phosphonate derivatives are potent inhibitors of aspartic proteases (APs). The affinity for the enzyme might be caused by the presence of low barrier hydrogen bonds between the ligand and the catalytic Asp dyad in the cleavage site. We have used density functional theory calculations along with hybrid quantum mechanics/molecular mechanics Car-Parrinello molecular dynamics simulations to investigate the hydrogen-bonding pattern at the binding site of the complexes of human immunodeficiency virus type-1 AP and the eukaryotic endothiapepsin and penicillopepsin. Our calculations are in fair agreement with the NMR data available for endothiapepsin (Coates et al. J. Mol. Biol. 2002, 318, 1405-1415) and show that the most stable active site configuration is the diprotonated, negatively charged form. In the viral complex both protons are located at the catalytic Asp dyad, while in the eukaryotic complexes the proton shared by the closest oxygen atoms is located at the phosphinic/phosphonic group.
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Affiliation(s)
- Pietro Vidossich
- International School for Advanced Studies and INFM-Democritos Modeling Center for Research in Atomistic Simulation, via Beirut 2-4 34014 Trieste, Italy
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65
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Neri M, Anselmi C, Cascella M, Maritan A, Carloni P. Coarse-grained model of proteins incorporating atomistic detail of the active site. PHYSICAL REVIEW LETTERS 2005; 95:218102. [PMID: 16384187 DOI: 10.1103/physrevlett.95.218102] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2005] [Indexed: 05/05/2023]
Abstract
We present a novel approach to explore the conformational space of globular proteins near their native state. It combines the advantages of coarse-grained models with those of all-atoms simulations, required to treat molecular recognition processes. The comparison between calculated structural properties with those obtained with all-atoms molecular dynamics simulations establishes the accuracy of the model. Our method has the potential to be extended to molecular recognition processes in systems whose characteristic size and time scale prevent an analysis based on all-atoms molecular dynamics.
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Affiliation(s)
- Marilisa Neri
- SISSA/ISAS and INFM-DEMOCRITOS Modeling Center, Via Beirut 4, I-34014 Trieste, Italy
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66
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Guo H, Wlodawer A, Guo H. A General Acid−Base Mechanism for the Stabilization of a Tetrahedral Adduct in a Serine−Carboxyl Peptidase: A Computational Study. J Am Chem Soc 2005; 127:15662-3. [PMID: 16277482 DOI: 10.1021/ja0520565] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The QM/MM MD and free energy simulations show that serine-carboxyl peptidases (sedolisins) may stabilize the tetrahedral intermediates and tetrahedral adducts primarily through a general acid-base mechanism involving Asp (Asp164 for kumamolisin-As) rather than the oxyanion-hole interactions as in the cases of serine proteases.
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Affiliation(s)
- Haobo Guo
- Department of Biochemistry and Cellular and Molecular Biology and Center of Excellence for Structural Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
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