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Sarkar A, Roitberg AE. pH-Dependent Conformational Changes Lead to a Highly Shifted p Ka for a Buried Glutamic Acid Mutant of SNase. J Phys Chem B 2020; 124:11072-11080. [PMID: 33259714 DOI: 10.1021/acs.jpcb.0c07136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ionizable residues are rarely present in the hydrophobic interior of proteins, but when they are, they play important roles in biological processes such as energy transduction and enzyme catalysis. Internal ionizable residues have anomalous experimental pKa values with respect to their pKa in bulk water. This work investigates the atomistic cause of the highly shifted pKa of the internal Glu23 in the artificially mutated variant V23E of Staphylococcal Nuclease (SNase) using pH replica exchange molecular dynamics (pH-REMD) simulations. The pKa of Glu23 obtained from our calculations is 6.55, which is elevated with respect to the glutamate pKa of 4.40 in bulk water. The calculated value is close to the experimental pKa of 7.10. Our simulations show that the highly shifted pKa of Glu23 is the product of a pH-dependent conformational change, which has been observed experimentally and also seen in our simulations. We carry out an analysis of this pH-dependent conformational change in response to the protonation state change of Glu23. Using a four-state thermodynamic model, we estimate the two conformation-specific pKa values of Glu23 and describe the coupling between the conformational and ionization equilibria.
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Affiliation(s)
- Ankita Sarkar
- Department of Physics, University of Florida, Gainesville, Florida 32611, United States
| | - Adrian E Roitberg
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
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Liu J, Swails J, Zhang JZH, He X, Roitberg AE. A Coupled Ionization-Conformational Equilibrium Is Required To Understand the Properties of Ionizable Residues in the Hydrophobic Interior of Staphylococcal Nuclease. J Am Chem Soc 2018; 140:1639-1648. [PMID: 29308643 DOI: 10.1021/jacs.7b08569] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Ionizable residues in the interior of proteins play essential roles, especially in biological energy transduction, but are relatively rare and seem incompatible with the complex and polar environment. We perform a comprehensive study of the internal ionizable residues on 21 variants of staphylococcal nuclease with internal Lys, Glu, or Asp residues. Using pH replica exchange molecular dynamics simulations, we find that, in most cases, the pKa values of these internal ionizable residues are shifted significantly from their values in solution. Our calculated results are in excellent agreement with the experimental observations of the Garcia-Moreno group. We show that the interpretation of the experimental pKa values requires the study of not only protonation changes but also conformational changes. The coupling between the protonation and conformational equilibria suggests a mechanism for efficient pH-sensing and regulation in proteins. This study provides new physical insights into how internal ionizable residues behave in the hydrophobic interior of proteins.
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Affiliation(s)
- Jinfeng Liu
- School of Chemistry and Molecular Engineering, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, East China Normal University , Shanghai, 200062, China.,Department of Chemistry, University of Florida , Gainesville, Florida 32611, United States.,Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University , Nanjing, 210009, China
| | - Jason Swails
- Department of Chemistry and Chemical Biology and BioMaPS Institute, Rutgers University , Piscataway, New Jersey 08854, United States
| | - John Z H Zhang
- School of Chemistry and Molecular Engineering, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, East China Normal University , Shanghai, 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai, 200062, China
| | - Xiao He
- School of Chemistry and Molecular Engineering, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, East China Normal University , Shanghai, 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai, 200062, China
| | - Adrian E Roitberg
- Department of Chemistry, University of Florida , Gainesville, Florida 32611, United States
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Wu X, Lee J, Brooks BR. Origin of pK a Shifts of Internal Lysine Residues in SNase Studied Via Equal-Molar VMMS Simulations in Explicit Water. J Phys Chem B 2016; 121:3318-3330. [PMID: 27700118 DOI: 10.1021/acs.jpcb.6b08249] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein internal ionizable groups can exhibit large shifts in pKa values. Although the environment and interaction changes have been extensively studied both experimentally and computationally, direct calculation of pKa values of these internal ionizable groups in explicit water is challenging due to energy barriers in solvent interaction and in conformational transition. The virtual mixture of multiple states (VMMS) method is a new approach designed to study chemical state equilibrium. This method constructs a virtual mixture of multiple chemical states in order to sample the conformational space of all states simultaneously and to avoid crossing energy barriers related to state transition. By applying VMMS to 25 variants of staphylococcal nuclease with lysine residues at internal positions, we obtained the pKa values of these lysine residues and investigated the physics underlining the pKa shifts. Our calculation results agree reasonably well with experimental measurements, validating the VMMS method for pKa calculation and providing molecular details of the protonation equilibrium for protein internal ionizable groups. Based on our analyses of protein conformation relaxation, lysine side chain flexibility, water penetration, and the microenvironment, we conclude that the hydrophobicity of the microenvironment around the lysine side chain (which affects water penetration differently for different protonation states) plays an important role in the pKa shifts.
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Affiliation(s)
- Xiongwu Wu
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH) , Bethesda, Maryland 20892, United States
| | - Juyong Lee
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH) , Bethesda, Maryland 20892, United States
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH) , Bethesda, Maryland 20892, United States
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Who cares for the protons? Bioorg Med Chem 2012; 20:5453-60. [PMID: 22464682 DOI: 10.1016/j.bmc.2012.03.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 02/29/2012] [Accepted: 03/02/2012] [Indexed: 11/20/2022]
Abstract
It is tempting to use standard protonation states for the analysis of protein-ligand interactions. Two different pK(a) calculation methods, PROPKA (protein pK(a)) and MCCE (multi conformation continuum electrostatics), were applied to challenge this convenient behavior. As data basis, we selected five recently approved drugs for which structural information of the protein-drug complex is available. We analyzed the pK(a) calculations in terms of a measure termed BIPS (binary protonation states) recently introduced by us. Both methods agree in detecting the majority of the sites with atypical BIPS values. However, when using only one method, some of the atypcial BIPS value would have been missed. Therefore, we recommend using both methods to set such an interpretation on a solid basis.
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Nielsen JE, Gunner MR, Bertrand García-Moreno E. The pKa Cooperative: a collaborative effort to advance structure-based calculations of pKa values and electrostatic effects in proteins. Proteins 2011; 79:3249-59. [PMID: 22002877 PMCID: PMC3375608 DOI: 10.1002/prot.23194] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 09/13/2011] [Indexed: 12/13/2022]
Abstract
The pK(a) Cooperative (http://www.pkacoop.org) was organized to advance development of accurate and useful computational methods for structure-based calculation of pK(a) values and electrostatic energies in proteins. The Cooperative brings together laboratories with expertise and interest in theoretical, computational, and experimental studies of protein electrostatics. To improve structure-based energy calculations, it is necessary to better understand the physical character and molecular determinants of electrostatic effects. Thus, the Cooperative intends to foment experimental research into fundamental aspects of proteins that depend on electrostatic interactions. It will maintain a depository for experimental data useful for critical assessment of methods for structure-based electrostatics calculations. To help guide the development of computational methods, the Cooperative will organize blind prediction exercises. As a first step, computational laboratories were invited to reproduce an unpublished set of experimental pK(a) values of acidic and basic residues introduced in the interior of staphylococcal nuclease by site-directed mutagenesis. The pK(a) values of these groups are unique and challenging to simulate owing to the large magnitude of their shifts relative to normal pK(a) values in water. Many computational methods were tested in this first Blind Prediction Challenge and critical assessment exercise. A workshop was organized in the Telluride Science Research Center to objectively assess the performance of many computational methods tested on this one extensive data set. This volume of Proteins: Structure, Function, and Bioinformatics introduces the pK(a) Cooperative, presents reports submitted by participants in the Blind Prediction Challenge, and highlights some of the problems in structure-based calculations identified during this exercise.
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Affiliation(s)
- Jens E. Nielsen
- School of Biomolecular and Biomedical Science, Centre for Synthesis and Chemical Biology, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - M. R. Gunner
- Department of Physics, City College of New York, New York, NY 10031
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