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Chakravorty A, Hussain A, Cervantes LF, Lai TT, Brooks CL. Exploring the Limits of the Generalized CHARMM and AMBER Force Fields through Predictions of Hydration Free Energy of Small Molecules. J Chem Inf Model 2024; 64:4089-4101. [PMID: 38717640 DOI: 10.1021/acs.jcim.4c00126] [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: 05/28/2024]
Abstract
Accurate force field parameters, potential energy functions, and receptor-ligand models are essential for modeling the solvation and binding of drug-like molecules to a receptor. A large and ever-growing chemical space of medicinally relevant scaffolds has also required these factors, especially force field parameters, to be highly transferable. Generalized force fields such as the CHARMM General Force Field (CGenFF) and the generalized AMBER force field (GAFF) have accomplished this feat along with other contemporaneous ones like OPLS. Here, we analyze the limits in the parametrization of drug-like small molecules by CGenFF and GAFF in terms of the various functional groups represented within them. Specifically, we link the presence of specific functional groups to the error in the absolute hydration free energy of over 600 small molecules, predicted by alchemical free energy methods implemented in the CHARMM program. Our investigation reveals that molecules with (i) a nitro group in CGenFF and GAFF are, respectively, over- or undersolubilized in aqueous medium, (ii) amine groups are undersolubilized more so in CGenFF than in GAFF, and (iii) carboxyl groups are more oversolubilized in GAFF than in CGenFF. We present our analyses of the potential factors underlying these trends. We also showcase the use of a machine-learning-based approach combined with the SHapley Additive exPlanations framework to attribute these trends to specific functional groups, which can be easily adopted to explore the limits of other general force fields.
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Affiliation(s)
- Arghya Chakravorty
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Azam Hussain
- Department of Macromolecular Science and Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Luis F Cervantes
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Thanh T Lai
- Biophysics Program, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Charles L Brooks
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Biophysics Program, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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2
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Helmick H, Tonner T, Hauersperger D, Okos M, Kokini JL. Comparison of the specific mechanical energy, specific thermal energy, and functional properties of cold and hot extruded pea protein isolate. Food Res Int 2023; 174:113603. [PMID: 37986466 DOI: 10.1016/j.foodres.2023.113603] [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: 08/09/2023] [Revised: 10/13/2023] [Accepted: 10/14/2023] [Indexed: 11/22/2023]
Abstract
Pea protein is a popular source of plant-based protein, though its application in meat and dairy analog products is still lacking. This is particularly true in the development of products with fatty and creamy textures. Cold denaturation may be a way to induce these types of textures in food since this is a universal phenomenon in protein that occurs due to a weakening of hydrophobic interactions at cold temperatures. This work utilizes a single screw extruder to systematically study the impacts of moisture content (50-65 %) and pH (2,4.5,8) on the outlet temperatures, specific mechanical energy, specific thermal energy, and texture of cold-extruded pea protein. It was found that at pH 2 and moistures of 60 % and greater, the temperature of the product exiting the extruder is <5.5 °C, and also produced 13.7 %-36.5 % more specific thermal energy, indicating the occurrence of cold denaturation in these products. Based on these findings, a comparison of hot and cold extrusion was conducted as a function of pH and oil content. It was found that cold extrusion imparts 43.0 %-56.2 % more mechanical energy into the protein than hot extrusion, and the cold extruded protein had higher values of Young's modulus and breaking stress. The protein extruded at low temperatures was also able to bind 32.93 % more oil than hot extruded proteins when extruded with 10 % added oil, which may aid in the formation of protein-based fat memetics for the food industry.
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Affiliation(s)
- Harrison Helmick
- Department of Food Science, Purdue University, 745 Agriculture Mall Dr, West Lafayette, IN 47907, United States
| | - Troy Tonner
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, IN 47907, United States
| | - Daniel Hauersperger
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, IN 47907, United States
| | - Martin Okos
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, IN 47907, United States
| | - Jozef L Kokini
- Department of Food Science, Purdue University, 745 Agriculture Mall Dr, West Lafayette, IN 47907, United States.
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3
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da Rocha L, Baptista AM, Campos SRR. Computational Study of the pH-Dependent Ionic Environment around β-Lactoglobulin. J Phys Chem B 2022; 126:9123-9136. [PMID: 36321840 PMCID: PMC9776516 DOI: 10.1021/acs.jpcb.2c03797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Ions are involved in multiple biological processes and may exist bound to biomolecules or may be associated with their surface. Although the presence of ions in nucleic acids has traditionally gained more interest, ion-protein interactions, often with a marked dependency on pH, are beginning to gather attention. Here we present a detailed analysis on the binding and distribution of ions around β-lactoglobulin using a constant-pH MD (CpHMD) method, at a pH range 3-8, and compare it with the more traditional Poisson-Boltzmann (PB) model and the existing experimental data. Most analyses used ion concentration maps built around the protein, obtained from either the CpHMD simulations or PB calculations. The requirements of approximate charge neutrality and ionic strength equal to bulk, imposed on the MD box, imply that the absolute value of the ion excess should be half the protein charge, which is in agreement with experimental observation on other proteins ( Proc. Natl. Acad. Sci. U.S.A. 2021, 118, e2015879118) and lends support to this protocol. In addition, the protein total charge (including territorially bound ions) estimated with MD is in excellent agreement with electrophoretic measurements. Overall, the CpHMD simulations show good agreement with the nonlinear form of the PB (NLPB) model but not with its linear form, which involves a theoretical inconsistency in the calculation of the concentration maps. In several analyses, the observed pH-dependent trends for the counterions and co-ions are those generally expected, and the ion concentration maps correctly converge to the bulk ionic strength as one moves away from the protein. Despite the overall similarity, the CpHMD and NLPB approaches show some discrepancies when analyzed in more detail, which may be related to an apparent overestimation of counterion excess and underestimation of co-ion exclusion by the NLPB model, particularly at short distances from the protein.
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4
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Helmick H, Hartanto C, Bhunia A, Liceaga A, Kokini JL. Validation of Bioinformatic Modeling for the Zeta Potential of Vicilin, Legumin, and Commercial Pea Protein Isolate. FOOD BIOPHYS 2021. [DOI: 10.1007/s11483-021-09686-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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5
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Bai X, Wang C, Wang X, Jia T, Sun B, Yang S, Li D, Li J, Li H. Strong electron affinity PDI supramolecules form anion radicals for the degradation of organic pollutants via direct electrophilic attack. Catal Sci Technol 2021. [DOI: 10.1039/d0cy01982h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Strong electron affinity PDI supramolecules degrade organic pollutants efficiently through directly electrophilic attack.
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Affiliation(s)
- Xiaojuan Bai
- Key Laboratory of Urban Stormwater System and Water Environment (Beijing University of Civil Engineering and Architecture)
- Ministry of Education
- China
- Beijing Engineering Research Center of Sustainable Urban Sewage System Construction and Risk Control
- Beijing University of Civil Engineering and Architecture
| | - Cong Wang
- Key Laboratory of Urban Stormwater System and Water Environment (Beijing University of Civil Engineering and Architecture)
- Ministry of Education
- China
| | - Xuyu Wang
- Key Laboratory of Urban Stormwater System and Water Environment (Beijing University of Civil Engineering and Architecture)
- Ministry of Education
- China
| | - Tianqi Jia
- Key Laboratory of Urban Stormwater System and Water Environment (Beijing University of Civil Engineering and Architecture)
- Ministry of Education
- China
| | - Boxuan Sun
- Key Laboratory of Urban Stormwater System and Water Environment (Beijing University of Civil Engineering and Architecture)
- Ministry of Education
- China
| | - Shengqi Yang
- Key Laboratory of Urban Stormwater System and Water Environment (Beijing University of Civil Engineering and Architecture)
- Ministry of Education
- China
| | - Di Li
- School of Chemistry and Chemical Engineering
- Xi'an University of Architecture and Technology
- Xi'an
- China
| | - Junqi Li
- Key Laboratory of Urban Stormwater System and Water Environment (Beijing University of Civil Engineering and Architecture)
- Ministry of Education
- China
- Beijing Engineering Research Center of Sustainable Urban Sewage System Construction and Risk Control
- Beijing University of Civil Engineering and Architecture
| | - Haiyan Li
- Key Laboratory of Urban Stormwater System and Water Environment (Beijing University of Civil Engineering and Architecture)
- Ministry of Education
- China
- Beijing Engineering Research Center of Sustainable Urban Sewage System Construction and Risk Control
- Beijing University of Civil Engineering and Architecture
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6
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Shashikala HBM, Chakravorty A, Panday SK, Alexov E. BION-2: Predicting Positions of Non-Specifically Bound Ions on Protein Surface by a Gaussian-Based Treatment of Electrostatics. Int J Mol Sci 2020; 22:ijms22010272. [PMID: 33383946 PMCID: PMC7794834 DOI: 10.3390/ijms22010272] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 12/25/2020] [Accepted: 12/26/2020] [Indexed: 01/16/2023] Open
Abstract
Ions play significant roles in biological processes—they may specifically bind to a protein site or bind non-specifically on its surface. Although the role of specifically bound ions ranges from actively providing structural compactness via coordination of charge–charge interactions to numerous enzymatic activities, non-specifically surface-bound ions are also crucial to maintaining a protein’s stability, responding to pH and ion concentration changes, and contributing to other biological processes. However, the experimental determination of the positions of non-specifically bound ions is not trivial, since they may have a low residential time and experience significant thermal fluctuation of their positions. Here, we report a new release of a computational method, the BION-2 method, that predicts the positions of non-specifically surface-bound ions. The BION-2 utilizes the Gaussian-based treatment of ions within the framework of the modified Poisson–Boltzmann equation, which does not require a sharp boundary between the protein and water phase. Thus, the predictions are done by the balance of the energy of interaction between the protein charges and the corresponding ions and the de-solvation penalty of the ions as they approach the protein. The BION-2 is tested against experimentally determined ion’s positions and it is demonstrated that it outperforms the old BION and other available tools.
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Affiliation(s)
- H. B. Mihiri Shashikala
- Department of Physics, Clemson University, Clemson, SC 29634, USA; (H.B.M.S.); (A.C.); (S.K.P.)
| | - Arghya Chakravorty
- Department of Physics, Clemson University, Clemson, SC 29634, USA; (H.B.M.S.); (A.C.); (S.K.P.)
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shailesh Kumar Panday
- Department of Physics, Clemson University, Clemson, SC 29634, USA; (H.B.M.S.); (A.C.); (S.K.P.)
| | - Emil Alexov
- Department of Physics, Clemson University, Clemson, SC 29634, USA; (H.B.M.S.); (A.C.); (S.K.P.)
- Correspondence:
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7
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Chakravorty A, Pandey S, Pahari S, Zhao S, Alexov E. Capturing the Effects of Explicit Waters in Implicit Electrostatics Modeling: Qualitative Justification of Gaussian-Based Dielectric Models in DelPhi. J Chem Inf Model 2020; 60:2229-2246. [PMID: 32155062 PMCID: PMC9883665 DOI: 10.1021/acs.jcim.0c00151] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Our group has implemented a smooth Gaussian-based dielectric function in DelPhi (J. Chem. Theory Comput. 2013, 9 (4), 2126-2136) which models the solute as an object with inhomogeneous dielectric permittivity and provides a smooth transition of dielectric permittivity from surface-bound water to bulk solvent. Although it is well-understood that the protein hydrophobic core is less polarizable than the hydrophilic protein surface, less attention is paid to the polarizability of water molecules inside the solute and on its surface. Here, we apply explicit water simulations to study the behavior of water molecules buried inside a protein and on the surface of that protein and contrast it with the behavior of the bulk water. We selected a protein that is experimentally shown to have five cavities, most of which are occupied by water molecules. We demonstrate through molecular dynamics (MD) simulations that the behavior of water in the cavity is drastically different from that in the bulk. These observations were made by comparing the mean residence times, dipole orientation relaxation times, and average dipole moment fluctuations. We also show that the bulk region has a nonuniform distribution of these tempo-spatial properties. From the perspective of continuum electrostatics, we argue that the dielectric "constant" in water-filled cavities of proteins and the space close to the molecular surface should differ from that assigned to the bulk water. This provides support for the Gaussian-based smooth dielectric model for solving electrostatics in the Poisson-Boltzmann equation framework. Furthermore, we demonstrate that using a well-parametrized Gaussian-based model with a single energy-minimized configuration of a protein can also reproduce its ensemble-averaged polar solvation energy. Thus, we argue that the Gaussian-based smooth dielectric model not only captures accurate physics but also provides an efficient way of computing ensemble-averaged quantities.
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Affiliation(s)
- Arghya Chakravorty
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, United States,Corresponding Authors:,
| | - Shailesh Pandey
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, United States
| | - Swagata Pahari
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, United States
| | - Shan Zhao
- Department of Mathematics, University of Alabama, Tuscaloosa, Alabama 35487, Unites States
| | - Emil Alexov
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, United States,Corresponding Authors:,
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8
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Kalayan J, Henchman RH, Warwicker J. Model for Counterion Binding and Charge Reversal on Protein Surfaces. Mol Pharm 2020; 17:595-603. [PMID: 31887056 DOI: 10.1021/acs.molpharmaceut.9b01047] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The structural stability and solubility of proteins in liquid therapeutic formulations is important, especially since new generations of therapeutics are designed for efficacy before consideration of stability. We introduce an electrostatic binding model to measure the net charge of proteins with bound ions in solution. The electrostatic potential on a protein surface is used to separately group together acidic and basic amino acids into patches, which are then iteratively bound with oppositely charged counterions. This model is aimed toward formulation chemists for initial screening of a range of conditions prior to lab-work. Computed results compare well with experimental zeta potential measurements from the literature covering a range of solution conditions. Importantly, the binding model reproduces the charge reversal phenomenon that is observed with polyvalent ion binding to proteins and its dependence on ion charge and concentration. Intriguingly, protein sequence can be used to give similarly good agreement with experiment as protein structure, interpreted as resulting from the close proximity of charged side chains on a protein surface. Further, application of the model to human proteins suggests that polyanion binding and overcharging, including charge reversal for cationic proteins, is a general feature. These results add to evidence that addition of polyanions to protein formulations could be a general mechanism for modulating solution stability.
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Affiliation(s)
- Jas Kalayan
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom, and School of Chemistry , The University of Manchester , Oxford Road , Manchester M13 9PL , United Kingdom
| | - Richard H Henchman
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom, and School of Chemistry , The University of Manchester , Oxford Road , Manchester M13 9PL , United Kingdom
| | - Jim Warwicker
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom, and School of Chemistry , The University of Manchester , Oxford Road , Manchester M13 9PL , United Kingdom
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9
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Li C, Jia Z, Chakravorty A, Pahari S, Peng Y, Basu S, Koirala M, Panday SK, Petukh M, Li L, Alexov E. DelPhi Suite: New Developments and Review of Functionalities. J Comput Chem 2019; 40:2502-2508. [PMID: 31237360 PMCID: PMC6771749 DOI: 10.1002/jcc.26006] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 05/07/2019] [Accepted: 06/09/2019] [Indexed: 12/25/2022]
Abstract
Electrostatic potential, energies, and forces affect virtually any process in molecular biology, however, computing these quantities is a difficult task due to irregularly shaped macromolecules and the presence of water. Here, we report a new edition of the popular software package DelPhi along with describing its functionalities. The new DelPhi is a C++ object-oriented package supporting various levels of multiprocessing and memory distribution. It is demonstrated that multiprocessing results in significant improvement of computational time. Furthermore, for computations requiring large grid size (large macromolecular assemblages), the approach of memory distribution is shown to reduce the requirement of RAM and thus permitting large-scale modeling to be done on Linux clusters with moderate architecture. The new release comes with new features, whose functionalities and applications are described as well. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.
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Affiliation(s)
- Chuan Li
- Department of MathematicsWest Chester University of PennsylvaniaWest ChesterPennsylvania19383
| | - Zhe Jia
- Department of Physics and AstronomyClemson UniversityClemsonSouth Carolina29634
| | - Arghya Chakravorty
- Department of Physics and AstronomyClemson UniversityClemsonSouth Carolina29634
| | - Swagata Pahari
- Department of Physics and AstronomyClemson UniversityClemsonSouth Carolina29634
| | - Yunhui Peng
- Department of Physics and AstronomyClemson UniversityClemsonSouth Carolina29634
| | - Sankar Basu
- Department of Physics and AstronomyClemson UniversityClemsonSouth Carolina29634
| | - Mahesh Koirala
- Department of Physics and AstronomyClemson UniversityClemsonSouth Carolina29634
| | | | - Marharyta Petukh
- Department of BiologyPresbyterian CollegeClintonSouth Carolina29325
| | - Lin Li
- Department of PhysicsUniversity of Texas at EI PasoTexas79968
| | - Emil Alexov
- Department of Physics and AstronomyClemson UniversityClemsonSouth Carolina29634
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10
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Kutnowski N, Shmulevich F, Davidov G, Shahar A, Bar-Zvi D, Eichler J, Zarivach R, Shaanan B. Specificity of protein-DNA interactions in hypersaline environment: structural studies on complexes of Halobacterium salinarum oxidative stress-dependent protein hsRosR. Nucleic Acids Res 2019; 47:8860-8873. [PMID: 31310308 PMCID: PMC7145548 DOI: 10.1093/nar/gkz604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 06/13/2019] [Accepted: 07/02/2019] [Indexed: 12/21/2022] Open
Abstract
Interactions between proteins and DNA are crucial for all biological systems. Many studies have shown the dependence of protein–DNA interactions on the surrounding salt concentration. How these interactions are maintained in the hypersaline environments that halophiles inhabit remains puzzling. Towards solving this enigma, we identified the DNA motif recognized by the Halobactrium salinarum ROS-dependent transcription factor (hsRosR), determined the structure of several hsRosR–DNA complexes and investigated the DNA-binding process under extreme high-salt conditions. The picture that emerges from this work contributes to our understanding of the principles underlying the interplay between electrostatic interactions and salt-mediated protein–DNA interactions in an ionic environment characterized by molar salt concentrations.
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Affiliation(s)
- Nitzan Kutnowski
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410510, Israel
| | - Fania Shmulevich
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410510, Israel
| | - Geula Davidov
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410510, Israel.,National Institute of Biotechnology in the Negev, Ben-Gurion University, Beer Sheva 8410510, Israel
| | - Anat Shahar
- Macromolecular Crystallography Research Center, National Institute of Biotechnology in the Negev, Ben-Gurion University, Beer Sheva 8410510, Israel
| | - Dudy Bar-Zvi
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410510, Israel
| | - Jerry Eichler
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410510, Israel
| | - Raz Zarivach
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410510, Israel.,National Institute of Biotechnology in the Negev, Ben-Gurion University, Beer Sheva 8410510, Israel
| | - Boaz Shaanan
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410510, Israel
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11
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Tolokh IS, Thomas DG, Onufriev AV. Explicit ions/implicit water generalized Born model for nucleic acids. J Chem Phys 2018; 148:195101. [PMID: 30307229 DOI: 10.1063/1.5027260] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The ion atmosphere around highly charged nucleic acid molecules plays a significant role in their dynamics, structure, and interactions. Here we utilized the implicit solvent framework to develop a model for the explicit treatment of ions interacting with nucleic acid molecules. The proposed explicit ions/implicit water model is based on a significantly modified generalized Born (GB) model and utilizes a non-standard approach to define the solute/solvent dielectric boundary. Specifically, the model includes modifications to the GB interaction terms for the case of multiple interacting solutes-disconnected dielectric boundary around the solute-ion or ion-ion pairs. A fully analytical description of all energy components for charge-charge interactions is provided. The effectiveness of the approach is demonstrated by calculating the potential of mean force for Na+-Cl- ion pair and by carrying out a set of Monte Carlo (MC) simulations of mono- and trivalent ions interacting with DNA and RNA duplexes. The monovalent (Na+) and trivalent (CoHex3+) counterion distributions predicted by the model are in close quantitative agreement with all-atom explicit water molecular dynamics simulations used as reference. Expressed in the units of energy, the maximum deviations of local ion concentrations from the reference are within k B T. The proposed explicit ions/implicit water GB model is able to resolve subtle features and differences of CoHex distributions around DNA and RNA duplexes. These features include preferential CoHex binding inside the major groove of the RNA duplex, in contrast to CoHex biding at the "external" surface of the sugar-phosphate backbone of the DNA duplex; these differences in the counterion binding patters were earlier shown to be responsible for the observed drastic differences in condensation propensities between short DNA and RNA duplexes. MC simulations of CoHex ions interacting with the homopolymeric poly(dA·dT) DNA duplex with modified (de-methylated) and native thymine bases are used to explore the physics behind CoHex-thymine interactions. The simulations suggest that the ion desolvation penalty due to proximity to the low dielectric volume of the methyl group can contribute significantly to CoHex-thymine interactions. Compared to the steric repulsion between the ion and the methyl group, the desolvation penalty interaction has a longer range and may be important to consider in the context of methylation effects on DNA condensation.
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Affiliation(s)
- Igor S Tolokh
- Department of Computer Science, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Dennis G Thomas
- Computational Biology, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Alexey V Onufriev
- Departments of Computer Science and Physics, Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia 24061, USA
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12
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Maddigan NK, Tarzia A, Huang DM, Sumby CJ, Bell SG, Falcaro P, Doonan CJ. Protein surface functionalisation as a general strategy for facilitating biomimetic mineralisation of ZIF-8. Chem Sci 2018; 9:4217-4223. [PMID: 29780551 PMCID: PMC5942038 DOI: 10.1039/c8sc00825f] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 03/09/2018] [Indexed: 12/17/2022] Open
Abstract
The surface charge and chemistry of a protein determines its ability to facilitate biomimetic mineralisation.
The durability of enzymes in harsh conditions can be enhanced by encapsulation within metal–organic frameworks (MOFs) via a process called biomimetic mineralisation. Herein we show that the surface charge and chemistry of a protein determines its ability to seed MOF growth. We demonstrate that chemical modification of amino acids on the protein surface is an effective method for systematically controlling biomimetic mineralisation by zeolitic imidazolate framework-8 (ZIF-8). Reaction of surface lysine residues with succinic (or acetic) anhydride facilitates biomimetic mineralisation by increasing the surface negative charge, whereas reaction of surface carboxylate moieties with ethylenediamine affords a more positively charged protein and hinders the process. Moreover, computational studies confirm that the surface electrostatic potential of a protein is a good indicator of its ability to induce biomimetic mineralisation. This study highlights the important role played by protein surface chemistry in encapsulation and outlines a general method for facilitating the biomimetic mineralisation of proteins.
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Affiliation(s)
- Natasha K Maddigan
- Department of Chemistry and the Centre for Advanced Nanomaterials , The University of Adelaide , Adelaide , South Australia 5005 , Australia .
| | - Andrew Tarzia
- Department of Chemistry and the Centre for Advanced Nanomaterials , The University of Adelaide , Adelaide , South Australia 5005 , Australia .
| | - David M Huang
- Department of Chemistry and the Centre for Advanced Nanomaterials , The University of Adelaide , Adelaide , South Australia 5005 , Australia .
| | - Christopher J Sumby
- Department of Chemistry and the Centre for Advanced Nanomaterials , The University of Adelaide , Adelaide , South Australia 5005 , Australia .
| | - Stephen G Bell
- Department of Chemistry and the Centre for Advanced Nanomaterials , The University of Adelaide , Adelaide , South Australia 5005 , Australia .
| | - Paolo Falcaro
- Department of Chemistry and the Centre for Advanced Nanomaterials , The University of Adelaide , Adelaide , South Australia 5005 , Australia . .,Institute of Physical and Theoretical Chemistry , Graz University of Technology , Stremayrgasse 9 , Graz 8010 , Austria
| | - Christian J Doonan
- Department of Chemistry and the Centre for Advanced Nanomaterials , The University of Adelaide , Adelaide , South Australia 5005 , Australia .
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13
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Li M, Zhang H, Chen B, Wu Y, Guan L. Prediction of pKa Values for Neutral and Basic Drugs based on Hybrid Artificial Intelligence Methods. Sci Rep 2018; 8:3991. [PMID: 29507318 PMCID: PMC5838250 DOI: 10.1038/s41598-018-22332-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 02/21/2018] [Indexed: 11/23/2022] Open
Abstract
The pKa value of drugs is an important parameter in drug design and pharmacology. In this paper, an improved particle swarm optimization (PSO) algorithm was proposed based on the population entropy diversity. In the improved algorithm, when the population entropy was higher than the set maximum threshold, the convergence strategy was adopted; when the population entropy was lower than the set minimum threshold the divergence strategy was adopted; when the population entropy was between the maximum and minimum threshold, the self-adaptive adjustment strategy was maintained. The improved PSO algorithm was applied in the training of radial basis function artificial neural network (RBF ANN) model and the selection of molecular descriptors. A quantitative structure-activity relationship model based on RBF ANN trained by the improved PSO algorithm was proposed to predict the pKa values of 74 kinds of neutral and basic drugs and then validated by another database containing 20 molecules. The validation results showed that the model had a good prediction performance. The absolute average relative error, root mean square error, and squared correlation coefficient were 0.3105, 0.0411, and 0.9685, respectively. The model can be used as a reference for exploring other quantitative structure-activity relationships.
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Affiliation(s)
- Mengshan Li
- College of Physics and Electronic Information, Gannan Normal University, Ganzhou, Jiangxi, 341000, China.
| | - Huaijing Zhang
- College of Physics and Electronic Information, Gannan Normal University, Ganzhou, Jiangxi, 341000, China
| | - Bingsheng Chen
- College of Physics and Electronic Information, Gannan Normal University, Ganzhou, Jiangxi, 341000, China
| | - Yan Wu
- College of Physics and Electronic Information, Gannan Normal University, Ganzhou, Jiangxi, 341000, China
| | - Lixin Guan
- College of Physics and Electronic Information, Gannan Normal University, Ganzhou, Jiangxi, 341000, China
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