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Tantipanjaporn A, Wong MK. Development and Recent Advances in Lysine and N-Terminal Bioconjugation for Peptides and Proteins. Molecules 2023; 28:molecules28031083. [PMID: 36770752 PMCID: PMC9953373 DOI: 10.3390/molecules28031083] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/24/2023] Open
Abstract
The demand for creation of protein diversity and regulation of protein function through native protein modification and post-translational modification has ignited the development of selective chemical modification methods for peptides and proteins. Chemical bioconjugation offers selective functionalization providing bioconjugates with desired properties and functions for diverse applications in chemical biology, medicine, and biomaterials. The amino group existing at the lysine residue and N-terminus of peptides and proteins has been extensively studied in bioconjugation because of its good nucleophilicity and high surface exposure. Herein, we review the development of chemical methods for modification of the amino groups on lysine residue and N-terminus featuring excellent selectivity, mild reaction conditions, short reaction time, high conversion, biocompatibility, and preservation of protein integrity. This review is organized based on the chemoselectivity and site-selectivity of the chemical bioconjugation reagents to the amino acid residues aiming to provide guidance for the selection of appropriate bioconjugation methods.
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2
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Chen AY, Lee J, Damjanovic A, Brooks BR. Protein p Ka Prediction by Tree-Based Machine Learning. J Chem Theory Comput 2022; 18:2673-2686. [PMID: 35289611 PMCID: PMC10510853 DOI: 10.1021/acs.jctc.1c01257] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Protonation states of ionizable protein residues modulate many essential biological processes. For correct modeling and understanding of these processes, it is crucial to accurately determine their pKa values. Here, we present four tree-based machine learning models for protein pKa prediction. The four models, Random Forest, Extra Trees, eXtreme Gradient Boosting (XGBoost), and Light Gradient Boosting Machine (LightGBM), were trained on three experimental PDB and pKa datasets, two of which included a notable portion of internal residues. We observed similar performance among the four machine learning algorithms. The best model trained on the largest dataset performs 37% better than the widely used empirical pKa prediction tool PROPKA and 15% better than the published result from the pKa prediction method DelPhiPKa. The overall root-mean-square error (RMSE) for this model is 0.69, with surface and buried RMSE values being 0.56 and 0.78, respectively, considering six residue types (Asp, Glu, His, Lys, Cys, and Tyr), and 0.63 when considering Asp, Glu, His, and Lys only. We provide pKa predictions for proteins in human proteome from the AlphaFold Protein Structure Database and observed that 1% of Asp/Glu/Lys residues have highly shifted pKa values close to the physiological pH.
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Affiliation(s)
- Ada Y. Chen
- Department of Physics & Astronomy, Johns Hopkins
University, Baltimore, Maryland, 21218
- Laboratory of Computational Biology, National Heart, Lung
and Blood Institute, National Institutes of Health, Bethesda, Maryland, 20892
| | - Juyong Lee
- Department of Chemistry, Division of Chemistry and
Biochemistry, Kangwon National University, 1 Gangwondaehak-gil, Chuncheon, 24341,
Republic of Korea
| | - Ana Damjanovic
- Department of Biophysics, Johns Hopkins University,
Baltimore, Maryland, 21218
| | - Bernard R. Brooks
- Laboratory of Computational Biology, National Heart, Lung
and Blood Institute, National Institutes of Health, Bethesda, Maryland, 20892
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3
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Nair AG, Perumalla DS, Anjukandi P. Towards solvent regulated self-activation of N-terminal disulfide bond oxidoreductase-D. Phys Chem Chem Phys 2022; 24:7691-7699. [PMID: 35311864 DOI: 10.1039/d1cp05819c] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
N-terminal disulfide bond oxidoreductase-D (nDsbD), an essential redox enzyme in Gram-negative bacteria, consists of a single disulfide bond (Cys103-Cys109) in its active site. The enzymatic functions are believed to be regulated by an electron transfer mediated redox switching of the disulfide bond, which is vital in controlling bacterial virulence factors. In light of the disulfide bond's inclination towards nucleophilic cleavage, it is also plausible that an internal nucleophile could second the existing electron transfer mechanism in nDsbD. Using QM/MM MD metadynamics simulations, we explore different possibilities of generating an internal nucleophile near the nDsbD active site, which could serve as a fail-over mechanism in cleaving the disulfide bond. The simulations show the formation of the internal nucleophile Tyr42O- (F ≈ 9 kcal mol-1) and its stabilization through the solvent medium. The static gas-phase calculations show that Tyr42O- could be a potential nucleophile for cleaving the S-S bond. Most strikingly, it is also seen that Tyr42O- and Asp68OH communicate with each other through a proton-hole like water wire (F ≈ 12 kcal mol-1), thus modulating the nucleophile formation. Accordingly, we propose the role of a solvent in regulating the internal nucleophilic reactions and the subsequent self-activation of nDsbD. We believe that this could be deterministic while designing enzyme-targeted inhibitor compounds.
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Affiliation(s)
- Aparna G Nair
- Department of Chemistry, Indian Institute of Technology, Palakkad-678557, Kerala, India.
| | | | - Padmesh Anjukandi
- Department of Chemistry, Indian Institute of Technology, Palakkad-678557, Kerala, India.
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4
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Zhorov BS. Possible Mechanism of Ion Selectivity in Eukaryotic Voltage-Gated Sodium Channels. J Phys Chem B 2021; 125:2074-2088. [DOI: 10.1021/acs.jpcb.0c11181] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Boris S. Zhorov
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8K 4K1, Canada
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, St. Petersburg 194223, Russian Federation
- Almazov National Medical Research Centre, St. Petersburg 197341, Russian Federation
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5
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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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6
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Han CT, Song J, Chan T, Pruett C, Han S. Electrostatic Environment of Proteorhodopsin Affects the pKa of Its Buried Primary Proton Acceptor. Biophys J 2020; 118:1838-1849. [PMID: 32197061 DOI: 10.1016/j.bpj.2020.02.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 01/27/2020] [Accepted: 02/27/2020] [Indexed: 01/18/2023] Open
Abstract
The protonation state of embedded charged residues in transmembrane proteins (TMPs) can control the onset of protein function. It is understood that interactions between an embedded charged residue and other charged or polar residues in the moiety would influence its pKa, but how the surrounding environment in which the TMP resides affects the pKa of these residues is unclear. Proteorhodopsin (PR), a light-responsive proton pump from marine bacteria, was used as a model to examine externally accessible factors that tune the pKa of its embedded charged residue, specifically its primary proton acceptor D97. The pKa of D97 was compared between PR reconstituted in liposomes with different net headgroup charges and equilibrated in buffer with different ion concentrations. For PR reconstituted in net positively charged compared to net negatively charged liposomes in low-salt buffer solutions, a drop of the apparent pKa from 7.6 to 5.6 was observed, whereas intrinsic pKa modeled with surface pH calculated from Gouy-Chapman predictions found an opposite trend for the pKa change, suggesting that surface pH does not account for the main changes observed in the apparent pKa. This difference in the pKa of D97 observed from PR reconstituted in oppositely charged liposome environments disappeared when the NaCl concentration was increased to 150 mM. We suggest that protein-intrinsic structural properties must play a role in adjusting the local microenvironment around D97 to affect its pKa, as corroborated with observations of changes in protein side-chain and hydration dynamics around the E-F loop of PR. Understanding the effect of externally controllable factors in tuning the pKa of TMP-embedded charged residues is important for bioengineering and biomedical applications relying on TMP systems, in which the onset of functions can be controlled by the protonation state of embedded residues.
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Affiliation(s)
- Chung-Ta Han
- Department of Chemical Engineering, University of California, Santa Barbara, California
| | - Jichao Song
- Department of Chemical Engineering, University of California, Santa Barbara, California
| | - Tristan Chan
- Department of Chemistry, University of California, Santa Barbara, California
| | - Christine Pruett
- Department of Chemical Engineering, University of California, Santa Barbara, California
| | - Songi Han
- Department of Chemical Engineering, University of California, Santa Barbara, California; Department of Chemistry, University of California, Santa Barbara, California.
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7
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Jiang D, Shi H, Tonggu L, Gamal El-Din TM, Lenaeus MJ, Zhao Y, Yoshioka C, Zheng N, Catterall WA. Structure of the Cardiac Sodium Channel. Cell 2019; 180:122-134.e10. [PMID: 31866066 DOI: 10.1016/j.cell.2019.11.041] [Citation(s) in RCA: 163] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/18/2019] [Accepted: 11/27/2019] [Indexed: 12/19/2022]
Abstract
Voltage-gated sodium channel Nav1.5 generates cardiac action potentials and initiates the heartbeat. Here, we report structures of NaV1.5 at 3.2-3.5 Å resolution. NaV1.5 is distinguished from other sodium channels by a unique glycosyl moiety and loss of disulfide-bonding capability at the NaVβ subunit-interaction sites. The antiarrhythmic drug flecainide specifically targets the central cavity of the pore. The voltage sensors are partially activated, and the fast-inactivation gate is partially closed. Activation of the voltage sensor of Domain III allows binding of the isoleucine-phenylalanine-methionine (IFM) motif to the inactivation-gate receptor. Asp and Ala, in the selectivity motif DEKA, line the walls of the ion-selectivity filter, whereas Glu and Lys are in positions to accept and release Na+ ions via a charge-delocalization network. Arrhythmia mutation sites undergo large translocations during gating, providing a potential mechanism for pathogenic effects. Our results provide detailed insights into Nav1.5 structure, pharmacology, activation, inactivation, ion selectivity, and arrhythmias.
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Affiliation(s)
- Daohua Jiang
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Hui Shi
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Lige Tonggu
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | | | - Michael J Lenaeus
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA; Division of General Internal Medicine, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Yan Zhao
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Craig Yoshioka
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Ning Zheng
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
| | - William A Catterall
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA.
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8
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Manandhar A, Chakraborty K, Tang PK, Kang M, Zhang P, Cui H, Loverde SM. Rational Coarse-Grained Molecular Dynamics Simulations of Supramolecular Anticancer Nanotubes. J Phys Chem B 2019; 123:10582-10593. [DOI: 10.1021/acs.jpcb.9b07417] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Anjela Manandhar
- Department of Chemistry, College of Staten Island, City University of New York, New York 10314, United States
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York 10016, United States
| | - Kaushik Chakraborty
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York 10016, United States
| | - Phu K. Tang
- Department of Chemistry, College of Staten Island, City University of New York, New York 10314, United States
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York 10016, United States
| | - Myungshim Kang
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York 10016, United States
| | - Pengcheng Zhang
- Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Honggang Cui
- Department of Chemical and Biomolecular Engineering and Institute for NanoBioTechnology, The Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Oncology and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Sharon M. Loverde
- Department of Chemistry, College of Staten Island, City University of New York, New York 10314, United States
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York 10016, United States
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9
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Spencer P, Ye Q, Song L, Parthasarathy R, Boone K, Misra A, Tamerler C. Threats to adhesive/dentin interfacial integrity and next generation bio-enabled multifunctional adhesives. J Biomed Mater Res B Appl Biomater 2019; 107:2673-2683. [PMID: 30895695 PMCID: PMC6754319 DOI: 10.1002/jbm.b.34358] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 02/07/2019] [Accepted: 02/20/2019] [Indexed: 12/27/2022]
Abstract
Nearly 100 million of the 170 million composite and amalgam restorations placed annually in the United States are replacements for failed restorations. The primary reason both composite and amalgam restorations fail is recurrent decay, for which composite restorations experience a 2.0-3.5-fold increase compared to amalgam. Recurrent decay is a pernicious problem-the standard treatment is replacement of defective composites with larger restorations that will also fail, initiating a cycle of ever-larger restorations that can lead to root canals, and eventually, to tooth loss. Unlike amalgam, composite lacks the inherent capability to seal discrepancies at the restorative material/tooth interface. The low-viscosity adhesive that bonds the composite to the tooth is intended to seal the interface, but the adhesive degrades, which can breach the composite/tooth margin. Bacteria and bacterial by-products such as acids and enzymes infiltrate the marginal gaps and the composite's inability to increase the interfacial pH facilitates cariogenic and aciduric bacterial outgrowth. Together, these characteristics encourage recurrent decay, pulpal damage, and composite failure. This review article examines key biological and physicochemical interactions involved in the failure of composite restorations and discusses innovative strategies to mitigate the negative effects of pathogens at the adhesive/dentin interface. © 2019 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater 107B:2466-2475, 2019.
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Affiliation(s)
- Paulette Spencer
- Institute for Bioengineering Research, School of Engineering, University of Kansas, 1530 W. 15th Street, Lawrence, KS 66045-7609, USA
- Department of Mechanical Engineering, University of Kansas,1530 W. 15th Street, Lawrence, KS 66045-7609, USA
| | - Qiang Ye
- Institute for Bioengineering Research, School of Engineering, University of Kansas, 1530 W. 15th Street, Lawrence, KS 66045-7609, USA
| | - Linyong Song
- Institute for Bioengineering Research, School of Engineering, University of Kansas, 1530 W. 15th Street, Lawrence, KS 66045-7609, USA
| | - Ranganathan Parthasarathy
- Department of Civil Engineering, Tennessee State University, 3500 John A Merritt Blvd, Nashville, TN 37209, USA
| | - Kyle Boone
- Institute for Bioengineering Research, School of Engineering, University of Kansas, 1530 W. 15th Street, Lawrence, KS 66045-7609, USA
| | - Anil Misra
- Institute for Bioengineering Research, School of Engineering, University of Kansas, 1530 W. 15th Street, Lawrence, KS 66045-7609, USA
- Department of Civil Engineering, University of Kansas, 1530 W. 15th Street, Lawrence, KS 66045-7609, USA
| | - Candan Tamerler
- Institute for Bioengineering Research, School of Engineering, University of Kansas, 1530 W. 15th Street, Lawrence, KS 66045-7609, USA
- Department of Mechanical Engineering, University of Kansas,1530 W. 15th Street, Lawrence, KS 66045-7609, USA
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10
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Cvitkovic JP, Pauplis CD, Kaminski GA. PKA17-A Coarse-Grain Grid-Based Methodology and Web-Based Software for Predicting Protein pK a Shifts. J Comput Chem 2019; 40:1718-1726. [PMID: 30895643 DOI: 10.1002/jcc.25826] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 02/26/2019] [Indexed: 11/09/2022]
Abstract
We have developed and tested PKA17, a coarse-grain grid-based model for predicting protein pK a shifts. Our pK a predictor is currently deployed via a website interface. We have carried out parameter fitting using 442 Asp, Glu, His, Lys, and Arg residues for which experimental results are available in the literature. PROPKA software has been used for benchmarking. The average unsigned error and root-mean-square deviation (RMSD) have been found to be 0.628 and 0.831 pH units, respectively, for PKA17. The corresponding results with PROPKA are 0.761 and 1.063 units. We have assessed the robustness of the developed PKA17 methodology with a number of tests and have also explored the possibility of using a combination of PROPKA and PKA17 calculations in order to improve the accuracy of predicted pK a values for protein residues. We have also once again confirmed that protein acidity constants are influenced almost entirely by residues in the immediate spatial proximity of the ionizable amino acids. The resulting PKA17 software has been deployed online with a web-based interface at http://users.wpi.edu/~jpcvitkovic/pka_calc.html. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- John P Cvitkovic
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 100 Institute Rd., Worcester, Massachusetts, 01609
| | - Connor D Pauplis
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 100 Institute Rd., Worcester, Massachusetts, 01609
| | - George A Kaminski
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 100 Institute Rd., Worcester, Massachusetts, 01609
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11
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Song L, Ge X, Ye Q, Boone K, Xie SX, Misra A, Tamerler C, Spencer P. Modulating pH through lysine integrated dental adhesives. Dent Mater 2018; 34:1652-1660. [PMID: 30201287 DOI: 10.1016/j.dental.2018.08.293] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 08/07/2018] [Accepted: 08/27/2018] [Indexed: 10/28/2022]
Abstract
OBJECTIVES The objective of this study was to explore the effect of lysine integration to dental adhesives with respect to the polymerization kinetics, neutralization capacities in the acidic microenvironment, dynamic mechanical properties, and thermal properties. MATERIALS AND METHOD Lysine was incorporated into liquid resin formulations at 2.5 and 5.0wt % with additional water/ethanol co-solvents. The co-monomer system contained 2-hydroxyethyl-methacrylate (HEMA) and Bisphenol A glycerolate dimethacrylate (BisGMA) with a mass ratio of 45/55. The kinetics of photopolymerization, neutralization capacities, lysine-leaching, dynamic mechanical properties and thermal properties of the control and experimental adhesives were analyzed. RESULTS The degree of conversion of the experimental adhesive was increased substantially at 2.5wt% lysine as compared to the control. The experimental polymers provided acute neutralization of the acidic microenvironment. Approximately half of the lysine was released from the polymer network within one month. Under dry conditions and physiologic temperatures, the incorporation of lysine did not compromise the storage modulus. Comparison of the thermal properties suggests that the more compact structure of the control adhesive inhibits movement of the polymer chains resulting in increased Tg. SIGNIFICANCE Incorporating lysine in the adhesive formulations led to promising results regarding modulating pH, which may serve as one aspect of a multi-spectrum approach for enhancing the durability of composite restorations. The results provide insight and lay a foundation for incorporating amino acids or peptides into adhesive formulations for pH modulation or desired bioactivity at the interfacial margin between the composite and tooth.
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Affiliation(s)
- Linyong Song
- Institute for Bioengineering Research, School of Engineering, University of Kansas, 1530 W. 15th Street, Lawrence, KS 66045-7609, USA
| | - Xueping Ge
- Institute for Bioengineering Research, School of Engineering, University of Kansas, 1530 W. 15th Street, Lawrence, KS 66045-7609, USA
| | - Qiang Ye
- Institute for Bioengineering Research, School of Engineering, University of Kansas, 1530 W. 15th Street, Lawrence, KS 66045-7609, USA
| | - Kyle Boone
- Institute for Bioengineering Research, School of Engineering, University of Kansas, 1530 W. 15th Street, Lawrence, KS 66045-7609, USA
| | - Sheng-Xue Xie
- Institute for Bioengineering Research, School of Engineering, University of Kansas, 1530 W. 15th Street, Lawrence, KS 66045-7609, USA
| | - Anil Misra
- Institute for Bioengineering Research, School of Engineering, University of Kansas, 1530 W. 15th Street, Lawrence, KS 66045-7609, USA; Department of Civil Engineering, University of Kansas, 1530 W. 15th Street, Lawrence, KS 66045-7609, USA
| | - Candan Tamerler
- Institute for Bioengineering Research, School of Engineering, University of Kansas, 1530 W. 15th Street, Lawrence, KS 66045-7609, USA; Department of Mechanical Engineering, University of Kansas, 1530 W. 15th Street, Lawrence, KS 66045-7609, USA
| | - Paulette Spencer
- Institute for Bioengineering Research, School of Engineering, University of Kansas, 1530 W. 15th Street, Lawrence, KS 66045-7609, USA; Department of Mechanical Engineering, University of Kansas, 1530 W. 15th Street, Lawrence, KS 66045-7609, USA.
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12
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Damjanovic A, Miller BT, Okur A, Brooks BR. Reservoir pH replica exchange. J Chem Phys 2018; 149:072321. [PMID: 30134701 PMCID: PMC6005788 DOI: 10.1063/1.5027413] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 05/30/2018] [Indexed: 11/15/2022] Open
Abstract
We present the reservoir pH replica exchange (R-pH-REM) method for constant pH simulations. The R-pH-REM method consists of a two-step procedure; the first step involves generation of one or more reservoirs of conformations. Each reservoir is obtained from a standard or enhanced molecular dynamics simulation with a constrained (fixed) protonation state. In the second step, fixed charge constraints are relaxed, as the structures from one or more reservoirs are periodically injected into a constant pH or a pH-replica exchange (pH-REM) simulation. The benefit of this two-step process is that the computationally intensive part of conformational search can be decoupled from constant pH simulations, and various techniques for enhanced conformational sampling can be applied without the need to integrate such techniques into the pH-REM framework. Simulations on blocked Lys, KK, and KAAE peptides were used to demonstrate an agreement between pH-REM and R-pH-REM simulations. While the reservoir simulations are not needed for these small test systems, the real need arises in cases when ionizable molecules can sample two or more conformations separated by a large energy barrier, such that adequate sampling is not achieved on a time scale of standard constant pH simulations. Such problems might be encountered in protein systems that exploit conformational transitions for function. A hypothetical case is studied, a small molecule with a large torsional barrier; while results of pH-REM simulations depend on the starting structure, R-pH-REM calculations on this model system are in excellent agreement with a theoretical model.
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Affiliation(s)
- Ana Damjanovic
- Author to whom correspondence should be addressed: . Tel.: (410) 516-5390. FAX: (410) 516-4118
| | - Benjamin T. Miller
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892-5690, USA
| | - Asim Okur
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892-5690, USA
| | - Bernard R. Brooks
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892-5690, USA
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13
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Takahashi KZ, Nozawa T, Yasuoka K. A fast and accurate computational method for the linear-combination-based isotropic periodic sum. Sci Rep 2018; 8:11880. [PMID: 30089878 PMCID: PMC6082916 DOI: 10.1038/s41598-018-30364-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 07/16/2018] [Indexed: 12/13/2022] Open
Abstract
An isotropic periodic sum (IPS) is a powerful technique to reasonably calculate intermolecular interactions for wide range of molecular systems under periodic boundary conditions. A linear-combination-based IPS (LIPS) has been developed to attain computational accuracy close to an exact lattice sum, such as the Ewald sum. The algorithm of the original LIPS method has a high computational cost because it needs long-range interaction calculations in real space. This becomes a performance bottleneck for long-time molecular simulations. In this work, the combination of an LIPS and fast Fourier transform (FFT) was developed, and evaluated on homogeneous and heterogeneous molecular systems. This combinational approach of LIPS/FFT attained computational efficiency close to that of a smooth particle mesh Ewald while maintaining the same high accuracy as the original LIPS. We concluded that LIPS/FFT has great potential to extend the capability of IPS techniques for the fast and accurate computation of many types of molecular systems.
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Affiliation(s)
- Kazuaki Z Takahashi
- Research Center for Computational Design of Advanced Functional Materials, National Institute of Advanced Industrial Science and Technology (AIST), Central 2, 1-1-1 Umezono, Tsukuba, Ibaraki, 305-8568, Japan.
| | - Takuma Nozawa
- Department of Mechanical Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
| | - Kenji Yasuoka
- Department of Mechanical Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
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14
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Wu X, Brooks BR. Hydronium Ions Accompanying Buried Acidic Residues Lead to High Apparent Dielectric Constants in the Interior of Proteins. J Phys Chem B 2018; 122:6215-6223. [PMID: 29771522 DOI: 10.1021/acs.jpcb.8b04584] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Internal ionizable groups are known to play important roles in protein functions. A mystery that has attracted decades of extensive experimental and theoretical studies is the apparent dielectric constants experienced by buried ionizable groups, which are much higher than values expected for protein interiors. Many interpretations have been proposed, such as water penetration, conformational relaxation, local unfolding, protein intrinsic backbone fluctuations, etc. However, these interpretations conflict with many experimental observations. The virtual mixture of multiple states (VMMS) simulation method developed in our lab provides a direct approach for studying the equilibrium of multiple chemical states and can monitor p Ka values along simulation trajectories. Through VMMS simulations of staphylococcal nuclease (SNase) variants with internal Asp or Glu residues, we discovered that cations were attracted to buried deprotonated acidic groups and the presence of the nearby cations were essential to reproduce experimentally measured p Ka values. This finding, combined with structural analysis and validation simulations, suggests that the proton released from a deprotonation process stays near the deprotonated group inside proteins, possibly in the form of a hydronium ion. The existence of a proton near a buried charge has many implications in our understanding of protein functions.
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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
| | - 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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Abstract
Truncation is still chosen for many long-range intermolecular interaction calculations to efficiently compute free-boundary systems, macromolecular systems and net-charge molecular systems, for example. Advanced truncation methods have been developed for long-range intermolecular interactions. Every truncation method can be implemented as one of two basic cut-off schemes, namely either an atom-based or a group-based cut-off scheme. The former computes interactions of “atoms” inside the cut-off radius, whereas the latter computes interactions of “molecules” inside the cut-off radius. In this work, the effect of group-based cut-off is investigated for isotropic periodic sum (IPS) techniques, which are promising cut-off treatments to attain advanced accuracy for many types of molecular system. The effect of group-based cut-off is clearly different from that of atom-based cut-off, and severe artefacts are observed in some cases. However, no severe discrepancy from the Ewald sum is observed with the extended IPS techniques.
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16
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Kougentakis CM, Grasso EM, Robinson AC, Caro JA, Schlessman JL, Majumdar A, García-Moreno E B. Anomalous Properties of Lys Residues Buried in the Hydrophobic Interior of a Protein Revealed with 15N-Detect NMR Spectroscopy. J Phys Chem Lett 2018; 9:383-387. [PMID: 29266956 DOI: 10.1021/acs.jpclett.7b02668] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Ionizable residues buried in hydrophobic environments in proteins are essential for many fundamental biochemical processes. These residues titrate with anomalous pKa values that are challenging to reproduce with structure-based calculations owing to the conformational reorganization coupled to their ionization. Detailed characterization of this conformational reorganization is of interest; unfortunately, the properties of buried Lys residues are difficult to study experimentally. Here we demonstrate the utility of 15N NMR spectroscopy to gain insight into the protonation state, state of hydration and conformational dynamics of the Nζ amino group of buried Lys residues. The experiments were applied to five variants of staphylococcal nuclease, with internal Lys residues that titrate with pKa values ranging from 6.2 to 8.1. Direct detection of buried Lys residues with these NMR spectroscopy methods will enable correlation between thermodynamic and structural data as well as unprecedented examination of how conformational transitions coupled to their ionization affect their pKa values.
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Affiliation(s)
| | | | | | | | - Jamie L Schlessman
- Chemistry Department, United States Naval Academy , 572M Holloway Rd MS 9B, Annapolis, Maryland 21402, United States
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17
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Takahashi KZ. Combined use of periodic reaction field and coarse-grained molecular dynamics simulations. I. phospholipid monolayer systems. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2016.1271948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Kazuaki Z. Takahashi
- Multi-scale Soft-matter Simulation Team, Research Center for Computational Design of Advanced Functional Materials, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
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18
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Borosky GL. Quantum-Mechanical Study on the Catalytic Mechanism of Alkaline Phosphatases. J Chem Inf Model 2017; 57:540-549. [DOI: 10.1021/acs.jcim.6b00755] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gabriela L. Borosky
- INFIQC, CONICET and Departamento
de Química Teórica y Computacional, Facultad de Ciencias
Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba 5000, Argentina
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