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Niu X, Yuan M, Zhao R, Wang L, Liu Y, Zhao H, Li H, Yang X, Wang K. Fabrication strategies for chiral self-assembly surface. Mikrochim Acta 2024; 191:202. [PMID: 38492117 DOI: 10.1007/s00604-024-06278-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/05/2024] [Indexed: 03/18/2024]
Abstract
Chiral self-assembly is the spontaneous organization of individual building blocks from chiral (bio)molecules to macroscopic objects into ordered superstructures. Chiral self-assembly is ubiquitous in nature, such as DNA and proteins, which formed the foundation of biological structures. In addition to chiral (bio) molecules, chiral ordered superstructures constructed by self-assembly have also attracted much attention. Chiral self-assembly usually refers to the process of forming chiral aggregates in an ordered arrangement under various non-covalent bonding such as H-bond, π-π interactions, van der Waals forces (dipole-dipole, electrostatic effects, etc.), and hydrophobic interactions. Chiral assembly involves the spontaneous process, which followed the minimum energy rule. It is essentially an intermolecular interaction force. Self-assembled chiral materials based on chiral recognition in electrochemistry, chiral catalysis, optical sensing, chiral separation, etc. have a broad application potential with the research development of chiral materials in recent years.
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Affiliation(s)
- Xiaohui Niu
- College of Petrochemical Technology, Lanzhou University of Technology, 730050, Lanzhou, People's Republic of China.
| | - Mei Yuan
- College of Petrochemical Technology, Lanzhou University of Technology, 730050, Lanzhou, People's Republic of China
| | - Rui Zhao
- College of Petrochemical Technology, Lanzhou University of Technology, 730050, Lanzhou, People's Republic of China
| | - Luhua Wang
- College of Petrochemical Technology, Lanzhou University of Technology, 730050, Lanzhou, People's Republic of China
| | - Yongqi Liu
- College of Petrochemical Technology, Lanzhou University of Technology, 730050, Lanzhou, People's Republic of China
| | - Hongfang Zhao
- College of Petrochemical Technology, Lanzhou University of Technology, 730050, Lanzhou, People's Republic of China
| | - Hongxia Li
- College of Petrochemical Technology, Lanzhou University of Technology, 730050, Lanzhou, People's Republic of China
| | - Xing Yang
- School of Materials Science and Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, People's Republic of China.
| | - Kunjie Wang
- College of Petrochemical Technology, Lanzhou University of Technology, 730050, Lanzhou, People's Republic of China.
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2
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Chhetri KB, Jang YH, Lansac Y, Maiti PK. DNA groove preference shift upon phosphorylation of a protamine-like cationic peptide. Phys Chem Chem Phys 2023; 25:31335-31345. [PMID: 37960891 DOI: 10.1039/d3cp03803c] [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: 11/15/2023]
Abstract
Protamines, arginine-rich DNA-binding proteins, are responsible for chromatin compaction in sperm cells, but their DNA groove preference, major or minor, is not clearly identified. We herein study the DNA groove preference of a short protamine-like cationic peptide before and after phosphorylation, using all-atom molecular dynamics and umbrella sampling simulations. According to various thermodynamic and structural analyses, a peptide in its non-phosphorylated native state prefers the minor groove over the major groove, but phosphorylation of the peptide bound to the minor groove not only reduces its binding affinity but also brings a serious deformation of the minor groove, eliminating the minor-groove preference. As protamines are heavily phosphorylated before binding to DNA, we expect that the structurally disordered phosphorylated protamines would prefer major grooves to enter into DNA during spermatogenesis.
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Affiliation(s)
- Khadka B Chhetri
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
- Department of Physics, Prithvinarayan Campus, Tribhuvan University, Pokhara, Nepal
| | - Yun Hee Jang
- Department of Energy Science and Engineering, DGIST, Daegu 42988, Korea
- GREMAN, CNRS UMR 7347, Université de Tours, 37200 Tours, France
- Laboratoire de Physique des Solides, CNRS UMR 8502, Université Paris Saclay, 91405 Orsay, France
| | - Yves Lansac
- GREMAN, CNRS UMR 7347, Université de Tours, 37200 Tours, France
- Laboratoire de Physique des Solides, CNRS UMR 8502, Université Paris Saclay, 91405 Orsay, France
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
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3
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Onufriev AV. Biologically relevant small variations of intra-cellular pH can have significant effect on stability of protein-DNA complexes, including the nucleosome. Front Mol Biosci 2023; 10:1067787. [PMID: 37143824 PMCID: PMC10151541 DOI: 10.3389/fmolb.2023.1067787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/16/2023] [Indexed: 05/06/2023] Open
Abstract
Stability of a protein-ligand complex may be sensitive to pH of its environment. Here we explore, computationally, stability of a set of protein-nucleic acid complexes using fundamental thermodynamic linkage relationship. The nucleosome, as well as an essentially random selection of 20 protein complexes with DNA or RNA, are included in the analysis. An increase in intra-cellular/intra-nuclear pH destabilizes most complexes, including the nucleosome. We propose to quantify the effect by ΔΔG0.3-the change in the binding free energy due to pH increase of 0.3 units, corresponding to doubling of the H + activity; variations of pH of this amplitude can occur in living cells, including in the course of the cell cycle, and in cancer cells relative to normal ones. We suggest, based on relevant experimental findings, a threshold of biological significance of 1 2 k B T ( ∼ 0.3 k c a l / m o l ) for changes of stability of chromatin-related protein-DNA complexes: a change in the binding affinity above the threshold may have biological consequences. We find that for 70% of the examined complexes, Δ Δ G 0.3 > 1 2 k B T (for 10%, ΔΔG0.3 is between 3 and 4 k B T). Thus, small but relevant variations of intra-nuclear pH of 0.3 may have biological consequences for many protein-nucleic acid complexes. The binding affinity between the histone octamer and its DNA, which directly affects the DNA accessibility in the nucleosome, is predicted to be highly sensitive to intra-nuclear pH. A variation of 0.3 units results in ΔΔG0.3 ∼ 10k B T ( ∼ 6 k c a l / m o l ) ; for spontaneous unwrapping of 20 bp long entry/exit fragments of the nucleosomal DNA, ΔΔG0.3 = 2.2k B T; partial disassembly of the nucleosome into the tetrasome is characterized by ΔΔG0.3 = 5.2k B T. The predicted pH -induced modulations of the nucleosome stability are significant enough to suggest that they may have consequences relevant to the biological function of the nucleosome. Accessibility of the nucleosomal DNA is predicted to positively correlate with pH variations during the cell cycle; an increase in intra-cellular pH seen in cancer cells is predicted to lead to a more accessible nucleosomal DNA; a drop in pH associated with apoptosis is predicted to make nucleosomal DNA less accessible. We speculate that processes that depend on accessibility to the DNA in the nucleosomes, such as transcription or DNA replication, might become upregulated due to relatively small, but nevertheless realistic increases of intra-nuclear pH.
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Affiliation(s)
- Alexey V. Onufriev
- Department of Physics, Virginia Tech, Blacksburg, Blacksburg, VA, United States
- Department of Computer Science, Virginia Tech, Blacksburg, Blacksburg, VA, United States
- Center from Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA, United States
- *Correspondence: Alexey V. Onufriev,
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4
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Li Z, Chan KC, Nickels JD, Cheng X. Electrostatic Contributions to the Binding Free Energy of Nicotine to the Acetylcholine Binding Protein. J Phys Chem B 2022; 126:8669-8679. [PMID: 36260486 PMCID: PMC10056799 DOI: 10.1021/acs.jpcb.2c04641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Biomolecular binding relies on specific attractive interactions between two partner molecules, including electrostatics, dispersion, hydrophobicity, and solvation. Assessing the contributions of electrostatic interactions to binding is key to the understanding of ligand binding mechanisms and the design of improved biomolecular binders. For example, nicotine is a well-known agonist of nicotinic acetylcholine receptors (nAChRs), but the molecular mechanisms for the differential action of nicotine on brain and muscle nAChRs remain elusive. In this work, we have chosen the acetylcholine binding protein (AChBP) in complex with nicotine as a model system to interrogate the electrostatic contributions to nicotine binding. Our absolute binding free energy simulations confirm that nicotine binds AChBP predominantly in its protonated (charged) form. By comparing energetic contributions from decomposed interactions for either neutral or charged nicotine, our calculations shed light on the nature of the binding of nicotine to the AChBP. The preferred binding of charged nicotine over neutral nicotine originates from its stronger electrostatic interactions with AChBP, a cation-π interaction to a tryptophan residue and a hydrogen bond between nicotine and the backbone carbonyl of the tryptophan, whereas the major force driving the binding process appears to be van der Waals interactions. The various nonelectrostatic terms can also indirectly modulate the electrostatic interactions through fine-tuning the binding pose of the ligand in the binding site, providing an explanation of why the binding specificity of nicotine to the brain versus muscle nAChRs is driven by electrostatic interaction, given that the immediate binding site residues, including the key tryptophan residue, are identical in the two receptors.
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Affiliation(s)
- Zoe Li
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy at The Ohio State University, Columbus, Ohio43210, United States
| | - Kevin C Chan
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy at The Ohio State University, Columbus, Ohio43210, United States
| | - Jonathan D Nickels
- Department of Chemical and Environmental Engineering, University of Cincinnati, Cincinnati, Ohio45221, United States
| | - Xiaolin Cheng
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy at The Ohio State University, Columbus, Ohio43210, United States
- Translational Data Analytics Institute (TDAI) at The Ohio State University, Columbus, Ohio43210, United States
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5
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Procyk J, Poppleton E, Šulc P. Coarse-grained nucleic acid-protein model for hybrid nanotechnology. SOFT MATTER 2021; 17:3586-3593. [PMID: 33398312 DOI: 10.1039/d0sm01639j] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The emerging field of hybrid DNA-protein nanotechnology brings with it the potential for many novel materials which combine the addressability of DNA nanotechnology with the versatility of protein interactions. However, the design and computational study of these hybrid structures is difficult due to the system sizes involved. To aid in the design and in silico analysis process, we introduce here a coarse-grained DNA/RNA-protein model that extends the oxDNA/oxRNA models of DNA/RNA with a coarse-grained model of proteins based on an anisotropic network model representation. Fully equipped with analysis scripts and visualization, our model aims to facilitate hybrid nanomaterial design towards eventual experimental realization, as well as enabling study of biological complexes. We further demonstrate its usage by simulating DNA-protein nanocage, DNA wrapped around histones, and a nascent RNA in polymerase.
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Affiliation(s)
- Jonah Procyk
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, Arizona 85281, USA.
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6
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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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7
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Acosta-Silva C, Bertran J, Branchadell V, Oliva A. Phosphoryl-Transfer Reaction in RNA under Alkaline Conditions. Chemistry 2018; 24:13565-13572. [PMID: 29943454 DOI: 10.1002/chem.201802332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 06/20/2018] [Indexed: 11/09/2022]
Abstract
The phosphoryl-transfer reaction in RNA under alkaline conditions by exploring the influence of several solvents theoretically was studied. The calculations were carried out by using the M06-2X functional and the solvents were taken as a continuum by using the solvent model density (SMD) method. The main findings show that the O2'-P-O5' angle in the reactants, the free activation energies, and the reaction mechanism are clearly dependent on the dielectric constant of the environment, thus showing that the electrostatic term is the determining factor for this chemical system with two negative charges. Our study seems to indicate that water, the solvent with the greatest dielectric constant, would be the solvent that increases the reaction rate the most. As this outcome was not the case in enzymatic catalysis, one has to conclude that, in the case of proteins as well as for ribozymes, the enzymatic catalysis is not mainly due to the solvent reaction field, but to local electrical fields as a result of enzyme preorganization.
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Affiliation(s)
- Carles Acosta-Silva
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Joan Bertran
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Vicenç Branchadell
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Antoni Oliva
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
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8
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Chu X, Muñoz V. Roles of conformational disorder and downhill folding in modulating protein-DNA recognition. Phys Chem Chem Phys 2018; 19:28527-28539. [PMID: 29044255 DOI: 10.1039/c7cp04380e] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Transcription factors are thought to efficiently search for their target DNA site via a combination of conventional 3D diffusion and 1D diffusion along the DNA molecule mediated by non-specific electrostatic interactions. This process requires the DNA-binding protein to quickly exchange between a search competent and a target recognition mode, but little is known as to how these two binding modes are encoded in the conformational properties of the protein. Here, we investigate this issue on the engrailed homeodomain (EngHD), a DNA-binding domain that folds ultrafast and exhibits a complex conformational behavior consistent with the downhill folding scenario. We explore the interplay between folding and DNA recognition using a coarse-grained computational model that allows us to manipulate the folding properties of the protein and monitor its non-specific and specific binding to DNA. We find that conformational disorder increases the search efficiency of EngHD by promoting a fast gliding search mode in addition to sliding. When gliding, EngHD remains loosely bound to DNA moving linearly along its length. A partially disordered EngHD also binds more dynamically to the target site, reducing the half-life of the specific complex via a spring-loaded mechanism. These findings apply to all conditions leading to partial disorder. However, we also find that at physiologically relevant temperatures EngHD is well folded and can only obtain the conformational flexibility required to accelerate 1D diffusion when it folds/unfolds within the downhill scenario (crossing a marginal free energy barrier). In addition, the conformational flexibility of native downhill EngHD enables its fast reconfiguration to lock into the specific binding site upon arrival, thereby affording finer control of the on- and off-rates of the specific complex. Our results provide key mechanistic insights into how DNA-binding domains optimize specific DNA recognition through the control of their conformational dynamics and folding mechanism.
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Affiliation(s)
- Xiakun Chu
- IMDEA Nanosciences, Faraday 9, Campus de Cantoblanco, Madrid, 28049, Spain
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9
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Acosta-Silva C, Bertran J, Branchadell V, Oliva A. Phosphoryl Transfer Reaction in RNA: Is the Substrate-Assisted Catalysis a Possible Mechanism in Certain Solvents? J Phys Chem A 2017; 121:8525-8534. [PMID: 29039953 DOI: 10.1021/acs.jpca.7b09156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A proton shuttle mechanism for the phosphoryl transfer reaction in RNA, in which a proton is transferred from the nucleophile to the leaving group through a nonbridged oxygen atom of the phosphate, was explored using the MO6-2X density functional method and the solvent continuum model. This reaction is the initial step of the RNA hydrolysis. We used different solvents characterized by their dielectric constant, and, for each of them, we studied the nuclear and electronic relaxation, produced by the solvent reaction field, for the stationary points. Given that RNA has a poor leaving group, the bond breaking corresponds to the rate-determining step. If the O atom is substituted by a S atom, the leaving group is now good, and the rate-determining step is now the nucleophilic attack concerted with the proton transfer. The most relevant result we found is that none of the solvents we studied has a free energy of activation that is smaller than the one in water. This suggests that the enzyme catalysis following this mechanism must be due to the permanent electric field that is created by a preorganized charge distribution but not to the solvent reaction field.
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Affiliation(s)
- Carles Acosta-Silva
- Department of Chemistry, Universitat Autònoma de Barcelona , 08193 Bellaterra, Spain
| | - Joan Bertran
- Department of Chemistry, Universitat Autònoma de Barcelona , 08193 Bellaterra, Spain
| | - Vicenç Branchadell
- Department of Chemistry, Universitat Autònoma de Barcelona , 08193 Bellaterra, Spain
| | - Antoni Oliva
- Department of Chemistry, Universitat Autònoma de Barcelona , 08193 Bellaterra, Spain
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10
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Theoretical study of a proton wire mechanism for the peptide bond formation in the ribosome. Theor Chem Acc 2017. [DOI: 10.1007/s00214-017-2066-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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11
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Casalino L, Palermo G, Abdurakhmonova N, Rothlisberger U, Magistrato A. Development of Site-Specific Mg(2+)-RNA Force Field Parameters: A Dream or Reality? Guidelines from Combined Molecular Dynamics and Quantum Mechanics Simulations. J Chem Theory Comput 2016; 13:340-352. [PMID: 28001405 DOI: 10.1021/acs.jctc.6b00905] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The vital contribution of Mg2+ ions to RNA biology is challenging to dissect at the experimental level. This calls for the integrative support of atomistic simulations, which at the classical level are plagued by limited accuracy. Indeed, force fields intrinsically neglect nontrivial electronic effects that Mg2+ exerts on its surrounding ligands in varying RNA coordination environments. Here, we present a combined computational study based on classical molecular dynamics (MD) and Density Functional Theory (DFT) calculations, aimed at characterizing (i) the performance of five Mg2+ force field (FF) models in RNA systems and (ii) how charge transfer and polarization affect the binding of Mg2+ ions in different coordination motifs. As a result, a total of ∼2.5 μs MD simulations (100/200 ns for each run) for two prototypical Mg2+-dependent ribozymes showed remarkable differences in terms of populations of inner-sphere coordination site types. Most importantly, complementary DFT calculations unveiled that differences in charge transfer and polarization among recurrent Mg2+-RNA coordination motifs are surprisingly small. In particular, the charge of the Mg2+ ions substantially remains constant through different coordination sites, suggesting that the common philosophy of developing site-specific Mg2+ ion parameters is not in line with the physical origin of the Mg2+-RNA MD simulations inaccuracies. Overall, this study constitutes a guideline for an adept use of current Mg2+ models and provides novel insights for the rational development of next-generation Mg2+ FFs to be employed for atomistic simulations of RNA.
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Affiliation(s)
- Lorenzo Casalino
- International School for Advanced Studies (SISSA) , Trieste, Italy
| | - Giulia Palermo
- Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne , CH-1015 Lausanne, Switzerland
| | - Nodira Abdurakhmonova
- International School for Advanced Studies (SISSA) , Trieste, Italy.,Università degli Studi di Trieste , Trieste, Italy
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne , CH-1015 Lausanne, Switzerland
| | - Alessandra Magistrato
- CNR-IOM-Democritos National Simulation Center c/o SISSA , via Bonomea 265, Trieste, Italy
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12
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Sushko ML, Thomas DG, Pabit SA, Pollack L, Onufriev AV, Baker NA. The Role of Correlation and Solvation in Ion Interactions with B-DNA. Biophys J 2016; 110:315-326. [PMID: 26789755 DOI: 10.1016/j.bpj.2015.12.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 11/30/2015] [Accepted: 12/07/2015] [Indexed: 01/28/2023] Open
Abstract
The ionic atmospheres around nucleic acids play important roles in biological function. Large-scale explicit solvent simulations coupled to experimental assays such as anomalous small-angle x-ray scattering can provide important insights into the structure and energetics of such atmospheres but are time- and resource intensive. In this article, we use classical density functional theory to explore the balance among ion-DNA, ion-water, and ion-ion interactions in ionic atmospheres of RbCl, SrCl2, and CoHexCl3 (cobalt hexamine chloride) around a B-form DNA molecule. The accuracy of the classical density functional theory calculations was assessed by comparison between simulated and experimental anomalous small-angle x-ray scattering curves, demonstrating that an accurate model should take into account ion-ion correlation and ion hydration forces, DNA topology, and the discrete distribution of charges on the DNA backbone. As expected, these calculations revealed significant differences among monovalent, divalent, and trivalent cation distributions around DNA. Approximately half of the DNA-bound Rb(+) ions penetrate into the minor groove of the DNA and half adsorb on the DNA backbone. The fraction of cations in the minor groove decreases for the larger Sr(2+) ions and becomes zero for CoHex(3+) ions, which all adsorb on the DNA backbone. The distribution of CoHex(3+) ions is mainly determined by Coulomb and steric interactions, while ion-correlation forces play a central role in the monovalent Rb(+) distribution and a combination of ion-correlation and hydration forces affect the Sr(2+) distribution around DNA. This does not imply that correlations in CoHex solutions are weaker or stronger than for other ions. Steric inaccessibility of the grooves to large CoHex ions leads to their binding at the DNA surface. In this binding mode, first-order electrostatic interactions (Coulomb) dominate the overall binding energy as evidenced by low sensitivity of ionic distribution to the presence or absence of second-order electrostatic correlation interactions.
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Affiliation(s)
- Maria L Sushko
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Dennis G Thomas
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Suzette A Pabit
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York
| | - Alexey V Onufriev
- Department of Computer Science and Department of Physics, Virginia Tech, Blacksburg, Virginia
| | - Nathan A Baker
- Computational and Statistical Analytics Division, Pacific Northwest National Laboratory, Richland, Washington; Division of Applied Mathematics, Brown University, Providence, Rhode Island.
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13
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Rubinstein AI, Sabirianov RF, Namavar F. Effects of the dielectric properties of the ceramic-solvent interface on the binding of proteins to oxide ceramics: a non-local electrostatic approach. NANOTECHNOLOGY 2016; 27:415703. [PMID: 27585807 DOI: 10.1088/0957-4484/27/41/415703] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The rapid development of nanoscience and nanotechnology has raised many fundamental questions that significantly impede progress in these fields. In particular, understanding the physicochemical processes at the interface in aqueous solvents requires the development and application of efficient and accurate methods. In the present work we evaluate the electrostatic contribution to the energy of model protein-ceramic complex formation in an aqueous solvent. We apply a non-local (NL) electrostatic approach that accounts for the effects of the short-range structure of the solvent on the electrostatic interactions of the interfacial systems. In this approach the aqueous solvent is considered as a non-ionic liquid, with the rigid and strongly correlated dipoles of the water molecules. We have found that an ordered interfacial aqueous solvent layer at the protein- and ceramic-solvent interfaces reduces the charging energy of both the ceramic and the protein in the solvent, and significantly increases the electrostatic contribution to their association into a complex. This contribution in the presented NL approach was found to be significantly shifted with respect to the classical model at any dielectric constant value of the ceramics. This implies a significant increase of the adsorption energy in the protein-ceramic complex formation for any ceramic material. We show that for several biocompatible ceramics (for example HfO2, ZrO2, and Ta2O5) the above effect predicts electrostatically induced protein-ceramic complex formation. However, in the framework of the classical continuum electrostatic model (the aqueous solvent as a uniform dielectric medium with a high dielectric constant ∼80) the above ceramics cannot be considered as suitable for electrostatically induced complex formation. Our results also show that the protein-ceramic electrostatic interactions can be strong enough to compensate for the unfavorable desolvation effect in the process of protein-ceramic complex formation.
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Affiliation(s)
- Alexander I Rubinstein
- Department of Physics, Laboratory of Applied Spectroscopy, Ariel University, Ariel 40700, West Bank. Department of Physics, University of Nebraska at Omaha, Omaha, NE 68182, USA
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14
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Kawaguchi K, Nakagawa S, Kinoshita S, Wada M, Saito H, Nagao H. A simple coarse-grained model for interacting protein complex. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1234652] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Kazutomo Kawaguchi
- Institute of Science and Engineering, Kanazawa University , Kanazawa, Japan
| | - Satoshi Nakagawa
- Institute of Science and Engineering, Kanazawa University , Kanazawa, Japan
| | - Shogo Kinoshita
- Institute of Science and Engineering, Kanazawa University , Kanazawa, Japan
| | - Makoto Wada
- Institute of Science and Engineering, Kanazawa University , Kanazawa, Japan
| | - Hiroaki Saito
- Institute of Science and Engineering, Kanazawa University , Kanazawa, Japan
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15
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Kim MO, McCammon JA. Computation of pH-dependent binding free energies. Biopolymers 2016; 105:43-9. [PMID: 26202905 PMCID: PMC4623928 DOI: 10.1002/bip.22702] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 07/20/2015] [Indexed: 01/21/2023]
Abstract
Protein-ligand binding accompanies changes in the surrounding electrostatic environments of the two binding partners and may lead to changes in protonation upon binding. In cases where the complex formation results in a net transfer of protons, the binding process is pH-dependent. However, conventional free energy computations or molecular docking protocols typically employ fixed protonation states for the titratable groups in both binding partners set a priori, which are identical for the free and bound states. In this review, we draw attention to these important yet largely ignored binding-induced protonation changes in protein-ligand association by outlining physical origins and prevalence of the protonation changes upon binding. Following a summary of various theoretical methods for pKa prediction, we discuss the theoretical framework to examine the pH dependence of protein-ligand binding processes.
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Affiliation(s)
- M. Olivia Kim
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92093, USA
| | - J. Andrew McCammon
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92093, USA
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093, USA
- National Biomedical Computation Resource, University of California San Diego, La Jolla, CA 92093, USA
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16
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Cell-penetrating compounds preferentially bind glycosaminoglycans over plasma membrane lipids in a charge density- and stereochemistry-dependent manner. Biophys Chem 2015; 207:40-50. [DOI: 10.1016/j.bpc.2015.08.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 08/14/2015] [Accepted: 08/17/2015] [Indexed: 11/19/2022]
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17
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Abstract
We investigate the electrostatics, energetics, and dynamics of dendrimer-DNA interactions that mimic protein-DNA complexes as a means to design facilitated mechanisms by which dendrimers can slide and search DNA for targets. By using all-atom molecular dynamics simulations, we calculated the free energy profiles of dendrimer-binding around the DNA via umbrella sampling. We also calculated electrostatic interaction maps in comparison to proteins, as well as the dynamical changes induced by DNA-dendrimer interactions via NMR-measurable order parameters. Our results show that for dendrimers to go around DNA, there is a free-energy barrier of 8.5 kcal/mol from the DNA major groove to DNA minor groove, with a minimum in the major groove. This barrier height makes it unlikely for an all-amine dendrimer to slide along DNA longitudinally, but following a helical path may be possible along the major groove. Comparison of the nonbonded interaction energy and the interaction free-energy profiles reveal a considerable entropic cost as the dendrimer binds to DNA. This is also supported by the mobility patterns obtained from NMR-measurable order parameter values, which show a decreased mobility of the dendrimer N-H bond vectors in the DNA-binding mode.
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Affiliation(s)
- Emel Ficici
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Ioan Andricioaei
- Department of Chemistry, University of California, Irvine, California 92697, United States
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18
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Kim MO, Blachly PG, Kaus JW, McCammon JA. Protocols utilizing constant pH molecular dynamics to compute pH-dependent binding free energies. J Phys Chem B 2014; 119:861-72. [PMID: 25134690 PMCID: PMC4306499 DOI: 10.1021/jp505777n] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
![]()
In protein–ligand binding,
the electrostatic environments
of the two binding partners may vary significantly in bound and unbound
states, which may lead to protonation changes upon binding. In cases
where ligand binding results in a net uptake or release of protons,
the free energy of binding is pH-dependent. Nevertheless, conventional
free energy calculations and molecular docking protocols typically
do not rigorously account for changes in protonation that may occur
upon ligand binding. To address these shortcomings, we present a simple
methodology based on Wyman’s binding polynomial formalism to
account for the pH dependence of binding free energies and demonstrate
its use on cucurbit[7]uril (CB[7]) host–guest systems. Using
constant pH molecular dynamics and a reference binding free energy
that is taken either from experiment or from thermodynamic integration
computations, the pH-dependent binding free energy is determined.
This computational protocol accurately captures the large pKa shifts observed experimentally upon CB[7]:guest
association and reproduces experimental binding free energies at different
levels of pH. We show that incorrect assignment of fixed protonation
states in free energy computations can give errors of >2 kcal/mol
in these host–guest systems. Use of the methods presented here
avoids such errors, thus suggesting their utility in computing proton-linked
binding free energies for protein–ligand complexes.
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Affiliation(s)
- M Olivia Kim
- Department of Chemistry and Biochemistry, University of California San Diego , La Jolla, California 92093, United States
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19
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Robbins TJ, Ziebarth JD, Wang Y. Comparison of monovalent and divalent ion distributions around a DNA duplex with molecular dynamics simulation and a Poisson-Boltzmann approach. Biopolymers 2014; 101:834-48. [PMID: 24443090 PMCID: PMC4102171 DOI: 10.1002/bip.22461] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 11/22/2013] [Accepted: 01/15/2014] [Indexed: 12/15/2022]
Abstract
The ion atmosphere created by monovalent (Na(+) ) or divalent (Mg(2+) ) cations surrounding a B-form DNA duplex were examined using atomistic molecular dynamics (MD) simulations and the nonlinear Poisson-Boltzmann (PB) equation. The ion distributions predicted by the two methods were compared using plots of radial and two-dimensional cation concentrations and by calculating the total number of cations and net solution charge surrounding the DNA. Na(+) ion distributions near the DNA were more diffuse in PB calculations than in corresponding MD simulations, with PB calculations predicting lower concentrations near DNA groove sites and phosphate groups and a higher concentration in the region between these locations. Other than this difference, the Na(+) distributions generated by the two methods largely agreed, as both predicted similar locations of high Na(+) concentration and nearly identical values of the number of cations and the net solution charge at all distances from the DNA. In contrast, there was greater disagreement between the two methods for Mg(2+) cation concentration profiles, as both the locations and magnitudes of peaks in Mg(2+) concentration were different. Despite experimental and simulation observations that Mg(2+) typically maintains its first solvation shell when interacting with nucleic acids, modeling Mg(2+) as an unsolvated ion during PB calculations improved the agreement of the Mg(2+) ion atmosphere predicted by the two methods and allowed for values of the number of bound ions and net solution charge surrounding the DNA from PB calculations that approached the values observed in MD simulations.
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20
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Nakano M, Tateishi-Karimata H, Tanaka S, Sugimoto N. Affinity of Molecular Ions for DNA Structures Is Determined by Solvent-Accessible Surface Area. J Phys Chem B 2014; 118:9583-94. [DOI: 10.1021/jp505107g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
| | | | - Shigenori Tanaka
- Graduate
School of System Informatics, Department of Computational Science, Kobe University, 1-1, Rokkodai, Nada-ku, Kobe 657-8501, Japan
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21
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Miyoshi D, Ueda YM, Shimada N, Nakano SI, Sugimoto N, Maruyama A. Drastic stabilization of parallel DNA hybridizations by a polylysine comb-type copolymer with hydrophilic graft chain. ChemMedChem 2014; 9:2156-63. [PMID: 25045164 DOI: 10.1002/cmdc.201402157] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Indexed: 11/08/2022]
Abstract
Electrostatic interactions play a major role in protein-DNA interactions. As a model system of a cationic protein, herein we focused on a comb-type copolymer of a polycation backbone and dextran side chains, poly(L-lysine)-graft-dextran (PLL-g-Dex), which has been reported to form soluble interpolyelectrolyte complexes with DNA strands. We investigated the effects of PLL-g-Dex on the conformation and thermodynamics of DNA oligonucleotides forming various secondary structures. Thermodynamic analysis of the DNA structures showed that the parallel conformations involved in both DNA duplexes and triplexes were significantly and specifically stabilized by PLL-g-Dex. On the basis of thermodynamic parameters, it was further possible to design DNA switches that undergo structural transition responding to PLL-g-Dex from an antiparallel duplex to a parallel triplex even with mismatches in the third strand hybridization. These results suggest that polycationic molecules are able to induce structural polymorphism of DNA oligonucleotides, because of the conformation-selective stabilization effects.
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Affiliation(s)
- Daisuke Miyoshi
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047 (Japan).
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22
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Terakawa T, Takada S. RESPAC: Method to Determine Partial Charges in Coarse-Grained Protein Model and Its Application to DNA-Binding Proteins. J Chem Theory Comput 2014; 10:711-21. [DOI: 10.1021/ct4007162] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tsuyoshi Terakawa
- Department of Biophysics,
Graduate School of Science, Kyoto University, Kitashirakawa Owake-cho, Sakyo, Kyoto, 606-8501, Japan
| | - Shoji Takada
- Department of Biophysics,
Graduate School of Science, Kyoto University, Kitashirakawa Owake-cho, Sakyo, Kyoto, 606-8501, Japan
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23
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Gasbarri C, Angelini G. Spectroscopic investigation of fluorinated phenols as pH-sensitive probes in mixed liposomal systems. RSC Adv 2014. [DOI: 10.1039/c4ra01507j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The pKa values of three fluorinated phenols, 2,4,6-trifluorophenol (3FP), 2,3,5,6-tetrafluorophenol (4FP) and 2,3,4,5,6-pentafluorophenol (5FP) have been measured by using UV-vis and 19F-NMR spectroscopy at 25 °C in water and in the presence of pure POPC, pure DDAB and mixed POPC–DDAB liposomes.
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Affiliation(s)
- Carla Gasbarri
- Dipartimento di Farmacia
- Università G. d'Annunzio di Chieti-Pescara
- 66100 Chieti, Italy
| | - Guido Angelini
- Dipartimento di Farmacia
- Università G. d'Annunzio di Chieti-Pescara
- 66100 Chieti, Italy
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24
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Marcovitz A, Levy Y. Weak frustration regulates sliding and binding kinetics on rugged protein-DNA landscapes. J Phys Chem B 2013; 117:13005-14. [PMID: 23668488 DOI: 10.1021/jp402296d] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A fundamental step in gene-regulatory activities, such as repression, transcription, and recombination, is the binding of regulatory DNA-binding proteins (DBPs) to specific targets in the genome. To rapidly localize their regulatory genomic sites, DBPs reduce the dimensionality of the search space by combining three-dimensional (3D) diffusion in solution with one-dimensional (1D) sliding along DNA. However, the requirement to form a thermodynamically stable protein-DNA complex at the cognate genomic target sequence imposes a challenge on the protein because, as it navigates one-dimensionally along the genome, it may come in close contact with sites that share partial or even complete sequence similarity with the functional DNA sequence. This puzzling issue creates a conflict between two basic requirements: finding the cognate site quickly and stably binding it. Here, we structurally assessed the interface adopted by a variety of DBPs to bind DNA specifically and nonspecifically, and found that many DBPs utilize one interface to specifically recognize a DNA sequence and another to assist in propagating along the DNA through nonspecific associations. While these two interfaces overlap each other in some proteins, they present partial overlap in others and frustrate the protein-DNA interface. Using coarse-grained molecular dynamics simulations, we demonstrate that the existence of frustration in DBPs is a compromise between rapid 1D diffusion along other regions in the genome (high frustration smoothens the landscape for sliding) and rapid formation of a stable and essentially active protein-DNA complex (low frustration reduces the free energy barrier for switching between the two binding modes).
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Affiliation(s)
- Amir Marcovitz
- Department of Structural Biology, Weizmann Institute of Science , Rehovot, 76100, Israel
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25
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Abstract
Formation of protein-ligand complexes causes various changes in both the receptor and the ligand. This review focuses on changes in pK and protonation states of ionizable groups that accompany protein-ligand binding. Physical origins of these effects are outlined, followed by a brief overview of the computational methods to predict them and the associated corrections to receptor-ligand binding affinities. Statistical prevalence, magnitude and spatial distribution of the pK and protonation state changes in protein-ligand binding are discussed in detail, based on both experimental and theoretical studies. While there is no doubt that these changes occur, they do not occur all the time; the estimated prevalence varies, both between individual complexes and by method. The changes occur not only in the immediate vicinity of the interface but also sometimes far away. When receptor-ligand binding is associated with protonation state change at particular pH, the binding becomes pH dependent: we review the interplay between sub-cellular characteristic pH and optimum pH of receptor-ligand binding. It is pointed out that there is a tendency for protonation state changes upon binding to be minimal at physiologically relevant pH for each complex (no net proton uptake/release), suggesting that native receptor-ligand interactions have evolved to reduce the energy cost associated with ionization changes. As a result, previously reported statistical prevalence of these changes - typically computed at the same pH for all complexes - may be higher than what may be expected at optimum pH specific to each complex. We also discuss whether proper account of protonation state changes appears to improve practical docking and scoring outcomes relevant to structure-based drug design. An overview of some of the existing challenges in the field is provided in conclusion.
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Affiliation(s)
- Alexey V Onufriev
- Department of Computer Science and Physics, 2050 Torgersen Hall, Virginia Tech, Blacksburg, VA 24061, USA.
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26
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El Jarroudi M, Brillard A. Asymptotic analysis of the Poisson-Boltzmann equation in biological membrane channels. Math Biosci 2013; 243:46-56. [PMID: 23429183 DOI: 10.1016/j.mbs.2013.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 01/23/2013] [Accepted: 01/25/2013] [Indexed: 11/29/2022]
Abstract
The Poisson-Boltzmann equation has been increasingly used for the description of biomolecular systems in order to derive their electrostatic properties. We here consider a domain consisting of two living cells which communicate through a system of proteins which assemble at specific membrane areas building microchannels called gap junctions. We describe the asymptotic behavior of the solution of the Poisson-Boltzmann equation posed in this domain. Using Γ-convergence tools, we derive some electrostatic properties of the biological membrane with respect to a vanishing parameter which is simultaneously associated to the membrane thinness, to the diameter of the gap junction microchannels and to the Debye length parameter which characterizes the spatial scale electrostatic interactions between particles within the gap junctions.
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Affiliation(s)
- Mustapha El Jarroudi
- Université Abdelmalek Essadi, FST Tanger, Département de Mathématiques, BP 416 Tanger, Morocco
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27
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Spassov VZ, Yan L. pH-selective mutagenesis of protein-protein interfaces: in silico design of therapeutic antibodies with prolonged half-life. Proteins 2013; 81:704-14. [PMID: 23239118 PMCID: PMC3601434 DOI: 10.1002/prot.24230] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 11/13/2012] [Accepted: 11/28/2012] [Indexed: 11/09/2022]
Abstract
Understanding the effects of mutation on pH-dependent protein binding affinity is important in protein design, especially in the area of protein therapeutics. We propose a novel method for fast in silico mutagenesis of protein–protein complexes to calculate the effect of mutation as a function of pH. The free energy differences between the wild type and mutants are evaluated from a molecular mechanics model, combined with calculations of the equilibria of proton binding. The predicted pH-dependent energy profiles demonstrate excellent agreement with experimentally measured pH-dependency of the effect of mutations on the dissociation constants for the complex of turkey ovomucoid third domain (OMTKY3) and proteinase B. The virtual scanning mutagenesis identifies all hotspots responsible for pH-dependent binding of immunoglobulin G (IgG) to neonatal Fc receptor (FcRn) and the results support the current understanding of the salvage mechanism of the antibody by FcRn based on pH-selective binding. The method can be used to select mutations that change the pH-dependent binding profiles of proteins and guide the time consuming and expensive protein engineering experiments. As an application of this method, we propose a computational strategy to search for mutations that can alter the pH-dependent binding behavior of IgG to FcRn with the aim of improving the half-life of therapeutic antibodies in the target organism.
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Affiliation(s)
- Velin Z Spassov
- Accelrys, 10188 Telesis Court, San Diego, California 92121, USA.
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28
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Saito H, Iwayama M, Mizukami T, Kang J, Tateno M, Nagao H. Molecular dynamics study on binding free energy of Azurin–Cytochrome c551 complex. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2012.12.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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29
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Wang L, Zhang Z, Rocchia W, Alexov E. Using DelPhi capabilities to mimic protein's conformational reorganization with amino acid specific dielectric constants. COMMUNICATIONS IN COMPUTATIONAL PHYSICS 2013; 13:13-30. [PMID: 24683422 PMCID: PMC3966310 DOI: 10.4208/cicp.300611.120911s] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Many molecular events are associated with small or large conformational changes occurring in the corresponding proteins. Modeling such changes is a challenge and requires significant amount of computing time. From point of view of electrostatics, these changes can be viewed as a reorganization of local charges and dipoles in response to the changes of the electrostatic field, if the cause is insertion or deletion of a charged amino acid. Here we report a large scale investigation of modeling the changes of the folding energy due to single mutations involving charged group. This allows the changes of the folding energy to be considered mostly electrostatics in origin and to be calculated with DelPhi assigning residue-specific value of the internal dielectric constant of protein. The predicted energy changes are benchmarked against experimentally measured changes of the folding energy on a set of 257 single mutations. The best fit between experimental values and predicted changes is used to find out the effective value of the internal dielectric constant for each type of amino acid. The predicted folding free energy changes with the optimal, amino acid specific, dielectric constants are within RMSD=0.86 kcal/mol from experimentally measured changes.
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Affiliation(s)
- Lin Wang
- Computational Biophysics and bioinformatics, Department of Physics, Clemson University, Clemson, SC 29634, USA
| | - Zhe Zhang
- Computational Biophysics and bioinformatics, Department of Physics, Clemson University, Clemson, SC 29634, USA
| | | | - Emil Alexov
- Computational Biophysics and bioinformatics, Department of Physics, Clemson University, Clemson, SC 29634, USA
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30
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Osypov AA, Krutinin GG, Krutinina EA, Kamzolova SG. DEPPDB - DNA electrostatic potential properties database. Electrostatic properties of genome DNA elements. J Bioinform Comput Biol 2012; 10:1241004. [PMID: 22809340 DOI: 10.1142/s0219720012410041] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Electrostatic properties of genome DNA are important to its interactions with different proteins, in particular, related to transcription. DEPPDB - DNA Electrostatic Potential (and other Physical) Properties Database - provides information on the electrostatic and other physical properties of genome DNA combined with its sequence and annotation of biological and structural properties of genomes and their elements. Genomes are organized on taxonomical basis, supporting comparative and evolutionary studies. Currently, DEPPDB contains all completely sequenced bacterial, viral, mitochondrial, and plastids genomes according to the NCBI RefSeq, and some model eukaryotic genomes. Data for promoters, regulation sites, binding proteins, etc., are incorporated from established DBs and literature. The database is complemented by analytical tools. User sequences calculations are available. Case studies discovered electrostatics complementing DNA bending in E.coli plasmid BNT2 promoter functioning, possibly affecting host-environment metabolic switch. Transcription factors binding sites gravitate to high potential regions, confirming the electrostatics universal importance in protein-DNA interactions beyond the classical promoter-RNA polymerase recognition and regulation. Other genome elements, such as terminators, also show electrostatic peculiarities. Most intriguing are gene starts, exhibiting taxonomic correlations. The necessity of the genome electrostatic properties studies is discussed.
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Affiliation(s)
- Alexander A Osypov
- Laboratory of Mechanisms of the Cell Genome Functioning, Institute of Cell Biophysics RAS, Pushchino, 142290, Russia.
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31
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Huang Q, Herrmann A. Calculating pH-dependent free energy of proteins by using Monte Carlo protonation probabilities of ionizable residues. Protein Cell 2012; 3:230-8. [PMID: 22467263 DOI: 10.1007/s13238-012-2035-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 01/09/2012] [Indexed: 11/30/2022] Open
Abstract
Protein folding, stability, and function are usually influenced by pH. And free energy plays a fundamental role in analysis of such pH-dependent properties. Electrostatics-based theoretical framework using dielectric solvent continuum model and solving Poisson-Boltzmann equation numerically has been shown to be very successful in understanding the pH-dependent properties. However, in this approach the exact computation of pH-dependent free energy becomes impractical for proteins possessing more than several tens of ionizable sites (e.g. > 30), because exact evaluation of the partition function requires a summation over a vast number of possible protonation microstates. Here we present a method which computes the free energy using the average energy and the protonation probabilities of ionizable sites obtained by the well-established Monte Carlo sampling procedure. The key feature is to calculate the entropy by using the protonation probabilities. We used this method to examine a well-studied protein (lysozyme) and produced results which agree very well with the exact calculations. Applications to the optimum pH of maximal stability of proteins and protein-DNA interactions have also resulted in good agreement with experimental data. These examples recommend our method for application to the elucidation of the pH-dependent properties of proteins.
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Affiliation(s)
- Qiang Huang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China.
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32
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Frustration in protein-DNA binding influences conformational switching and target search kinetics. Proc Natl Acad Sci U S A 2011; 108:17957-62. [PMID: 22003125 DOI: 10.1073/pnas.1109594108] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Rapid recognition of DNA target sites involves facilitated diffusion through which alternative sites are searched on genomic DNA. A key mechanism facilitating the localization of the target by a DNA-binding protein (DBP) is one-dimensional diffusion (sliding) in which electrostatic forces attract the protein to the DNA. As the protein reaches its target DNA site, it switches from purely electrostatic binding to a specific set of interactions with the DNA bases that also involves hydrogen bonding and van der Waals forces. High overlap between the DBP patches used for nonspecific and specific interactions with DNA may enable an immediate transition between the two binding modes following target site localization. By contrast, an imperfect overlap may result in greater frustration between the two potentially competing binding modes and consequently slower switching between them. A structural analysis of 125 DBPs indicates frustration between the two binding modes that results in a large difference between the orientations of the protein to the DNA when it slides compared to when it specifically interacts with DNA. Coarse-grained molecular dynamics simulations of in silico designed peptides comprising the full range of frustrations between the two interfaces show slower transition from nonspecific to specific DNA binding as the overlap between the patches involved in the two binding modes decreases. The complex search kinetics may regulate the search by eliminating trapping of the protein in semispecific sites while sliding.
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33
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Yang SY, Yang XL, Yao LF, Wang HB, Sun CK. Effect of CpG methylation on DNA binding protein: molecular dynamics simulations of the homeodomain PITX2 bound to the methylated DNA. J Mol Graph Model 2011; 29:920-7. [PMID: 21498098 DOI: 10.1016/j.jmgm.2011.03.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Revised: 03/02/2011] [Accepted: 03/03/2011] [Indexed: 10/18/2022]
Abstract
A large number of studies have argued that aberrant CpG methylation is associated with some human cancers. One possible mechanism of the cancer caused by CpG methylation is the gene repression, which is a binding-inhibition of the sequence-specific transcription factors bound to specific DNA-binding sites. Exploring the effects of CpG methylation on the structure and the thermodynamic property of DNA-binding transcription factors will help to gain an insight into how CpG methylation affects the repression of gene transcription in cancer. We have performed molecular dynamics (MD) simulations and free energy calculations of the protein bound to the native or the methylated DNA, in which the solution structure of the K50-class homeodomain PITX2 bound to DNA was used as a template. The simulation results indicate that the methylated CpG located at the DNA major groove can enhance the protein-DNA interactions, and the residue side-chains near the methylated CpG pair appear to have an unusually high affinity with DNA. The structural analysis and calculated energy values demonstrate that the binding-induced structural changes were further encouraged as the CpG methylation upon the complexation. Moreover, the CpG methylation may reduce the unfavorable effect of the conformational entropy and increase the electrostatic contribution to the binding free energy of DNA-PITX2. The changes in specific binding sites and the excessive affinity between DNA and protein caused by the CpG methylation could affect the gene transcriptional activity.
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Affiliation(s)
- Si-Ya Yang
- School of Chemistry and Chemical Engineering, Qujing Normal University, Sanjiang Road, Qinig District, Qujing City 655011, Yunnan Province, PR China.
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34
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Khazanov N, Levy Y. Sliding of p53 along DNA Can Be Modulated by Its Oligomeric State and by Cross-Talks between Its Constituent Domains. J Mol Biol 2011; 408:335-55. [DOI: 10.1016/j.jmb.2011.01.059] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Revised: 01/24/2011] [Accepted: 01/29/2011] [Indexed: 12/21/2022]
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35
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Sabirianov RF, Rubinstein A, Namavar F. Enhanced initial protein adsorption on engineered nanostructured cubic zirconia. Phys Chem Chem Phys 2011; 13:6597-609. [DOI: 10.1039/c0cp02389b] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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36
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Cherstvy AG. Electrostatic interactions in biological DNA-related systems. Phys Chem Chem Phys 2011; 13:9942-68. [DOI: 10.1039/c0cp02796k] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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37
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Zhou P, Tian F, Ren Y, Shang Z. Systematic classification and analysis of themes in protein-DNA recognition. J Chem Inf Model 2010; 50:1476-88. [PMID: 20726602 DOI: 10.1021/ci100145d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Protein-DNA recognition plays a central role in the regulation of gene expression. With the rapidly increasing number of protein-DNA complex structures available at atomic resolution in recent years, a systematic, complete, and intuitive framework to clarify the intrinsic relationship between the global binding modes of these complexes is needed. In this work, we modified, extended, and applied previously defined RNA-recognition themes to describe protein-DNA recognition and used a protocol that incorporates automatic methods into manual inspection to plant a comprehensive classification tree for currently available high-quality protein-DNA structures. Further, a nonredundant (representative) data set consisting of 200 thematically diverse complexes was extracted from the leaves of the classification tree by using a locally sensitive interface comparison algorithm. On the basis of the representative data set, various physical and chemical properties associated with protein-DNA interactions were analyzed using empirical or semiempirical methods. We also examined the individual energetic components involved in protein-DNA interactions and highlighted the importance of conformational entropy, which has been almost completely ignored in previous studies of protein-DNA binding energy.
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Affiliation(s)
- Peng Zhou
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China, College of Bioengineering, Chongqing University, Chongqing 400044, China
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Vuzman D, Polonsky M, Levy Y. Facilitated DNA search by multidomain transcription factors: cross talk via a flexible linker. Biophys J 2010; 99:1202-11. [PMID: 20713004 DOI: 10.1016/j.bpj.2010.06.007] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Revised: 05/30/2010] [Accepted: 06/02/2010] [Indexed: 10/19/2022] Open
Abstract
More than 70% of eukaryotic proteins are composed of multiple domains. However, most studies of the search for DNA focus on individual protein domains and do not consider potential cross talk within a multidomain transcription factor. In this study, the molecular features of the DNA search mechanism were explored for two multidomain transcription factors: human Pax6 and Oct-1. Using a simple computational model, we compared a DNA search of multidomain proteins with a search of isolated domains. Furthermore, we studied how manipulating the binding affinity of a single domain to DNA can affect the overall DNA search of the multidomain protein. Tethering the two domains via a flexible linker increases their affinity to the DNA, resulting in a higher propensity for sliding along the DNA, which is more significant for the domain with the weaker DNA-binding affinity. In this case, the domain that binds DNA more tightly anchors the multidomain protein to the DNA and, via the linker, increases the local concentration of the weak DNA-binding domain (DBD). The tethered domains directly exchange between two parallel DNA molecules via a bridged intermediate, where intersegmental transfer is promoted by the weaker DBD. We found that, in general, the relative affinity of the two domains can significantly affect the cross talk between them and thus their overall capability to search DNA efficiently. The results we obtained by examining various multidomain DNA-binding proteins support the necessity of discrepancies between the DNA-binding affinities of the constituent domains.
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Affiliation(s)
- Dana Vuzman
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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Privalov PL, Dragan AI, Crane-Robinson C. Interpreting protein/DNA interactions: distinguishing specific from non-specific and electrostatic from non-electrostatic components. Nucleic Acids Res 2010; 39:2483-91. [PMID: 21071403 PMCID: PMC3074165 DOI: 10.1093/nar/gkq984] [Citation(s) in RCA: 162] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
We discuss the effectiveness of existing methods for understanding the forces driving the formation of specific protein-DNA complexes. Theoretical approaches using the Poisson-Boltzmann (PB) equation to analyse interactions between these highly charged macromolecules to form known structures are contrasted with an empirical approach that analyses the effects of salt on the stability of these complexes and assumes that release of counter-ions associated with the free DNA plays the dominant role in their formation. According to this counter-ion condensation (CC) concept, the salt-dependent part of the Gibbs energy of binding, which is defined as the electrostatic component, is fully entropic and its dependence on the salt concentration represents the number of ionic contacts present in the complex. It is shown that although this electrostatic component provides the majority of the Gibbs energy of complex formation and does not depend on the DNA sequence, the salt-independent part of the Gibbs energy--usually regarded as non-electrostatic--is sequence specific. The CC approach thus has considerable practical value for studying protein/DNA complexes, while practical applications of PB analysis have yet to demonstrate their merit.
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Affiliation(s)
- Peter L Privalov
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
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Saito H, Matubayasi N, Nishikawa K, Nagao H. Hydration property of globular proteins: An analysis of solvation free energy by energy representation method. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.08.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Rubinstein A, Sabirianov RF, Mei WN, Namavar F, Khoynezhad A. Effect of the ordered interfacial water layer in protein complex formation: A nonlocal electrostatic approach. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 82:021915. [PMID: 20866845 DOI: 10.1103/physreve.82.021915] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Indexed: 05/29/2023]
Abstract
Using a nonlocal electrostatic approach that incorporates the short-range structure of the contacting media, we evaluated the electrostatic contribution to the energy of the complex formation of two model proteins. In this study, we have demonstrated that the existence of an ordered interfacial water layer at the protein-solvent interface reduces the charging energy of the proteins in the aqueous solvent, and consequently increases the electrostatic contribution to the protein binding (change in free energy upon the complex formation of two proteins). This is in contrast with the finding of the continuum electrostatic model, which suggests that electrostatic interactions are not strong enough to compensate for the unfavorable desolvation effects.
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Affiliation(s)
- A Rubinstein
- Department of Biomedical Sciences and Surgery, Creighton University Medical Center, Omaha, Nebraska 68131, USA.
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Osypov AA, Krutinin GG, Kamzolova SG. Deppdb--DNA electrostatic potential properties database: electrostatic properties of genome DNA. J Bioinform Comput Biol 2010; 8:413-25. [PMID: 20556853 DOI: 10.1142/s0219720010004811] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Revised: 01/28/2010] [Accepted: 02/12/2010] [Indexed: 11/18/2022]
Abstract
The electrostatic properties of genome DNA influence its interactions with different proteins, in particular, the regulation of transcription by RNA-polymerases. DEPPDB--DNA Electrostatic Potential Properties Database--was developed to hold and provide all available information on the electrostatic properties of genome DNA combined with its sequence and annotation of biological and structural properties of genome elements and whole genomes. Genomes in DEPPDB are organized on a taxonomical basis. Currently, the database contains all the completely sequenced bacterial and viral genomes according to NCBI RefSeq. General properties of the genome DNA electrostatic potential profile and principles of its formation are revealed. This potential correlates with the GC content but does not correspond to it exactly and strongly depends on both the sequence arrangement and its context (flanking regions). Analysis of the promoter regions for bacterial and viral RNA polymerases revealed a correspondence between the scale of these proteins' physical properties and electrostatic profile patterns. We also discovered a direct correlation between the potential value and the binding frequency of RNA polymerase to DNA, supporting the idea of the role of electrostatics in these interactions. This matches a pronounced tendency of the promoter regions to possess higher values of the electrostatic potential.
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Affiliation(s)
- Alexander A Osypov
- Laboratory of Mechanisms of the Cell Genome Functioning, Institute of Cell Biophysics RAS, Pushchino 142290, Russia.
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Xie F, Briggs JM, Dupureur CM. Nucleophile activation in PD...(D/E)xK metallonucleases: an experimental and computational pK(a) study. J Inorg Biochem 2010; 104:665-72. [PMID: 20347155 PMCID: PMC2913505 DOI: 10.1016/j.jinorgbio.2010.02.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Revised: 02/03/2010] [Accepted: 02/26/2010] [Indexed: 10/19/2022]
Abstract
Metallonucleases conduct metal-dependent nucleic acid hydrolysis. While metal ions serve in multiple mechanistic capacities in these enzymes, precisely how the attacking water is activated remains unclear for those lacking an obvious general base. All arguments hinge on appropriate pK(a)s for active site moieties very close to this species, and measurement of the pK(a) of a specific water molecule is difficult to access experimentally. Here we describe a computational approach for exploring the local electrostatic influences on the water-derived nucleophile in metallonucleases featuring the common PD...(D/E)xK motif. We utilized UHBD to predict the pK(a)s of active site groups, including that of a water molecule positioned to act as a nucleophile. The pK(a) of a Mg(II)-ligated water molecule hydrogen bonded to the conserved Lys70 in a Mg(II)-PvuII enzyme complex was calculated to be 6.5. The metal and the charge on the Lys group were removed in separate experiments; both resulted in the elevation of the pK(a) of this water molecule, consistent with contributions from both moieties to lowering this pK(a). This behavior is preserved among other PD...(D/E)xK metallonucleases. pK(a)s extracted from the pH dependence of the single turnover rate constant are compared to previous experimental data and the above predicted pK(a)s.
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Sotres J, Baró A. AFM imaging and analysis of electrostatic double layer forces on single DNA molecules. Biophys J 2010; 98:1995-2004. [PMID: 20441764 PMCID: PMC2862200 DOI: 10.1016/j.bpj.2009.12.4330] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Revised: 12/16/2009] [Accepted: 12/21/2009] [Indexed: 11/29/2022] Open
Abstract
Electrical double layer (EDL) forces develop between charged surfaces immersed in an electrolyte solution. Biological material surrounded by its physiological medium constitutes a case where these forces play a major role. Specifically, this work is focused on the study of the EDL force exerted by DNA molecules, a standard reference for the study of single biomolecules of nanometer size. The molecules deposited on plane substrates have been characterized by means of the atomic force microscope operated in the force spectroscopy imaging mode. Force spectroscopy imaging provides images of the topography of the DNA molecules, and of the EDL force spectrum. Due to the size of the molecule being much smaller than that of the tip, both the tip-substrate and tip-molecule interactions need to be considered in the analysis of the experimental results. We solve this problem by linearly superposing the two contributions. EDL force images are presented where DNA molecules are clearly resolved. The lateral resolution of the EDL force is discussed and compared with that of the topography. The method also allows the estimation of the DNA surface charge density, thereby obtaining reasonable values.
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Affiliation(s)
| | - A.M. Baró
- Instituto de Ciencia de Materiales de Madrid (Consejo Superior de Investigaciones Científicas), Madrid, Spain
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Michael LA, Chenault JA, Miller BR, Knolhoff AM, Nagan MC. Water, Shape Recognition, Salt Bridges, and Cation–Pi Interactions Differentiate Peptide Recognition of the HIV Rev-Responsive Element. J Mol Biol 2009; 392:774-86. [DOI: 10.1016/j.jmb.2009.07.047] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2009] [Revised: 07/06/2009] [Accepted: 07/16/2009] [Indexed: 10/20/2022]
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Blose JM, Proctor DJ, Veeraraghavan N, Misra VK, Bevilacqua PC. Contribution of the closing base pair to exceptional stability in RNA tetraloops: roles for molecular mimicry and electrostatic factors. J Am Chem Soc 2009; 131:8474-84. [PMID: 19476351 DOI: 10.1021/ja900065e] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hairpins are common RNA secondary structures that play multiple roles in nature. Tetraloops are the most frequent RNA hairpin loops and are often phylogenetically conserved. For both the UNCG and GNRA families, CG closing base pairs (cbps) confer exceptional thermodynamic stability but the molecular basis for this has remained unclear. We propose that, despite having very different overall folds, these two tetraloop families achieve stability by presenting the same functionalities to the major groove edge of the CG cbp. Thermodynamic contributions of this molecular mimicry were investigated using substitutions at the nucleobase and functional group levels. By either interrupting or deleting loop-cbp electrostatic interactions, which were identified by solving the nonlinear Poisson-Boltzmann (NLPB) equation, stability changed in a manner consistent with molecular mimicry. We also observed a linear relationship between DeltaG(o)(37) and log[Na(+)] for both families, and loops with a CG cbp had a decreased dependence of stability on salt. NLPB calculations revealed that, for both UUCG and GAAA tetraloops, the GC cbp form has a higher surface charge density, although it arises from changes in loop compaction for UUCG and changes in loop configuration for GAAA. Higher surface charge density leads to stronger interactions of GC cbp loops with solvent and salt, which explains the correlation between experimental and calculated trends of free energy with salt. Molecular mimicry as evidenced in these two stable but otherwise unrelated tetraloops may underlie common functional roles in other RNA and DNA motifs.
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Affiliation(s)
- Joshua M Blose
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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Ma PL, Lavertu M, Winnik FM, Buschmann MD. New Insights into Chitosan−DNA Interactions Using Isothermal Titration Microcalorimetry. Biomacromolecules 2009; 10:1490-9. [DOI: 10.1021/bm900097s] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Pei Lian Ma
- Department of Chemical and Biomedical Engineering, Ecole Polytechnique de Montréal, P.O. 6079 Succ. Centre-Ville, Montreal, Quebec, H3C 3A7, Canada, and Department of Chemistry and Faculty of Pharmacy, Université de Montréal, P.O. 6128 Succ. Centre-Ville, Montreal, Quebec, H3C 3J7, Canada
| | - Marc Lavertu
- Department of Chemical and Biomedical Engineering, Ecole Polytechnique de Montréal, P.O. 6079 Succ. Centre-Ville, Montreal, Quebec, H3C 3A7, Canada, and Department of Chemistry and Faculty of Pharmacy, Université de Montréal, P.O. 6128 Succ. Centre-Ville, Montreal, Quebec, H3C 3J7, Canada
| | - Françoise M. Winnik
- Department of Chemical and Biomedical Engineering, Ecole Polytechnique de Montréal, P.O. 6079 Succ. Centre-Ville, Montreal, Quebec, H3C 3A7, Canada, and Department of Chemistry and Faculty of Pharmacy, Université de Montréal, P.O. 6128 Succ. Centre-Ville, Montreal, Quebec, H3C 3J7, Canada
| | - Michael D. Buschmann
- Department of Chemical and Biomedical Engineering, Ecole Polytechnique de Montréal, P.O. 6079 Succ. Centre-Ville, Montreal, Quebec, H3C 3A7, Canada, and Department of Chemistry and Faculty of Pharmacy, Université de Montréal, P.O. 6128 Succ. Centre-Ville, Montreal, Quebec, H3C 3J7, Canada
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Chen C, Krause K, Pettitt BM. Advantage of being a dimer for Serratia marcescens endonuclease. J Phys Chem B 2009; 113:511-21. [PMID: 19053714 DOI: 10.1021/jp8057838] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The monomer and dimer of the bacterium Serratia marcescens endonuclease (SMnase) are each catalytically active, and the two subunits of the dimer function independently of each other. Nature, however, chooses the dimer form instead of the monomer. In order to explain this, we performed molecular dynamics (MD) simulations of both model-built complexes of a subunit of SMnase and the dimer with DNA in aqueous solution. We estimated the electrostatic binding energy, analyzed the distribution and dynamics of water around the complexes, identified water clusters in the protein, and related the dynamics of water to the protein's function. We find that the dimer form has an electrostatic advantage over the monomer to associate with DNA. Although Mg(2+) remains hexa-coordinated during the simulation, the binding pathway of DNA to Mg(2+) changes from inner-sphere binding in the monomer to outer-sphere in the dimer, which may be more energetically favorable. In addition, two water clusters in the active site of each monomer and in the dimer complex were identified and localized in two regions, named the "stabilizing" and "working" regions. Water in the "working" region in the dimer complex has larger fluctuations than that in the monomer.
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Affiliation(s)
- Chuanying Chen
- Department of Chemistry, University of Houston, Houston, Texas 77204-5003, USA
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49
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Protein Sliding along DNA: Dynamics and Structural Characterization. J Mol Biol 2009; 385:1087-97. [DOI: 10.1016/j.jmb.2008.11.016] [Citation(s) in RCA: 170] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2008] [Revised: 10/07/2008] [Accepted: 11/11/2008] [Indexed: 10/21/2022]
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50
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Abstract
Described here are several computational procedures for the analysis of electrostatic interactions in molecular complexes, all based on a continuum model of solvation. The first section describes how to compute the residual potential, a measure of how electrostatically complementary a ligand is for its receptor. The second procedure describes electrostatic component analysis, a method by which the electrostatic contribution to the binding free energy can be broken up into terms directly attributable to individual chemical groups. Finally, electrostatic affinity optimization is described. This procedure is particularly useful in determining what portions of a ligand are the most suboptimal, and thus provide the greatest opportunity for the design of improvements.
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Affiliation(s)
- David F Green
- Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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