1
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van Heesch T, Bolhuis PG, Vreede J. Decoding dissociation of sequence-specific protein-DNA complexes with non-equilibrium simulations. Nucleic Acids Res 2023; 51:12150-12160. [PMID: 37953329 PMCID: PMC10711434 DOI: 10.1093/nar/gkad1014] [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] [Received: 02/27/2023] [Revised: 10/13/2023] [Accepted: 10/19/2023] [Indexed: 11/14/2023] Open
Abstract
Sequence-specific protein-DNA interactions are crucial in processes such as DNA organization, gene regulation and DNA replication. Obtaining detailed insights into the recognition mechanisms of protein-DNA complexes through experiments is hampered by a lack of resolution in both space and time. Here, we present a molecular simulation approach to quantify the sequence specificity of protein-DNA complexes, that yields results fast, and is generally applicable to any protein-DNA complex. The approach is based on molecular dynamics simulations in combination with a sophisticated steering potential and results in an estimate of the free energy difference of dissociation. We provide predictions of the nucleotide specific binding affinity of the minor groove binding Histone-like Nucleoid Structuring (H-NS) protein, that are in agreement with experimental data. Furthermore, our approach offers mechanistic insight into the process of dissociation. Applying our approach to the major groove binding ETS domain in complex with three different nucleotide sequences identified the high affinity consensus sequence, quantitatively in agreement with experiments. Our protocol facilitates quantitative prediction of protein-DNA complex stability, while also providing high resolution insights into recognition mechanisms. As such, our simulation approach has the potential to yield detailed and quantitative insights into biological processes involving sequence-specific protein-DNA interactions.
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Affiliation(s)
- Thor van Heesch
- Van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, Netherlands
| | - Peter G Bolhuis
- Van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, Netherlands
| | - Jocelyne Vreede
- Van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, Netherlands
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2
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Popov AV, Endutkin AV, Yatsenko DD, Yudkina AV, Barmatov AE, Makasheva KA, Raspopova DY, Diatlova EA, Zharkov DO. Molecular dynamics approach to identification of new OGG1 cancer-associated somatic variants with impaired activity. J Biol Chem 2021; 296:100229. [PMID: 33361155 PMCID: PMC7948927 DOI: 10.1074/jbc.ra120.014455] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 01/02/2023] Open
Abstract
DNA of living cells is always exposed to damaging factors. To counteract the consequences of DNA lesions, cells have evolved several DNA repair systems, among which base excision repair is one of the most important systems. Many currently used antitumor drugs act by damaging DNA, and DNA repair often interferes with chemotherapy and radiotherapy in cancer cells. Tumors are usually extremely genetically heterogeneous, often bearing mutations in DNA repair genes. Thus, knowledge of the functionality of cancer-related variants of proteins involved in DNA damage response and repair is of great interest for personalization of cancer therapy. Although computational methods to predict the variant functionality have attracted much attention, at present, they are mostly based on sequence conservation and make little use of modern capabilities in computational analysis of 3D protein structures. We have used molecular dynamics (MD) to model the structures of 20 clinically observed variants of a DNA repair enzyme, 8-oxoguanine DNA glycosylase. In parallel, we have experimentally characterized the activity, thermostability, and DNA binding in a subset of these mutant proteins. Among the analyzed variants of 8-oxoguanine DNA glycosylase, three (I145M, G202C, and V267M) were significantly functionally impaired and were successfully predicted by MD. Alone or in combination with sequence-based methods, MD may be an important functional prediction tool for cancer-related protein variants of unknown significance.
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Affiliation(s)
- Aleksandr V Popov
- Laboratory of Genome and Protein Engineering, SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia.
| | - Anton V Endutkin
- Laboratory of Genome and Protein Engineering, SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Darya D Yatsenko
- Laboratory of Genome and Protein Engineering, SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia; Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Anna V Yudkina
- Laboratory of Genome and Protein Engineering, SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Alexander E Barmatov
- Laboratory of Genome and Protein Engineering, SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Kristina A Makasheva
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Darya Yu Raspopova
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Evgeniia A Diatlova
- Laboratory of Genome and Protein Engineering, SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Dmitry O Zharkov
- Laboratory of Genome and Protein Engineering, SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia; Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia.
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3
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Long P, Zhang L, Huang B, Chen Q, Liu H. Integrating genome sequence and structural data for statistical learning to predict transcription factor binding sites. Nucleic Acids Res 2020; 48:12604-12617. [PMID: 33264415 PMCID: PMC7736823 DOI: 10.1093/nar/gkaa1134] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/18/2020] [Accepted: 11/10/2020] [Indexed: 01/11/2023] Open
Abstract
We report an approach to predict DNA specificity of the tetracycline repressor (TetR) family transcription regulators (TFRs). First, a genome sequence-based method was streamlined with quantitative P-values defined to filter out reliable predictions. Then, a framework was introduced to incorporate structural data and to train a statistical energy function to score the pairing between TFR and TFR binding site (TFBS) based on sequences. The predictions benchmarked against experiments, TFBSs for 29 out of 30 TFRs were correctly predicted by either the genome sequence-based or the statistical energy-based method. Using P-values or Z-scores as indicators, we estimate that 59.6% of TFRs are covered with relatively reliable predictions by at least one of the two methods, while only 28.7% are covered by the genome sequence-based method alone. Our approach predicts a large number of new TFBs which cannot be correctly retrieved from public databases such as FootprintDB. High-throughput experimental assays suggest that the statistical energy can model the TFBSs of a significant number of TFRs reliably. Thus the energy function may be applied to explore for new TFBSs in respective genomes. It is possible to extend our approach to other transcriptional factor families with sufficient structural information.
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Affiliation(s)
- Pengpeng Long
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Lu Zhang
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Bin Huang
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Quan Chen
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
- Hefei National Laboratory for Physical Sciences at the Microscale, Hefei, Anhui 230026, China
| | - Haiyan Liu
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
- Hefei National Laboratory for Physical Sciences at the Microscale, Hefei, Anhui 230026, China
- School of Data Science, University of Science and Technology of China, Hefei, Anhui 230026, China
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4
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Abstract
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Molecular association of proteins with nucleic
acids is required
for many biological processes essential to life. Electrostatic interactions
via ion pairs (salt bridges) of nucleic acid phosphates and protein
side chains are crucial for proteins to bind to DNA or RNA. Counterions
around the macromolecules are also key constituents for the thermodynamics
of protein–nucleic acid association. Until recently, there
had been only a limited amount of experiment-based information about
how ions and ionic moieties behave in biological macromolecular processes.
In the past decade, there has been significant progress in quantitative
experimental research on ionic interactions with nucleic acids and
their complexes with proteins. The highly negatively charged surfaces
of DNA and RNA electrostatically attract and condense cations, creating
a zone called the ion atmosphere. Recent experimental studies were
able to examine and validate theoretical models on ions and their
mobility and interactions with macromolecules. The ionic interactions
are highly dynamic. The counterions rapidly diffuse within the ion
atmosphere. Some of the ions are released from the ion atmosphere
when proteins bind to nucleic acids, balancing the charge via intermolecular
ion pairs of positively charged side chains and negatively charged
backbone phosphates. Previously, the release of counterions had been
implicated indirectly by the salt-concentration dependence of the
association constant. Recently, direct detection of counterion
release by NMR spectroscopy
has become possible and enabled more accurate and quantitative analysis
of the counterion release and its entropic impact on the thermodynamics
of protein–nucleic acid association. Recent studies also revealed
the dynamic nature of ion pairs of protein side chains and nucleic
acid phosphates. These ion pairs undergo transitions between two major
states. In one of the major states, the cation and the anion are in
direct contact and form hydrogen bonds. In the other major state,
the cation and the anion are separated by water. Transitions between
these states rapidly occur on a picosecond to nanosecond time scale.
When proteins interact with nucleic acids, interfacial arginine (Arg)
and lysine (Lys) side chains exhibit considerably different behaviors.
Arg side chains show a higher propensity to form rigid contacts with
nucleotide bases, whereas Lys side chains tend to be more mobile at
the molecular interfaces. The dynamic ionic interactions may facilitate
adaptive molecular recognition and play both thermodynamic and kinetic
roles in protein–nucleic acid interactions.
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Affiliation(s)
- Binhan Yu
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, United States
| | - B. Montgomery Pettitt
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, United States
| | - Junji Iwahara
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, United States
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5
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Gapsys V, de Groot BL. Alchemical Free Energy Calculations for Nucleotide Mutations in Protein–DNA Complexes. J Chem Theory Comput 2017; 13:6275-6289. [DOI: 10.1021/acs.jctc.7b00849] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Vytautas Gapsys
- Computational Biomolecular
Dynamics Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Bert L. de Groot
- Computational Biomolecular
Dynamics Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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6
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Farrel A, Murphy J, Guo JT. Structure-based prediction of transcription factor binding specificity using an integrative energy function. Bioinformatics 2017; 32:i306-i313. [PMID: 27307632 PMCID: PMC4908348 DOI: 10.1093/bioinformatics/btw264] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
UNLABELLED Transcription factors (TFs) regulate gene expression through binding to specific target DNA sites. Accurate annotation of transcription factor binding sites (TFBSs) at genome scale represents an essential step toward our understanding of gene regulation networks. In this article, we present a structure-based method for computational prediction of TFBSs using a novel, integrative energy (IE) function. The new energy function combines a multibody (MB) knowledge-based potential and two atomic energy terms (hydrogen bond and π interaction) that might not be accurately captured by the knowledge-based potential owing to the mean force nature and low count problem. We applied the new energy function to the TFBS prediction using a non-redundant dataset that consists of TFs from 12 different families. Our results show that the new IE function improves the prediction accuracy over the knowledge-based, statistical potentials, especially for homeodomain TFs, the second largest TF family in mammals. CONTACT jguo4@uncc.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Alvin Farrel
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Jonathan Murphy
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Jun-Tao Guo
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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7
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Farrel A, Guo JT. An efficient algorithm for improving structure-based prediction of transcription factor binding sites. BMC Bioinformatics 2017; 18:342. [PMID: 28715997 PMCID: PMC5514533 DOI: 10.1186/s12859-017-1755-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Accepted: 07/12/2017] [Indexed: 01/07/2023] Open
Abstract
Background Gene expression is regulated by transcription factors binding to specific target DNA sites. Understanding how and where transcription factors bind at genome scale represents an essential step toward our understanding of gene regulation networks. Previously we developed a structure-based method for prediction of transcription factor binding sites using an integrative energy function that combines a knowledge-based multibody potential and two atomic energy terms. While the method performs well, it is not computationally efficient due to the exponential increase in the number of binding sequences to be evaluated for longer binding sites. In this paper, we present an efficient pentamer algorithm by splitting DNA binding sequences into overlapping fragments along with a simplified integrative energy function for transcription factor binding site prediction. Results A DNA binding sequence is split into overlapping pentamers (5 base pairs) for calculating transcription factor-pentamer interaction energy. To combine the results from overlapping pentamer scores, we developed two methods, Kmer-Sum and PWM (Position Weight Matrix) stacking, for full-length binding motif prediction. Our results show that both Kmer-Sum and PWM stacking in the new pentamer approach along with a simplified integrative energy function improved transcription factor binding site prediction accuracy and dramatically reduced computation time, especially for longer binding sites. Conclusion Our new fragment-based pentamer algorithm and simplified energy function improve both efficiency and accuracy. To our knowledge, this is the first fragment-based method for structure-based transcription factor binding sites prediction. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1755-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alvin Farrel
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223, USA
| | - Jun-Tao Guo
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223, USA.
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8
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Andrabi M, Hutchins AP, Miranda-Saavedra D, Kono H, Nussinov R, Mizuguchi K, Ahmad S. Predicting conformational ensembles and genome-wide transcription factor binding sites from DNA sequences. Sci Rep 2017; 7:4071. [PMID: 28642456 PMCID: PMC5481346 DOI: 10.1038/s41598-017-03199-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 04/26/2017] [Indexed: 12/24/2022] Open
Abstract
DNA shape is emerging as an important determinant of transcription factor binding beyond just the DNA sequence. The only tool for large scale DNA shape estimates, DNAshape was derived from Monte-Carlo simulations and predicts four broad and static DNA shape features, Propeller twist, Helical twist, Minor groove width and Roll. The contributions of other shape features e.g. Shift, Slide and Opening cannot be evaluated using DNAshape. Here, we report a novel method DynaSeq, which predicts molecular dynamics-derived ensembles of a more exhaustive set of DNA shape features. We compared the DNAshape and DynaSeq predictions for the common features and applied both to predict the genome-wide binding sites of 1312 TFs available from protein interaction quantification (PIQ) data. The results indicate a good agreement between the two methods for the common shape features and point to advantages in using DynaSeq. Predictive models employing ensembles from individual conformational parameters revealed that base-pair opening - known to be important in strand separation - was the best predictor of transcription factor-binding sites (TFBS) followed by features employed by DNAshape. Of note, TFBS could be predicted not only from the features at the target motif sites, but also from those as far as 200 nucleotides away from the motif.
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Affiliation(s)
- Munazah Andrabi
- National Institutes of Biomedical Innovation Health and Nutrition, 7-6-8, Saito-Asagi, Ibaraki, Osaka, 5670085, Japan
- Faculty of Biology,Medicine and Health, Michael Smith Building, The University of Manchester, Dover Street, Manchester, M13 9PT, UK
| | - Andrew Paul Hutchins
- Department of Biology, Southern University of Science and Technology of China, Shenzhen, 518055, China
| | - Diego Miranda-Saavedra
- World Premier International (WPI) Immunology Frontier Research Center (IFReC), Osaka University, 3-1 Yamadaoka, Suita, 565-0871, Osaka, Japan
- Centro de Biología Molecular Severo Ochoa, CSIC/Universidad Autónoma de Madrid, 28049, Madrid, Spain
- Department of Computer Science, University of Oxford Wolfson Building, Parks Road, OXFORD, OX1 3QD, United Kingdom
| | - Hidetoshi Kono
- Molecular Modeling and Simulation (MMS) Group, National Institutes for Quantum and Radiological Science and Technology, 8-1-7, Umemidai, Kizugawa, Kyoto, 619-0215, Japan
| | - Ruth Nussinov
- National Cancer Institute, Cancer and Inflammation Program, Leidos Biomedical Research, Inc. Frederick, Maryland, USA
- Department of Biochemistry and Human Genetics, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Kenji Mizuguchi
- National Institutes of Biomedical Innovation Health and Nutrition, 7-6-8, Saito-Asagi, Ibaraki, Osaka, 5670085, Japan
| | - Shandar Ahmad
- National Institutes of Biomedical Innovation Health and Nutrition, 7-6-8, Saito-Asagi, Ibaraki, Osaka, 5670085, Japan.
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi, 110067, India.
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9
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Khabiri M, Freddolino PL. Deficiencies in Molecular Dynamics Simulation-Based Prediction of Protein-DNA Binding Free Energy Landscapes. J Phys Chem B 2017; 121:5151-5161. [PMID: 28471184 PMCID: PMC5817055 DOI: 10.1021/acs.jpcb.6b12450] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Transcriptional regulation allows cells to match their gene expression profiles to their current requirements based on environment, cellular physiological state, and extracellular signals. DNA binding transcription factors are major agents of transcriptional regulation, and bind to DNA with a factor-specific sequence preference to exert regulatory effects. A crucial step in unraveling the logic of a regulatory network is determining the sequence-specific binding affinity landscapes for the transcription factors in it. While such landscapes can be measured experimentally, the ability to predict them computationally would both reduce the effort required to obtain the needed data and provide additional insight into the key interactions shaping protein-DNA interactions. Here we apply free energy calculations based on all-atom molecular dynamics simulations to predict the changes in binding free energy for all single base pair perturbations of the binding sites for four eukaryotic transcription factors for which high-quality experimental data exist. We find that the simulated results both vastly overestimate the magnitude of changes in binding free energy, and frequently predict the incorrect signs. These simulations will nevertheless serve as a jumping-off point for refining our current representation of protein-DNA interactions to allow quantitative reproduction of experimental data on such systems in the future.
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Affiliation(s)
- Morteza Khabiri
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI USA
| | - Peter L. Freddolino
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI USA
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10
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Jankowsky E, Harris ME. Mapping specificity landscapes of RNA-protein interactions by high throughput sequencing. Methods 2017; 118-119:111-118. [PMID: 28263887 DOI: 10.1016/j.ymeth.2017.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 02/07/2017] [Accepted: 03/01/2017] [Indexed: 12/28/2022] Open
Abstract
To function in a biological setting, RNA binding proteins (RBPs) have to discriminate between alternative binding sites in RNAs. This discrimination can occur in the ground state of an RNA-protein binding reaction, in its transition state, or in both. The extent by which RBPs discriminate at these reaction states defines RBP specificity landscapes. Here, we describe the HiTS-Kin and HiTS-EQ techniques, which combine kinetic and equilibrium binding experiments with high throughput sequencing to quantitatively assess substrate discrimination for large numbers of substrate variants at ground and transition states of RNA-protein binding reactions. We discuss experimental design, practical considerations and data analysis and outline how a combination of HiTS-Kin and HiTS-EQ allows the mapping of RBP specificity landscapes.
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Affiliation(s)
- Eckhard Jankowsky
- Center for RNA Molecular Biology, School of Medicine, Case Western Reserve University, 1099 Euclid Ave Cleveland, OH 44106, United States; Department of Biochemistry, School of Medicine, Case Western Reserve University, 1099 Euclid Ave Cleveland, OH 44106, United States.
| | - Michael E Harris
- Department of Biochemistry, School of Medicine, Case Western Reserve University, 1099 Euclid Ave Cleveland, OH 44106, United States
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11
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Qin W, Zhao G, Carson M, Jia C, Lu H. Knowledge-based three-body potential for transcription factor binding site prediction. IET Syst Biol 2016; 10:23-9. [PMID: 26816396 DOI: 10.1049/iet-syb.2014.0066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
A structure-based statistical potential is developed for transcription factor binding site (TFBS) prediction. Besides the direct contact between amino acids from TFs and DNA bases, the authors also considered the influence of the neighbouring base. This three-body potential showed better discriminate powers than the two-body potential. They validate the performance of the potential in TFBS identification, binding energy prediction and binding mutation prediction.
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Affiliation(s)
- Wenyi Qin
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
| | - Guijun Zhao
- Key Laboratory of Molecular Embryology, Ministry of Health & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai 200040, People's Republic of China
| | - Matthew Carson
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
| | - Caiyan Jia
- School of Computer and Information Technology & Beijing Key Lab of Traffic Data Analysis, Beijing Jiaotong University, Beijing, People's Republic of China
| | - Hui Lu
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA.
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12
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AlQuraishi M, Tang S, Xia X. An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system. BMC Bioinformatics 2015; 16:390. [PMID: 26586237 PMCID: PMC4653904 DOI: 10.1186/s12859-015-0819-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 11/11/2015] [Indexed: 11/28/2022] Open
Abstract
Background Molecular interactions between proteins and DNA molecules underlie many cellular processes, including transcriptional regulation, chromosome replication, and nucleosome positioning. Computational analyses of protein-DNA interactions rely on experimental data characterizing known protein-DNA interactions structurally and biochemically. While many databases exist that contain either structural or biochemical data, few integrate these two data sources in a unified fashion. Such integration is becoming increasingly critical with the rapid growth of structural and biochemical data, and the emergence of algorithms that rely on the synthesis of multiple data types to derive computational models of molecular interactions. Description We have developed an integrated affinity-structure database in which the experimental and quantitative DNA binding affinities of helix-turn-helix proteins are mapped onto the crystal structures of the corresponding protein-DNA complexes. This database provides access to: (i) protein-DNA structures, (ii) quantitative summaries of protein-DNA binding affinities using position weight matrices, and (iii) raw experimental data of protein-DNA binding instances. Critically, this database establishes a correspondence between experimental structural data and quantitative binding affinity data at the single basepair level. Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical environments at the interface between complexes. Using this unified coordinate system, we compute the statistics of atomic interactions at the protein-DNA interface of helix-turn-helix proteins. We provide an interactive website for visualization, querying, and analyzing this database, and a downloadable version to facilitate programmatic analysis. Conclusions This database will facilitate the analysis of protein-DNA interactions and the development of programmatic computational methods that capitalize on integration of structural and biochemical datasets. The database can be accessed at http://ProteinDNA.hms.harvard.edu.
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Affiliation(s)
- Mohammed AlQuraishi
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA. .,HMS Laboratory of Systems Pharmacology, Harvard Medical School, 200 Longwood Avenue, Boston, MA, 02115, USA.
| | - Shengdong Tang
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.,HMS Laboratory of Systems Pharmacology, Harvard Medical School, 200 Longwood Avenue, Boston, MA, 02115, USA
| | - Xide Xia
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.,HMS Laboratory of Systems Pharmacology, Harvard Medical School, 200 Longwood Avenue, Boston, MA, 02115, USA
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13
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Abstract
To fully understand the regulation of gene expression, it is critical to quantitatively define whether and how RNA-binding proteins (RBPs) discriminate between alternative binding sites in RNAs. Here, we describe new methods that measure protein binding to large numbers of RNA variants, and ways to analyse and interpret data obtained by these approaches, including affinity distributions and free energy landscapes. We discuss how the new methodologies and the associated concepts enable the development of inclusive, quantitative models for RNA-protein interactions that transcend the traditional binary classification of RBPs as either specific or nonspecific.
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14
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Hennig J, Sattler M. Deciphering the protein-RNA recognition code: Combining large-scale quantitative methods with structural biology. Bioessays 2015; 37:899-908. [DOI: 10.1002/bies.201500033] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Janosch Hennig
- Institute of Structural Biology; Helmholtz Zentrum M; ü; nchen; München Germany
- Department Chemie; Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy; Technische Universität München; Garching Germany
| | - Michael Sattler
- Institute of Structural Biology; Helmholtz Zentrum M; ü; nchen; München Germany
- Department Chemie; Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy; Technische Universität München; Garching Germany
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15
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Yan J, Friedrich S, Kurgan L. A comprehensive comparative review of sequence-based predictors of DNA- and RNA-binding residues. Brief Bioinform 2015; 17:88-105. [DOI: 10.1093/bib/bbv023] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Indexed: 01/07/2023] Open
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16
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Quantitative modeling of transcription factor binding specificities using DNA shape. Proc Natl Acad Sci U S A 2015; 112:4654-9. [PMID: 25775564 DOI: 10.1073/pnas.1422023112] [Citation(s) in RCA: 161] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
DNA binding specificities of transcription factors (TFs) are a key component of gene regulatory processes. Underlying mechanisms that explain the highly specific binding of TFs to their genomic target sites are poorly understood. A better understanding of TF-DNA binding requires the ability to quantitatively model TF binding to accessible DNA as its basic step, before additional in vivo components can be considered. Traditionally, these models were built based on nucleotide sequence. Here, we integrated 3D DNA shape information derived with a high-throughput approach into the modeling of TF binding specificities. Using support vector regression, we trained quantitative models of TF binding specificity based on protein binding microarray (PBM) data for 68 mammalian TFs. The evaluation of our models included cross-validation on specific PBM array designs, testing across different PBM array designs, and using PBM-trained models to predict relative binding affinities derived from in vitro selection combined with deep sequencing (SELEX-seq). Our results showed that shape-augmented models compared favorably to sequence-based models. Although both k-mer and DNA shape features can encode interdependencies between nucleotide positions of the binding site, using DNA shape features reduced the dimensionality of the feature space. In addition, analyzing the feature weights of DNA shape-augmented models uncovered TF family-specific structural readout mechanisms that were not revealed by the DNA sequence. As such, this work combines knowledge from structural biology and genomics, and suggests a new path toward understanding TF binding and genome function.
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Samant M, Jethva M, Hasija Y. INTERACT-O-FINDER: A Tool for Prediction of DNA-Binding Proteins Using Sequence Features. Int J Pept Res Ther 2014. [DOI: 10.1007/s10989-014-9446-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Pujato M, Kieken F, Skiles AA, Tapinos N, Fiser A. Prediction of DNA binding motifs from 3D models of transcription factors; identifying TLX3 regulated genes. Nucleic Acids Res 2014; 42:13500-12. [PMID: 25428367 PMCID: PMC4267649 DOI: 10.1093/nar/gku1228] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Proper cell functioning depends on the precise spatio-temporal expression of its genetic material. Gene expression is controlled to a great extent by sequence-specific transcription factors (TFs). Our current knowledge on where and how TFs bind and associate to regulate gene expression is incomplete. A structure-based computational algorithm (TF2DNA) is developed to identify binding specificities of TFs. The method constructs homology models of TFs bound to DNA and assesses the relative binding affinity for all possible DNA sequences using a knowledge-based potential, after optimization in a molecular mechanics force field. TF2DNA predictions were benchmarked against experimentally determined binding motifs. Success rates range from 45% to 81% and primarily depend on the sequence identity of aligned target sequences and template structures, TF2DNA was used to predict 1321 motifs for 1825 putative human TF proteins, facilitating the reconstruction of most of the human gene regulatory network. As an illustration, the predicted DNA binding site for the poorly characterized T-cell leukemia homeobox 3 (TLX3) TF was confirmed with gel shift assay experiments. TLX3 motif searches in human promoter regions identified a group of genes enriched in functions relating to hematopoiesis, tissue morphology, endocrine system and connective tissue development and function.
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Affiliation(s)
- Mario Pujato
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - Fabien Kieken
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA Macromolecular Therapeutics Development, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - Amanda A Skiles
- Molecular Neuroscience Laboratory, Geisinger Clinic, 100 North Academy Avenue, Danville, PA 17822, USA
| | - Nikos Tapinos
- Molecular Neuroscience Laboratory, Geisinger Clinic, 100 North Academy Avenue, Danville, PA 17822, USA
| | - Andras Fiser
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
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Slattery M, Zhou T, Yang L, Dantas Machado AC, Gordân R, Rohs R. Absence of a simple code: how transcription factors read the genome. Trends Biochem Sci 2014; 39:381-99. [PMID: 25129887 DOI: 10.1016/j.tibs.2014.07.002] [Citation(s) in RCA: 337] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/11/2014] [Accepted: 07/15/2014] [Indexed: 12/21/2022]
Abstract
Transcription factors (TFs) influence cell fate by interpreting the regulatory DNA within a genome. TFs recognize DNA in a specific manner; the mechanisms underlying this specificity have been identified for many TFs based on 3D structures of protein-DNA complexes. More recently, structural views have been complemented with data from high-throughput in vitro and in vivo explorations of the DNA-binding preferences of many TFs. Together, these approaches have greatly expanded our understanding of TF-DNA interactions. However, the mechanisms by which TFs select in vivo binding sites and alter gene expression remain unclear. Recent work has highlighted the many variables that influence TF-DNA binding, while demonstrating that a biophysical understanding of these many factors will be central to understanding TF function.
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Affiliation(s)
- Matthew Slattery
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812, USA; Developmental Biology Center, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Tianyin Zhou
- Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Lin Yang
- Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Ana Carolina Dantas Machado
- Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Raluca Gordân
- Center for Genomic and Computational Biology, Departments of Biostatistics and Bioinformatics, Computer Science, and Molecular Genetics and Microbiology, Duke University, Durham, NC 27708, USA.
| | - Remo Rohs
- Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA.
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Thomas CJ, Kotova E, Andrake M, Adolf-Bryfogle J, Glaser R, Regnard C, Tulin AV. Kinase-mediated changes in nucleosome conformation trigger chromatin decondensation via poly(ADP-ribosyl)ation. Mol Cell 2014; 53:831-42. [PMID: 24508391 DOI: 10.1016/j.molcel.2014.01.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 10/28/2013] [Accepted: 01/02/2014] [Indexed: 10/25/2022]
Abstract
Dynamically controlled posttranslational modifications of nucleosomal histones alter chromatin condensation to regulate transcriptional activation. We report that a nuclear tandem kinase, JIL-1, controls gene expression by activating poly(ADP-ribose) polymerase-1 (PARP-1). JIL-1 phosphorylates the C terminus of the H2Av histone variant, which stimulates PARP-1 enzymatic activity in the surrounding chromatin, leading to further modification of histones and chromatin loosening. The H2Av nucleosome has a higher surface representation of PARP-1 binding patch, consisting of H3 and H4 epitopes. Phosphorylation of H2Av by JIL-1 restructures this surface patch, leading to activation of PARP-1. Exposure of Val61 and Leu23 of the H4 histone is critical for PARP-1 binding on nucleosome and PARP-1 activation following H2Av phosphorylation. We propose that chromatin loosening and associated initiation of gene expression is activated by phosphorylation of H2Av in a nucleosome positioned in promoter regions of PARP-1-dependent genes.
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Affiliation(s)
- Colin J Thomas
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | - Elena Kotova
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | - Mark Andrake
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | | | - Robert Glaser
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA
| | - Catherine Regnard
- Adolf Butenandt Institute, Ludwig Maximilian University, Schillerstrasse 44, 80336 Munich, Germany
| | - Alexei V Tulin
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA.
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Sequence based prediction of DNA-binding proteins based on hybrid feature selection using random forest and Gaussian naïve Bayes. PLoS One 2014; 9:e86703. [PMID: 24475169 PMCID: PMC3901691 DOI: 10.1371/journal.pone.0086703] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Accepted: 12/10/2013] [Indexed: 11/22/2022] Open
Abstract
Developing an efficient method for determination of the DNA-binding proteins, due to their vital roles in gene regulation, is becoming highly desired since it would be invaluable to advance our understanding of protein functions. In this study, we proposed a new method for the prediction of the DNA-binding proteins, by performing the feature rank using random forest and the wrapper-based feature selection using forward best-first search strategy. The features comprise information from primary sequence, predicted secondary structure, predicted relative solvent accessibility, and position specific scoring matrix. The proposed method, called DBPPred, used Gaussian naïve Bayes as the underlying classifier since it outperformed five other classifiers, including decision tree, logistic regression, k-nearest neighbor, support vector machine with polynomial kernel, and support vector machine with radial basis function. As a result, the proposed DBPPred yields the highest average accuracy of 0.791 and average MCC of 0.583 according to the five-fold cross validation with ten runs on the training benchmark dataset PDB594. Subsequently, blind tests on the independent dataset PDB186 by the proposed model trained on the entire PDB594 dataset and by other five existing methods (including iDNA-Prot, DNA-Prot, DNAbinder, DNABIND and DBD-Threader) were performed, resulting in that the proposed DBPPred yielded the highest accuracy of 0.769, MCC of 0.538, and AUC of 0.790. The independent tests performed by the proposed DBPPred on completely a large non-DNA binding protein dataset and two RNA binding protein datasets also showed improved or comparable quality when compared with the relevant prediction methods. Moreover, we observed that majority of the selected features by the proposed method are statistically significantly different between the mean feature values of the DNA-binding and the non DNA-binding proteins. All of the experimental results indicate that the proposed DBPPred can be an alternative perspective predictor for large-scale determination of DNA-binding proteins.
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Dršata T, Kara M, Zacharias M, Lankaš F. Effect of 8-oxoguanine on DNA structure and deformability. J Phys Chem B 2013; 117:11617-22. [PMID: 24028561 DOI: 10.1021/jp407562t] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
8-Oxoguanine (oxoG) is an abundant product of oxidative DNA damage. It is removed by repair glycosylases, but exactly how the enzymes recognize oxoG in the large surplus of undamaged bases is not fully understood. The lesion may induce changes in the properties of naked DNA that facilitate the recognition. In this work, we assess the effect of oxoG on DNA structure and mechanical deformability. We performed extensive unrestrained, atomic resolution molecular dynamics simulations to parametrize a nonlocal, rigid base mechanical model of DNA. Our data indicate that oxoG induces unwinding of the base pair step at the 5'-side of the lesion. This brings the damaged DNA closer to its conformation in the initial complex with bacterial glycosylase MutM. The untwisting is partially caused by different BII substate populations and is further enhanced by the base-sugar repulsion within oxoG. On the other hand, our analysis shows that damaged and undamaged DNA have very similar harmonic stiffness. These results suggest an indirect readout component of the MutM-DNA initial complex formation. They also help one to understand the effect of oxoG on the formation of nucleosomes and looped gene regulatory complexes.
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Affiliation(s)
- Tomáš Dršata
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo náměstı́ 2, 166 10, Praha 6, Czech Republic
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Affiliation(s)
- Robert O J Weinzierl
- Department of Life Sciences, Division of Biomolecular Sciences, Imperial College London , Sir Alexander Fleming Building, Exhibition Road, London SW7 2AZ, United Kingdom
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Abstract
The physiological properties of biological soft matter are the product of collective interactions, which span many time and length scales. Recent computational modeling efforts have helped illuminate experiments that characterize the ways in which proteins modulate membrane physics. Linking these models across time and length scales in a multiscale model explains how atomistic information propagates to larger scales. This paper reviews continuum modeling and coarse-grained molecular dynamics methods, which connect atomistic simulations and single-molecule experiments with the observed microscopic or mesoscale properties of soft-matter systems essential to our understanding of cells, particularly those involved in sculpting and remodeling cell membranes.
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Affiliation(s)
- Ryan Bradley
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ravi Radhakrishnan
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
- Author to whom correspondence should be addressed; ; Tel.: +1-215-898-0487; Fax: +1-215-573-2071
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25
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Banavali NK. Partial base flipping is sufficient for strand slippage near DNA duplex termini. J Am Chem Soc 2013; 135:8274-82. [PMID: 23692220 DOI: 10.1021/ja401573j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Strand slippage is a structural mechanism by which insertion-deletion (indel) mutations are introduced during replication by polymerases. Three-dimensional atomic-resolution structural pathways are still not known for the decades-old template slippage description. The dynamic nature of the process and the higher energy intermediates involved increase the difficulty of studying these processes experimentally. In the present study, restrained and unrestrained molecular dynamics simulations, carried out using multiple nucleic acid force fields, are used to demonstrate that partial base-flipping can be sufficient for strand slippage at DNA duplex termini. Such strand slippage can occur in either strand, i.e. near either the 3' or the 5' terminus of a DNA strand, which suggests that similar structural flipping mechanisms can cause both primer and template slippage. In the repetitive mutation hot-spot sequence studied, non-canonical base-pairing with exposed DNA groove atoms of a neighboring G:C base-pair stabilizes a partially flipped state of the cytosine. For its base-pair partner guanine, a similar partially flipped metastable intermediate was not detected, and the propensity for sustained slippage was also found to be lower. This illustrates that a relatively small metastable DNA structural distortion in polymerase active sites could allow single base insertion or deletion mutations to occur, and stringent DNA groove molecular recognition may be required to maintain intrinsic DNA polymerase fidelity. The implications of a close relationship between base-pair dissociation, base unstacking, and strand slippage are discussed in the context of sequence dependence of indel mutations.
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Affiliation(s)
- Nilesh K Banavali
- Laboratory of Computational and Structural Biology, Division of Genetics, Wadsworth Center, New York State Department of Health , and Department of Biomedical Sciences, School of Public Health, State University of New York at Albany , CMS 2008, 150 New Scotland Avenue, Albany, New York 12208, United States
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van Dijk M, Visscher KM, Kastritis PL, Bonvin AMJJ. Solvated protein-DNA docking using HADDOCK. JOURNAL OF BIOMOLECULAR NMR 2013; 56:51-63. [PMID: 23625455 DOI: 10.1007/s10858-013-9734-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 04/20/2013] [Indexed: 06/02/2023]
Abstract
Interfacial water molecules play an important role in many aspects of protein-DNA specificity and recognition. Yet they have been mostly neglected in the computational modeling of these complexes. We present here a solvated docking protocol that allows explicit inclusion of water molecules in the docking of protein-DNA complexes and demonstrate its feasibility on a benchmark of 30 high-resolution protein-DNA complexes containing crystallographically-determined water molecules at their interfaces. Our protocol is capable of reproducing the solvation pattern at the interface and recovers hydrogen-bonded water-mediated contacts in many of the benchmark cases. Solvated docking leads to an overall improvement in the quality of the generated protein-DNA models for cases with limited conformational change of the partners upon complex formation. The applicability of this approach is demonstrated on real cases by docking a representative set of 6 complexes using unbound protein coordinates, model-built DNA and knowledge-based restraints. As HADDOCK supports the inclusion of a variety of NMR restraints, solvated docking is also applicable for NMR-based structure calculations of protein-DNA complexes.
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Affiliation(s)
- Marc van Dijk
- Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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27
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Li S, Bradley P. Probing the role of interfacial waters in protein-DNA recognition using a hybrid implicit/explicit solvation model. Proteins 2013; 81:1318-29. [PMID: 23444044 DOI: 10.1002/prot.24272] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 02/06/2013] [Indexed: 01/30/2023]
Abstract
When proteins bind to their DNA target sites, ordered water molecules are often present at the protein-DNA interface bridging protein and DNA through hydrogen bonds. What is the role of these ordered interfacial waters? Are they important determinants of the specificity of DNA sequence recognition, or do they act in binding in a primarily nonspecific manner, by improving packing of the interface, shielding unfavorable electrostatic interactions, and solvating unsatisfied polar groups that are inaccessible to bulk solvent? When modeling details of structure and binding preferences, can fully implicit solvent models be fruitfully applied to protein-DNA interfaces, or must the individualistic properties of these interfacial waters be accounted for? To address these questions, we have developed a hybrid implicit/explicit solvation model that specifically accounts for the locations and orientations of small numbers of DNA-bound water molecules, while treating the majority of the solvent implicitly. Comparing the performance of this model with that of its fully implicit counterpart, we find that explicit treatment of interfacial waters results in a modest but significant improvement in protein side-chain placement and DNA sequence recovery. Base-by-base comparison of the performance of the two models highlights DNA sequence positions whose recognition may be dependent on interfacial water. Our study offers large-scale statistical evidence for the role of ordered water for protein-DNA recognition, together with detailed examination of several well-characterized systems. In addition, our approach provides a template for modeling explicit water molecules at interfaces that should be extensible to other systems.
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Affiliation(s)
- Shen Li
- Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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