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Agosta F, Cozzini P. A Combined Molecular Dynamics and Hydropathic INTeraction (HINT) Approach to Investigate Protein Flexibility: The PPARγ Case Study. Molecules 2024; 29:2234. [PMID: 38792097 PMCID: PMC11124508 DOI: 10.3390/molecules29102234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 05/03/2024] [Accepted: 05/05/2024] [Indexed: 05/26/2024] Open
Abstract
Molecular Dynamics (MD) is a computational technique widely used to evaluate a molecular system's thermodynamic properties and conformational behavior over time. In particular, the energy analysis of a protein conformation ensemble produced though MD simulations plays a crucial role in explaining the relationship between protein dynamics and its mechanism of action. In this research work, the HINT (Hydropathic INTeractions) LogP-based scoring function was first used to handle MD trajectories and investigate the molecular basis behind the intricate PPARγ mechanism of activation. The Peroxisome Proliferator-Activated Receptor γ (PPARγ) is an emblematic example of a highly flexible protein due to the extended ω-loop delimiting the active site, and it is responsible for the receptor's ability to bind chemically different compounds. In this work, we focused on the PPARγ complex with Rosiglitazone, a common anti-diabetic compound and analyzed the molecular basis of the flexible ω-loop stabilization effect produced by the Oleic Acid co-binding. The HINT-based analysis of the produced MD trajectories allowed us to account for all of the energetic contributions involved in interconverting between conformational states and describe the intramolecular interactions between the flexible ω-loop and the helix H3 triggered by the allosteric binding mechanism.
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Affiliation(s)
| | - Pietro Cozzini
- Molecular Modelling Lab, Food and Drug Department, University of Parma, Parco Area delle Scienze, 17/A, 43121 Parma, Italy;
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2
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Kellogg GE, Marabotti A, Spyrakis F, Mozzarelli A. HINT, a code for understanding the interaction between biomolecules: a tribute to Donald J. Abraham. Front Mol Biosci 2023; 10:1194962. [PMID: 37351551 PMCID: PMC10282649 DOI: 10.3389/fmolb.2023.1194962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 05/24/2023] [Indexed: 06/24/2023] Open
Abstract
A long-lasting goal of computational biochemists, medicinal chemists, and structural biologists has been the development of tools capable of deciphering the molecule-molecule interaction code that produces a rich variety of complex biomolecular assemblies comprised of the many different simple and biological molecules of life: water, small metabolites, cofactors, substrates, proteins, DNAs, and RNAs. Software applications that can mimic the interactions amongst all of these species, taking account of the laws of thermodynamics, would help gain information for understanding qualitatively and quantitatively key determinants contributing to the energetics of the bimolecular recognition process. This, in turn, would allow the design of novel compounds that might bind at the intermolecular interface by either preventing or reinforcing the recognition. HINT, hydropathic interaction, was a model and software code developed from a deceptively simple idea of Donald Abraham with the close collaboration with Glen Kellogg at Virginia Commonwealth University. HINT is based on a function that scores atom-atom interaction using LogP, the partition coefficient of any molecule between two phases; here, the solvents are water that mimics the cytoplasm milieu and octanol that mimics the protein internal hydropathic environment. This review summarizes the results of the extensive and successful collaboration between Abraham and Kellogg at VCU and the group at the University of Parma for testing HINT in a variety of different biomolecular interactions, from proteins with ligands to proteins with DNA.
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Affiliation(s)
- Glen E. Kellogg
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, United States
| | - Anna Marabotti
- Department of Chemistry and Biology “A Zambelli”, University of Salerno, Fisciano (SA), Italy
| | - Francesca Spyrakis
- Department of Drug Science and Technology, University of Turin, Turin, Italy
| | - Andrea Mozzarelli
- Department of Food and Drug, University of Parma and Institute of Biophysics, Parma, Italy
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3
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The role of zinc finger linkers in zinc finger protein binding to DNA. J Comput Aided Mol Des 2021; 35:973-986. [PMID: 34350488 DOI: 10.1007/s10822-021-00413-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 07/26/2021] [Indexed: 10/20/2022]
Abstract
Zinc finger proteins (ZFP) play important roles in cellular processes. The DNA binding region of ZFP consists of 3 zinc finger DNA binding domains connected by amino acid linkers, the sequence TGQKP connects ZF1 and ZF2, and TGEKP connects ZF2 with ZF3. Linkers act to tune the zinc finger protein in the right position to bind its DNA target, the type of amino acid residues and length of linkers reflect on ZF1-ZF2-ZF3 interactions and contribute to the search and recognition process of ZF protein to its DNA target. Linker mutations and the affinity of the resulting mutants to specific and nonspecific DNA targets were studied by MD simulations and MM_GB(PB)SA. The affinity of mutants to DNA varied with type and position of amino acid residue. Mutation of K in TGQKP resulted in loss in affinity due to the loss of positive K interaction with phosphates, mutation of G showed loss in affinity to DNA, WT protein and all linker mutants showed loss in affinity to a nonspecific DNA target, this finding confirms previous reports which interpreted this loss in affinity as due to ZF1 having an anchoring role, and ZF3 playing an explorer role in the binding mechanism. The change in ZFP-DNA affinity with linker mutations is discussed in view of protein structure and role of linker residues in binding.
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4
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Corbella M, Liao Q, Moreira C, Parracino A, Kasson PM, Kamerlin SCL. The N-terminal Helix-Turn-Helix Motif of Transcription Factors MarA and Rob Drives DNA Recognition. J Phys Chem B 2021; 125:6791-6806. [PMID: 34137249 PMCID: PMC8279559 DOI: 10.1021/acs.jpcb.1c00771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
DNA-binding proteins
play an important role in gene regulation
and cellular function. The transcription factors MarA and Rob are
two homologous members of the AraC/XylS family that regulate multidrug
resistance. They share a common DNA-binding domain, and Rob possesses
an additional C-terminal domain that permits binding of low-molecular
weight effectors. Both proteins possess two helix-turn-helix (HTH)
motifs capable of binding DNA; however, while MarA interacts with
its promoter through both HTH-motifs, prior studies indicate that
Rob binding to DNA via a single HTH-motif is sufficient for tight
binding. In the present work, we perform microsecond time scale all-atom
simulations of the binding of both transcription factors to different
DNA sequences to understand the determinants of DNA recognition and
binding. Our simulations characterize sequence-dependent changes in
dynamical behavior upon DNA binding, showcasing the role of Arg40
of the N-terminal HTH-motif in allowing for specific tight binding.
Finally, our simulations demonstrate that an acidic C-terminal loop
of Rob can control the DNA binding mode, facilitating interconversion
between the distinct DNA binding modes observed in MarA and Rob. In
doing so, we provide detailed molecular insight into DNA binding and
recognition by these proteins, which in turn is an important step
toward the efficient design of antivirulence agents that target these
proteins.
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Affiliation(s)
- Marina Corbella
- Science for Life Laboratory, Department of Chemistry-BMC, Uppsala University, Uppsala, S-751 23, Sweden
| | - Qinghua Liao
- Science for Life Laboratory, Department of Chemistry-BMC, Uppsala University, Uppsala, S-751 23, Sweden
| | - Cátia Moreira
- Science for Life Laboratory, Department of Chemistry-BMC, Uppsala University, Uppsala, S-751 23, Sweden
| | - Antonietta Parracino
- Science for Life Laboratory, Department of Chemistry-BMC, Uppsala University, Uppsala, S-751 23, Sweden
| | - Peter M Kasson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, S-65124, Sweden.,Departments of Molecular Physiology and Biomedical Engineering, University of Virginia, Charlottesville, Virginia 22908, United States
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5
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Rational Design of a User-Friendly Aptamer/Peptide-Based Device for the Detection of Staphylococcus aureus. SENSORS 2020; 20:s20174977. [PMID: 32887407 PMCID: PMC7506613 DOI: 10.3390/s20174977] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/29/2020] [Accepted: 08/30/2020] [Indexed: 02/07/2023]
Abstract
The urgent need to develop a detection system for Staphylococcus aureus, one of the most common causes of infection, is prompting research towards novel approaches and devices, with a particular focus on point-of-care analysis. Biosensors are promising systems to achieve this aim. We coupled the selectivity and affinity of aptamers, short nucleic acids sequences able to recognize specific epitopes on bacterial surface, immobilized at high density on a nanostructured zirconium dioxide surface, with the rational design of specifically interacting fluorescent peptides to assemble an easy-to-use detection device. We show that the displacement of fluorescent peptides upon the competitive binding of S. aureus to immobilized aptamers can be detected and quantified through fluorescence loss. This approach could be also applied to the detection of other bacterial species once aptamers interacting with specific antigens will be identified, allowing the development of a platform for easy detection of a pathogen without requiring access to a healthcare environment.
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6
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Emamjomeh A, Choobineh D, Hajieghrari B, MahdiNezhad N, Khodavirdipour A. DNA-protein interaction: identification, prediction and data analysis. Mol Biol Rep 2019; 46:3571-3596. [PMID: 30915687 DOI: 10.1007/s11033-019-04763-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 03/14/2019] [Indexed: 12/30/2022]
Abstract
Life in living organisms is dependent on specific and purposeful interaction between other molecules. Such purposeful interactions make the various processes inside the cells and the bodies of living organisms possible. DNA-protein interactions, among all the types of interactions between different molecules, are of considerable importance. Currently, with the development of numerous experimental techniques, diverse methods are convenient for recognition and investigating such interactions. While the traditional experimental techniques to identify DNA-protein complexes are time-consuming and are unsuitable for genome-scale studies, the current high throughput approaches are more efficient in determining such interaction at a large-scale, but they are clearly too costly to be practice for daily applications. Hence, according to the availability of much information related to different biological sequences and clearing different dimensions of conditions in which such interactions are formed, with the developments related to the computer, mathematics, and statistics motivate scientists to develop bioinformatics tools for prediction the interaction site(s). Until now, there has been much progress in this field. In this review, the factors and conditions governing the interaction and the laboratory techniques for examining such interactions are addressed. In addition, developed bioinformatics tools are introduced and compared for this reason and, in the end, several suggestions are offered for the promotion of such tools in prediction with much more precision.
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Affiliation(s)
- Abbasali Emamjomeh
- Laboratory of Computational Biotechnology and Bioinformatics (CBB), Department of Plant Breeding and Biotechnology (PBB), University of Zabol, Zabol, 98615-538, Iran.
| | - Darush Choobineh
- Agricultural Biotechnology, Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran
| | - Behzad Hajieghrari
- Department of Agricultural Biotechnology, College of Agriculture, Jahrom University, Jahrom, 74135-111, Iran.
| | - Nafiseh MahdiNezhad
- Laboratory of Computational Biotechnology and Bioinformatics (CBB), Department of Plant Breeding and Biotechnology (PBB), University of Zabol, Zabol, 98615-538, Iran
| | - Amir Khodavirdipour
- Division of Human Genetics, Department of Anatomy, St. John's hospital, Bangalore, India
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7
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Synthesis and characterization of Ag+-decorated poly(glycidyl methacrylate) microparticle design for the adsorption of nucleic acids. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1081-1082:1-7. [DOI: 10.1016/j.jchromb.2018.02.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 02/05/2018] [Accepted: 02/15/2018] [Indexed: 11/18/2022]
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8
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Güette-Fernández JR, Meléndez E, Maldonado-Rojas W, Ortega-Zúñiga C, Olivero-Verbel J, Parés-Matos EI. A molecular docking study of the interactions between human transferrin and seven metallocene dichlorides. J Mol Graph Model 2017; 75:250-265. [PMID: 28609757 DOI: 10.1016/j.jmgm.2017.05.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Revised: 05/08/2017] [Accepted: 05/09/2017] [Indexed: 02/08/2023]
Abstract
Human Transferrin (hTf) is a metal-binding protein found in blood plasma and is well known for its role in iron delivery. With only a 30% of its capacity for Fe+3 binding, this protein has the potential ability to transport other metal ions or organometallic compounds from the blood stream to all cell tissues. In this perspective, recent studies have described seven metallocene dichlorides (Cp2M(IV)Cl2, M(IV)=V, Mo, W, Nb, Ti, Zr, Hf) suitable as anticancer drugs and less secondary effects than cisplatin. However, these studies have not provided enough data to clearly explain how hTf binds and transports these organometallic compounds into the cells. Thus, a computational docking study with native apo-hTf using Sybyl-X 2.0 program was conducted to explore the binding modes of these seven Cp2M(IV)Cl2 after their optimization and minimization using Gaussian 09. Our model showed that the first three Cp2M(IV)Cl2 (M(IV)=V, Mo, W) can interact with apo-hTf on a common binding site with the amino acid residues Leu-46, Ile-49, Arg-50, Leu-66, Asp-69, Ala-70, Leu-72, Ala-73, Pro-74 and Asn-75, while the next four Cp2M(IV)Cl2 (M(IV)=Nb, Ti, Zr, Hf) showed different binding sites, unknown until now. A decreasing order in the total score (equal to -log Kd) was observed from these docking studies: W (5.4356), Mo (5.2692), Nb (5.1672), V (4.5973), Ti (3.6529), Zr (2.0054) and Hf (1.8811). High and significant correlation between the affinity of these seven ligands (metallocenes) for apo-hTf and their bond angles CpMCp (r=0.94, p<0.01) and Cl-M-Cl (r=0.95, p<0.01) were observed, thus indicating the important role that these bond angles can play in ligand-protein interactions. Fluorescence spectra of apo-hTf, measured at pH 7.4, had a decrease in the fluorescence emission spectrum with increasing concentration of Cp2M(IV)Cl2. Experimental data has a good correlation between KA (r=0.84, p=0.027) and Kd (r=0.94, p=0.0014) values and the calculated total scores obtained from our docking experiments. In conclusion, these results suggest that the seven Cp2M(IV)Cl2 used for this study can interact with apo-hTf, and their affinity was directly and inversely proportional to their bond angles CpMCp and ClMCl, respectively. Our docking studies also suggest that the binding of the first three Cp2M(IV)Cl2 (M(IV)=V, Mo, W) to hTf could abrogate the formation of the hTf-receptor complex, and as a consequence the metallocene-hTf complex might require another transport mechanism in order to get into the cell.
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Affiliation(s)
- Jorge R Güette-Fernández
- Department of Chemistry at Mayagüez, University of Puerto Rico, Mayagüez, PR 00681; Environmental and Computational Chemistry Group, School of Pharmaceutical Sciences, Zaragocilla Campus, University of Cartagena, 130014, Cartagena, Colombia
| | - Enrique Meléndez
- Department of Chemistry at Mayagüez, University of Puerto Rico, Mayagüez, PR 00681
| | - Wilson Maldonado-Rojas
- Environmental and Computational Chemistry Group, School of Pharmaceutical Sciences, Zaragocilla Campus, University of Cartagena, 130014, Cartagena, Colombia
| | - Carlos Ortega-Zúñiga
- Department of Chemistry at Mayagüez, University of Puerto Rico, Mayagüez, PR 00681; Environmental and Computational Chemistry Group, School of Pharmaceutical Sciences, Zaragocilla Campus, University of Cartagena, 130014, Cartagena, Colombia
| | - Jesus Olivero-Verbel
- Environmental and Computational Chemistry Group, School of Pharmaceutical Sciences, Zaragocilla Campus, University of Cartagena, 130014, Cartagena, Colombia
| | - Elsie I Parés-Matos
- Department of Chemistry at Mayagüez, University of Puerto Rico, Mayagüez, PR 00681.
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9
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Spyrakis F, Ahmed MH, Bayden AS, Cozzini P, Mozzarelli A, Kellogg GE. The Roles of Water in the Protein Matrix: A Largely Untapped Resource for Drug Discovery. J Med Chem 2017; 60:6781-6827. [PMID: 28475332 DOI: 10.1021/acs.jmedchem.7b00057] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The value of thoroughly understanding the thermodynamics specific to a drug discovery/design study is well known. Over the past decade, the crucial roles of water molecules in protein structure, function, and dynamics have also become increasingly appreciated. This Perspective explores water in the biological environment by adopting its point of view in such phenomena. The prevailing thermodynamic models of the past, where water was seen largely in terms of an entropic gain after its displacement by a ligand, are now known to be much too simplistic. We adopt a set of terminology that describes water molecules as being "hot" and "cold", which we have defined as being easy and difficult to displace, respectively. The basis of these designations, which involve both enthalpic and entropic water contributions, are explored in several classes of biomolecules and structural motifs. The hallmarks for characterizing water molecules are examined, and computational tools for evaluating water-centric thermodynamics are reviewed. This Perspective's summary features guidelines for exploiting water molecules in drug discovery.
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Affiliation(s)
- Francesca Spyrakis
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino , Via Pietro Giuria 9, 10125 Torino, Italy
| | - Mostafa H Ahmed
- Department of Medicinal Chemistry & Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University , Richmond, Virginia 23298-0540, United States
| | - Alexander S Bayden
- CMD Bioscience , 5 Science Park, New Haven, Connecticut 06511, United States
| | - Pietro Cozzini
- Dipartimento di Scienze degli Alimenti e del Farmaco, Laboratorio di Modellistica Molecolare, Università degli Studi di Parma , Parco Area delle Scienze 59/A, 43121 Parma, Italy
| | - Andrea Mozzarelli
- Dipartimento di Scienze degli Alimenti e del Farmaco, Laboratorio di Biochimica, Università degli Studi di Parma , Parco Area delle Scienze 23/A, 43121 Parma, Italy.,Istituto di Biofisica, Consiglio Nazionale delle Ricerche , Via Moruzzi 1, 56124 Pisa, Italy
| | - Glen E Kellogg
- Department of Medicinal Chemistry & Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University , Richmond, Virginia 23298-0540, United States
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10
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Andrews CT, Campbell BA, Elcock AH. Direct Comparison of Amino Acid and Salt Interactions with Double-Stranded and Single-Stranded DNA from Explicit-Solvent Molecular Dynamics Simulations. J Chem Theory Comput 2017; 13:1794-1811. [PMID: 28288277 DOI: 10.1021/acs.jctc.6b00883] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Given the ubiquitous nature of protein-DNA interactions, it is important to understand the interaction thermodynamics of individual amino acid side chains for DNA. One way to assess these preferences is to perform molecular dynamics (MD) simulations. Here we report MD simulations of 20 amino acid side chain analogs interacting simultaneously with both a 70-base-pair double-stranded DNA and with a 70-nucleotide single-stranded DNA. The relative preferences of the amino acid side chains for dsDNA and ssDNA match well with values deduced from crystallographic analyses of protein-DNA complexes. The estimated apparent free energies of interaction for ssDNA, on the other hand, correlate well with previous simulation values reported for interactions with isolated nucleobases, and with experimental values reported for interactions with guanosine. Comparisons of the interactions with dsDNA and ssDNA indicate that, with the exception of the positively charged side chains, all types of amino acid side chain interact more favorably with ssDNA, with intercalation of aromatic and aliphatic side chains being especially notable. Analysis of the data on a base-by-base basis indicates that positively charged side chains, as well as sodium ions, preferentially bind to cytosine in ssDNA, and that negatively charged side chains, and chloride ions, preferentially bind to guanine in ssDNA. These latter observations provide a novel explanation for the lower salt dependence of DNA duplex stability in GC-rich sequences relative to AT-rich sequences.
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Affiliation(s)
- Casey T Andrews
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Brady A Campbell
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Adrian H Elcock
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
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11
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12
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Gerogiokas G, Southey MWY, Mazanetz MP, Heifetz A, Bodkin M, Law RJ, Henchman RH, Michel J. Assessment of Hydration Thermodynamics at Protein Interfaces with Grid Cell Theory. J Phys Chem B 2016; 120:10442-10452. [PMID: 27645529 DOI: 10.1021/acs.jpcb.6b07993] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Molecular dynamics simulations have been analyzed with the Grid Cell Theory (GCT) method to spatially resolve the binding enthalpies and entropies of water molecules at the interface of 17 structurally diverse proteins. Correlations between computed energetics and structural descriptors have been sought to facilitate the development of simple models of protein hydration. Little correlation was found between GCT-computed binding enthalpies and continuum electrostatics calculations. A simple count of contacts with functional groups in charged amino acids correlates well with enhanced water stabilization, but the stability of water near hydrophobic and polar residues depends markedly on its coordination environment. The positions of X-ray-resolved water molecules correlate with computed high-density hydration sites, but many unresolved waters are significantly stabilized at the protein surfaces. A defining characteristic of ligand-binding pockets compared to nonbinding pockets was a greater solvent-accessible volume, but average water thermodynamic properties were not distinctive from other interfacial regions. Interfacial water molecules are frequently stabilized by enthalpy and destabilized entropy with respect to bulk, but counter-examples occasionally occur. Overall detailed inspection of the local coordinating environment appears necessary to gauge the thermodynamic stability of water in protein structures.
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Affiliation(s)
- Georgios Gerogiokas
- EaStCHEM School of Chemistry , Joseph Black Building, The King's Buildings, Edinburgh EH9 3JJ, United Kingdom
| | - Michelle W Y Southey
- Evotec (U.K.) Limited , 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | - Michael P Mazanetz
- Evotec (U.K.) Limited , 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | - Alexander Heifetz
- Evotec (U.K.) Limited , 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | - Michael Bodkin
- Evotec (U.K.) Limited , 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | - Richard J Law
- Evotec (U.K.) Limited , 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | - Richard H Henchman
- Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom.,School of Chemistry, The University of Manchester , Oxford Road, Manchester M13 9PL, United Kingdom
| | - J Michel
- EaStCHEM School of Chemistry , Joseph Black Building, The King's Buildings, Edinburgh EH9 3JJ, United Kingdom
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13
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Chakraborty K, Bandyopadhyay S. Effects of protein-DNA complex formation on the intermolecular vibrational density of states of interfacial water. Phys Chem Chem Phys 2016; 18:7780-8. [PMID: 26912116 DOI: 10.1039/c5cp07562a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Single-stranded DNAs (ss-DNAs) are formed as intermediates during DNA metabolic processes. ss-DNA binding (SSB) proteins specifically bind to the single-stranded segments of the DNA and protect it from being degraded. We have performed room temperature molecular dynamics simulations of the aqueous solution of two DNA binding K homology (KH) domains (KH3 and KH4) of the far upstream element (FUSE) binding protein (FBP) complexed with two ss-DNA oligomers. Efforts have been made to explore the influence of complex formation on low-frequency vibrational density of states of the surface water molecules. It is revealed that increased back scattering of water confined around the complexed structures leads to significant blue shifts of the band corresponding to the O···O···O bending or restricted transverse motions of water, the effect being more for the bridged water molecules. Importantly, it is demonstrated that the formation of such complexed structures of a similar type may often influence the transverse and longitudinal degrees of freedom of the surrounding water molecules in a nonuniform manner.
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Affiliation(s)
- Kaushik Chakraborty
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur - 721302, India.
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur - 721302, India.
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14
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Spyrakis F, Cavasotto CN. Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description. Arch Biochem Biophys 2015; 583:105-19. [DOI: 10.1016/j.abb.2015.08.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 08/03/2015] [Accepted: 08/03/2015] [Indexed: 01/05/2023]
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15
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Chakraborty K, Bandyopadhyay S. Dynamics of water around the complex structures formed between the KH domains of far upstream element binding protein and single-stranded DNA molecules. J Chem Phys 2015; 143:045106. [DOI: 10.1063/1.4927568] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Kaushik Chakraborty
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
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16
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Ronda L, Bruno S, Bettati S, Storici P, Mozzarelli A. From protein structure to function via single crystal optical spectroscopy. Front Mol Biosci 2015; 2:12. [PMID: 25988179 PMCID: PMC4428442 DOI: 10.3389/fmolb.2015.00012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 03/31/2015] [Indexed: 11/23/2022] Open
Abstract
The more than 100,000 protein structures determined by X-ray crystallography provide a wealth of information for the characterization of biological processes at the molecular level. However, several crystallographic “artifacts,” including conformational selection, crystallization conditions and radiation damages, may affect the quality and the interpretation of the electron density maps, thus limiting the relevance of structure determinations. Moreover, for most of these structures, no functional data have been obtained in the crystalline state, thus posing serious questions on their validity in infereing protein mechanisms. In order to solve these issues, spectroscopic methods have been applied for the determination of equilibrium and kinetic properties of proteins in the crystalline state. These methods are UV-vis spectrophotometry, spectrofluorimetry, IR, EPR, Raman, and resonance Raman spectroscopy. Some of these approaches have been implemented with on-line instruments at X-ray synchrotron beamlines. Here, we provide an overview of investigations predominantly carried out in our laboratory by single crystal polarized absorption UV-vis microspectrophotometry, the most applied technique for the functional characterization of proteins in the crystalline state. Studies on hemoglobins, pyridoxal 5′-phosphate dependent enzymes and green fluorescent protein in the crystalline state have addressed key biological issues, leading to either straightforward structure-function correlations or limitations to structure-based mechanisms.
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Affiliation(s)
- Luca Ronda
- Department of Neurosciences, University of Parma Parma, Italy
| | - Stefano Bruno
- Department of Pharmacy, University of Parma Parma, Italy
| | - Stefano Bettati
- Department of Neurosciences, University of Parma Parma, Italy ; National Institute of Biostructures and Biosystems Rome, Italy
| | | | - Andrea Mozzarelli
- Department of Pharmacy, University of Parma Parma, Italy ; National Institute of Biostructures and Biosystems Rome, Italy ; Institute of Biophysics, Consiglio Nazionale delle Ricerche Pisa, Italy
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17
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Aranda J, Zinovjev K, Roca M, Tuñón I. Dynamics and Reactivity in Thermus aquaticus N6-Adenine Methyltransferase. J Am Chem Soc 2014; 136:16227-39. [DOI: 10.1021/ja5077124] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Juan Aranda
- Departament de Química
Física, Universitat de València, 46100 Burjassot, Spain
| | - Kirill Zinovjev
- Departament de Química
Física, Universitat de València, 46100 Burjassot, Spain
| | - Maite Roca
- Departament de Química
Física, Universitat de València, 46100 Burjassot, Spain
| | - Iñaki Tuñón
- Departament de Química
Física, Universitat de València, 46100 Burjassot, Spain
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18
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Biedermann F, Nau WM, Schneider HJ. Neues zum hydrophoben Effekt - Studien mit supramolekularen Komplexen zeigen hochenergetisches Wasser als nichtkovalente Bindungstriebkraft. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201310958] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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19
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Biedermann F, Nau WM, Schneider HJ. The hydrophobic effect revisited--studies with supramolecular complexes imply high-energy water as a noncovalent driving force. Angew Chem Int Ed Engl 2014; 53:11158-71. [PMID: 25070083 DOI: 10.1002/anie.201310958] [Citation(s) in RCA: 426] [Impact Index Per Article: 42.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Indexed: 01/14/2023]
Abstract
Traditional descriptions of the hydrophobic effect on the basis of entropic arguments or the calculation of solvent-occupied surfaces must be questioned in view of new results obtained with supramolecular complexes. In these studies, it was possible to separate hydrophobic from dispersive interactions, which are strongest in aqueous systems. Even very hydrophobic alkanes associate significantly only in cavities containing water molecules with an insufficient number of possible hydrogen bonds. The replacement of high-energy water in cavities by guest molecules is the essential enthalpic driving force for complexation, as borne out by data for complexes of cyclodextrins, cyclophanes, and cucurbiturils, for which complexation enthalpies of up to -100 kJ mol(-1) were reached for encapsulated alkyl residues. Water-box simulations were used to characterize the different contributions from high-energy water and enabled the calculation of the association free enthalpies for selected cucurbituril complexes to within a 10% deviation from experimental values. Cavities in artificial receptors are more apt to show the enthalpic effect of high-energy water than those in proteins or nucleic acids, because they bear fewer or no functional groups in the inner cavity to stabilize interior water molecules.
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Affiliation(s)
- Frank Biedermann
- ISIS-Institut de Science et d'Ingénierie Supramoléculaires, 67083 Strasbourg (France).
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20
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Spyrakis F, Cellini B, Bruno S, Benedetti P, Carosati E, Cruciani G, Micheli F, Felici A, Cozzini P, Kellogg GE, Voltattorni CB, Mozzarelli A. Targeting cystalysin, a virulence factor of treponema denticola-supported periodontitis. ChemMedChem 2014; 9:1501-11. [PMID: 24616267 DOI: 10.1002/cmdc.201300527] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 02/13/2014] [Indexed: 01/01/2023]
Abstract
Cystalysin from Treponema denticola is a pyridoxal 5'-phosphate dependent lyase that catalyzes the formation of pyruvate, ammonia, and sulfide from cysteine. It is a virulence factor in adult periodontitis because its reaction contributes to hemolysis, which sustains the pathogen. Therefore, it was proposed as a potential antimicrobial target. To identify specific inhibitors by structure-based in silico methods, we first validated the crystal structure of cystalysin as a reliable starting point for the design of ligands. By using single-crystal absorption microspectrophotometry, we found that the enzyme in the crystalline state, with respect to that in solution, exhibits: 1) the same absorption spectra for the catalytic intermediates, 2) a close pKa value for the residue controlling the keto enamine ionization, and 3) similar reactivity with glycine, L-serine, L-methionine, and the nonspecific irreversible inhibitor aminoethoxyvinylglycine. Next, we screened in silico a library of 9357 compounds with the Fingerprints for Ligands and Proteins (FLAP) software, by using the three-dimensional structure of cystalysin as a template. From the library, 17 compounds were selected and experimentally evaluated by enzyme assays and spectroscopic methods. Two compounds were found to competitively inhibit recombinant T. denticola cystalysin, with inhibition constant (Ki ) values of 25 and 37 μM. One of them exhibited a minimum inhibitory concentration (MIC) value of 64 μg mL(-1) on Moraxella catarrhalis ATCC 23246, which proves its ability to cross bacterial membranes.
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Affiliation(s)
- Francesca Spyrakis
- Department of Food Sciences, University of Parma, Parma (Italy); Current address: Department of Life Sciences, University of Modena and Reggio Emilia, Modena (Italy)
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21
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Ahmed MH, Kellogg GE, Selley DE, Safo MK, Zhang Y. Predicting the molecular interactions of CRIP1a-cannabinoid 1 receptor with integrated molecular modeling approaches. Bioorg Med Chem Lett 2014; 24:1158-65. [PMID: 24461351 PMCID: PMC4353595 DOI: 10.1016/j.bmcl.2013.12.119] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 12/26/2013] [Accepted: 12/29/2013] [Indexed: 12/14/2022]
Abstract
Cannabinoid receptors are a family of G-protein coupled receptors that are involved in a wide variety of physiological processes and diseases. One of the key regulators that are unique to cannabinoid receptors is the cannabinoid receptor interacting proteins (CRIPs). Among them CRIP1a was found to decrease the constitutive activity of the cannabinoid type-1 receptor (CB1R). The aim of this study is to gain an understanding of the interaction between CRIP1a and CB1R through using different computational techniques. The generated model demonstrated several key putative interactions between CRIP1a and CB1R, including the critical involvement of Lys130 in CRIP1a.
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Affiliation(s)
- Mostafa H Ahmed
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA; Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Glen E Kellogg
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA; Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23298, USA; Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Dana E Selley
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Martin K Safo
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA; Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Yan Zhang
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA.
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22
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Parikh HI, Kellogg GE. Intuitive, but not simple: including explicit water molecules in protein-protein docking simulations improves model quality. Proteins 2013; 82:916-32. [PMID: 24214407 DOI: 10.1002/prot.24466] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 10/18/2013] [Accepted: 10/22/2013] [Indexed: 11/06/2022]
Abstract
Characterizing the nature of interaction between proteins that have not been experimentally cocrystallized requires a computational docking approach that can successfully predict the spatial conformation adopted in the complex. In this work, the Hydropathic INTeractions (HINT) force field model was used for scoring docked models in a data set of 30 high-resolution crystallographically characterized "dry" protein-protein complexes and was shown to reliably identify native-like models. However, most current protein-protein docking algorithms fail to explicitly account for water molecules involved in bridging interactions that mediate and stabilize the association of the protein partners, so we used HINT to illuminate the physical and chemical properties of bridging waters and account for their energetic stabilizing contributions. The HINT water Relevance metric identified the "truly" bridging waters at the 30 protein-protein interfaces and we utilized them in "solvated" docking by manually inserting them into the input files for the rigid body ZDOCK program. By accounting for these interfacial waters, a statistically significant improvement of ∼24% in the average hit-count within the top-10 predictions the protein-protein dataset was seen, compared to standard "dry" docking. The results also show scoring improvement, with medium and high accuracy models ranking much better than incorrect ones. These improvements can be attributed to the physical presence of water molecules that alter surface properties and better represent native shape and hydropathic complementarity between interacting partners, with concomitantly more accurate native-like structure predictions.
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Affiliation(s)
- Hardik I Parikh
- Department of Medicinal Chemistry and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, Virginia, 23298-0540
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23
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Ahmed MH, Habtemariam M, Safo MK, Scarsdale JN, Spyrakis F, Cozzini P, Mozzarelli A, Kellogg GE. Unintended consequences? Water molecules at biological and crystallographic protein–protein interfaces. Comput Biol Chem 2013; 47:126-41. [DOI: 10.1016/j.compbiolchem.2013.08.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 08/27/2013] [Accepted: 08/27/2013] [Indexed: 01/31/2023]
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24
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Spyrakis F, Singh R, Cozzini P, Campanini B, Salsi E, Felici P, Raboni S, Benedetti P, Cruciani G, Kellogg GE, Cook PF, Mozzarelli A. Isozyme-specific ligands for O-acetylserine sulfhydrylase, a novel antibiotic target. PLoS One 2013; 8:e77558. [PMID: 24167577 PMCID: PMC3805590 DOI: 10.1371/journal.pone.0077558] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 09/03/2013] [Indexed: 01/06/2023] Open
Abstract
The last step of cysteine biosynthesis in bacteria and plants is catalyzed by O-acetylserine sulfhydrylase. In bacteria, two isozymes, O-acetylserine sulfhydrylase-A and O-acetylserine sulfhydrylase-B, have been identified that share similar binding sites, although the respective specific functions are still debated. O-acetylserine sulfhydrylase plays a key role in the adaptation of bacteria to the host environment, in the defense mechanisms to oxidative stress and in antibiotic resistance. Because mammals synthesize cysteine from methionine and lack O-acetylserine sulfhydrylase, the enzyme is a potential target for antimicrobials. With this aim, we first identified potential inhibitors of the two isozymes via a ligand- and structure-based in silico screening of a subset of the ZINC library using FLAP. The binding affinities of the most promising candidates were measured in vitro on purified O-acetylserine sulfhydrylase-A and O-acetylserine sulfhydrylase-B from Salmonella typhimurium by a direct method that exploits the change in the cofactor fluorescence. Two molecules were identified with dissociation constants of 3.7 and 33 µM for O-acetylserine sulfhydrylase-A and O-acetylserine sulfhydrylase-B, respectively. Because GRID analysis of the two isoenzymes indicates the presence of a few common pharmacophoric features, cross binding titrations were carried out. It was found that the best binder for O-acetylserine sulfhydrylase-B exhibits a dissociation constant of 29 µM for O-acetylserine sulfhydrylase-A, thus displaying a limited selectivity, whereas the best binder for O-acetylserine sulfhydrylase-A exhibits a dissociation constant of 50 µM for O-acetylserine sulfhydrylase-B and is thus 8-fold selective towards the former isozyme. Therefore, isoform-specific and isoform-independent ligands allow to either selectively target the isozyme that predominantly supports bacteria during infection and long-term survival or to completely block bacterial cysteine biosynthesis.
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Affiliation(s)
| | - Ratna Singh
- Department of Pharmacy, University of Parma, Parma, Italy
| | - Pietro Cozzini
- Department of Food Sciences, University of Parma, Parma, Italy
- National Institute of Biostructures and Biosystems, Rome, Italy
| | - Barbara Campanini
- Department of Pharmacy, University of Parma, Parma, Italy
- * E-mail: (BC); (AM)
| | - Enea Salsi
- Department of Pharmacy, University of Parma, Parma, Italy
| | - Paolo Felici
- Department of Pharmacy, University of Parma, Parma, Italy
| | - Samanta Raboni
- Department of Pharmacy, University of Parma, Parma, Italy
| | | | | | - Glen E. Kellogg
- Department of Medicinal Chemistry and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Paul F. Cook
- Department of Biochemistry, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Andrea Mozzarelli
- Department of Pharmacy, University of Parma, Parma, Italy
- National Institute of Biostructures and Biosystems, Rome, Italy
- * E-mail: (BC); (AM)
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25
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Vandeventer PE, Mejia J, Nadim A, Johal MS, Niemz A. DNA adsorption to and elution from silica surfaces: influence of amino acid buffers. J Phys Chem B 2013; 117:10742-9. [PMID: 23931415 DOI: 10.1021/jp405753m] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Solid phase extraction and purification of DNA from complex samples typically requires chaotropic salts that can inhibit downstream polymerase amplification if carried into the elution buffer. Amino acid buffers may serve as a more compatible alternative for modulating the interaction between DNA and silica surfaces. We characterized DNA binding to silica surfaces, facilitated by representative amino acid buffers, and the subsequent elution of DNA from the silica surfaces. Through bulk depletion experiments, we found that more DNA adsorbs to silica particles out of positively compared to negatively charged amino acid buffers. Additionally, the type of the silica surface greatly influences the amount of DNA adsorbed and the final elution yield. Quartz crystal microbalance experiments with dissipation monitoring (QCM-D) revealed multiphasic DNA adsorption out of stronger adsorbing conditions such as arginine, glycine, and glutamine, with DNA more rigidly bound during the early stages of the adsorption process. The DNA film adsorbed out of glutamate was more flexible and uniform throughout the adsorption process. QCM-D characterization of DNA elution from the silica surface indicates an uptake in water mass during the initial stage of DNA elution for the stronger adsorbing conditions, which suggests that for these conditions the DNA film is partly dehydrated during the prior adsorption process. Overall, several positively charged and polar neutral amino acid buffers show promise as an alternative to methods based on chaotropic salts for solid phase DNA extraction.
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Affiliation(s)
- Peter E Vandeventer
- Keck Graduate Institute of Applied Life Sciences , 535 Watson Drive, Claremont, California 91711, United States
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26
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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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Structures of complexes comprised of Fischerella transcription factor HetR with Anabaena DNA targets. Proc Natl Acad Sci U S A 2013; 110:E1716-23. [PMID: 23610410 DOI: 10.1073/pnas.1305971110] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
HetR is an essential regulator of heterocyst development in cyanobacteria. Many mutations in HetR render Anabaena incapable of nitrogen fixation. The protein binds to a DNA palindrome upstream of hetP and other genes. We have determined the crystal structures of HetR complexed with palindromic DNA targets, 21, 23, and 29 bp at 2.50-, 3.00-, and 3.25-Å resolution, respectively. The highest-resolution structure shows fine details of specific protein-DNA interactions. The lower-resolution structures with longer DNA duplexes have similar interaction patterns and show how the flap domains interact with DNA in a sequence nonspecific fashion. Fifteen of 15 protein-DNA contacts predicted on the basis of the structure were confirmed by single amino acid mutations that abolished binding in vitro and complementation in vivo. A striking feature of the structure is the association of glutamate 71 from each subunit of the HetR dimer with three successive cytosines in each arm of the palindromic target, a feature that is conserved among all known heterocyst-forming cyanobacteria sequenced to date.
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28
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Khandelwal G, Jayaram B. DNA-water interactions distinguish messenger RNA genes from transfer RNA genes. J Am Chem Soc 2012; 134:8814-6. [PMID: 22551381 DOI: 10.1021/ja3020956] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Physicochemical properties of DNA sequences as a guide to developing insights into genome organization has received little attention. Here, we utilize the energetics of DNA to further advance the knowledge on its language at a molecular level. Specifically, we ask the question whether physicochemical properties of different functional units on genomes differ. We extract intramolecular and solvation energies of different DNA base pair steps from a comprehensive set of molecular dynamics simulations. We then investigate the solvation behavior of DNA sequences coding for mRNAs and tRNAs. Distinguishing mRNA genes from tRNA genes is a tricky problem in genome annotation without assumptions on length of DNA and secondary structure of the product of transcription. We find that solvation energetics of DNA behaves as an extremely efficient property in discriminating 2,063,537 genes coding for mRNAs from 56,251 genes coding for tRNAs in all (~1500) completely sequenced prokaryotic genomes.
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Affiliation(s)
- Garima Khandelwal
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi-110016, India
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29
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Sinha SK, Bandyopadhyay S. Conformational fluctuations of a protein-DNA complex and the structure and ordering of water around it. J Chem Phys 2012; 135:245104. [PMID: 22225189 DOI: 10.1063/1.3670877] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Protein-DNA binding is an important process responsible for the regulation of genetic activities in living organisms. The most crucial issue in this problem is how the protein recognizes the DNA and identifies its target base sequences. Water molecules present around the protein and DNA are also expected to play an important role in mediating the recognition process and controlling the structure of the complex. We have performed atomistic molecular dynamics simulations of an aqueous solution of the protein-DNA complex formed between the DNA binding domain of human TRF1 protein and a telomeric DNA. The conformational fluctuations of the protein and DNA and the microscopic structure and ordering of water around them in the complex have been explored. In agreement with experimental studies, the calculations reveal conformational immobilization of the terminal segments of the protein on complexation. Importantly, it is discovered that both structural adaptations of the protein and DNA, and the subsequent correlation between them to bind, contribute to the net entropy loss associated with the complex formation. Further, it is found that water molecules around the DNA are more structured with significantly higher density and ordering than that around the protein in the complex.
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Affiliation(s)
- Sudipta Kumar Sinha
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur, India
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30
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Sinha SK, Bandyopadhyay S. Dynamic properties of water around a protein-DNA complex from molecular dynamics simulations. J Chem Phys 2012; 135:135101. [PMID: 21992339 DOI: 10.1063/1.3634004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Formation of protein-DNA complex is an important step in regulation of genes in living organisms. One important issue in this problem is the role played by water in mediating the protein-DNA interactions. In this work, we have carried out atomistic molecular dynamics simulations to explore the heterogeneous dynamics of water molecules present in different regions around a complex formed between the DNA binding domain of human TRF1 protein and a telomeric DNA. It is demonstrated that such heterogeneous water motions around the complex are correlated with the relaxation time scales of hydrogen bonds formed by those water molecules with the protein and DNA. The calculations reveal the existence of a fraction of extraordinarily restricted water molecules forming a highly rigid thin layer in between the binding motifs of the protein and DNA. It is further proved that higher rigidity of water layers around the complex originates from more frequent reformations of broken water-water hydrogen bonds. Importantly, it is found that the formation of the complex affects the transverse and longitudinal degrees of freedom of surrounding water molecules in a nonuniform manner.
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Affiliation(s)
- Sudipta Kumar Sinha
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur - 721302, India
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31
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Bound water at protein-protein interfaces: partners, roles and hydrophobic bubbles as a conserved motif. PLoS One 2011; 6:e24712. [PMID: 21961043 PMCID: PMC3178540 DOI: 10.1371/journal.pone.0024712] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Accepted: 08/17/2011] [Indexed: 12/18/2022] Open
Abstract
Background There is a great interest in understanding and exploiting protein-protein associations as new routes for treating human disease. However, these associations are difficult to structurally characterize or model although the number of X-ray structures for protein-protein complexes is expanding. One feature of these complexes that has received little attention is the role of water molecules in the interfacial region. Methodology A data set of 4741 water molecules abstracted from 179 high-resolution (≤ 2.30 Å) X-ray crystal structures of protein-protein complexes was analyzed with a suite of modeling tools based on the HINT forcefield and hydrogen-bonding geometry. A metric termed Relevance was used to classify the general roles of the water molecules. Results The water molecules were found to be involved in: a) (bridging) interactions with both proteins (21%), b) favorable interactions with only one protein (53%), and c) no interactions with either protein (26%). This trend is shown to be independent of the crystallographic resolution. Interactions with residue backbones are consistent for all classes and account for 21.5% of all interactions. Interactions with polar residues are significantly more common for the first group and interactions with non-polar residues dominate the last group. Waters interacting with both proteins stabilize on average the proteins' interaction (−0.46 kcal mol−1), but the overall average contribution of a single water to the protein-protein interaction energy is unfavorable (+0.03 kcal mol−1). Analysis of the waters without favorable interactions with either protein suggests that this is a conserved phenomenon: 42% of these waters have SASA ≤ 10 Å2 and are thus largely buried, and 69% of these are within predominantly hydrophobic environments or “hydrophobic bubbles”. Such water molecules may have an important biological purpose in mediating protein-protein interactions.
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32
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Cole JC, Korb O, Olsson TSG, Liebeschuetz J. The Basis for Target-Based Virtual Screening: Protein Structures. ACTA ACUST UNITED AC 2011. [DOI: 10.1002/9783527633326.ch4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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33
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Bueno M, Temiz NA, Camacho CJ. Novel modulation factor quantifies the role of water molecules in protein interactions. Proteins 2011; 78:3226-34. [PMID: 20665475 DOI: 10.1002/prot.22805] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Water molecules decrease the potential of mean force of a hydrogen bond (H-bond), as well as modulate (de)solvation forces, but exactly how much has not been easy to determine. Crystallographic water molecules provide snapshots of optimal solutions for the role of solvent in protein interactions, information that is often ignored by implicit solvent models. Motivated by high-resolution crystal structures, we describe a simple quantitative approach to explicitly incorporate the role of molecular water in protein interactions. Applications to protein-DNA interactions show that the accuracy of binding free-energy estimates improves significantly if a distinction is made between H-bonds that are desolvated (or only contact crystal waters), solvated by mobile waters trapped at the binding interface, or partially solvated through connections to bulk water. These different environments are modeled by a unique "water" scaling factor that decreases or increases the strength of hydrogen bonds depending on whether water contacts the acceptor or donor atoms or the bond is fully desolvated, respectively. Our empirical energies are fully consistent with mobile water molecules having a strong polarization effect in direct intermolecular interactions.
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Affiliation(s)
- Marta Bueno
- Department of Pathology, Division of Transplant Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania 15213, USA.
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34
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Boryskina OP, Tkachenko MY, Shestopalova AV. Protein-DNA complexes: specificity and DNA readout mechanisms. ACTA ACUST UNITED AC 2011. [DOI: 10.7124/bc.00007c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- O. P. Boryskina
- O. Ya. Usikov Institute for Radio Physics and Electronics, National Academy of Sciences of Ukraine
| | - M. Yu. Tkachenko
- O. Ya. Usikov Institute for Radio Physics and Electronics, National Academy of Sciences of Ukraine
| | - A. V. Shestopalova
- O. Ya. Usikov Institute for Radio Physics and Electronics, National Academy of Sciences of Ukraine
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35
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Joshi KB, Vijaya Krishna K, Verma S. Self-Assembled Morphologies from C2- and C3-Symmetric Biotin Conjugates. J Org Chem 2010; 75:4280-3. [DOI: 10.1021/jo100881r] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- K. B. Joshi
- Department of Chemistry, Indian Institute of Technology-Kanpur, Kanpur-208016 (UP), India
| | - K. Vijaya Krishna
- Department of Chemistry, Indian Institute of Technology-Kanpur, Kanpur-208016 (UP), India
| | - Sandeep Verma
- Department of Chemistry, Indian Institute of Technology-Kanpur, Kanpur-208016 (UP), India
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Naômé A, Schyman P, Laaksonen A, Vercauteren DP. Molecular Dynamics Simulation of 8-Oxoguanine Containing DNA Fragments Reveals Altered Hydration and Ion Binding Patterns. J Phys Chem B 2010; 114:4789-801. [DOI: 10.1021/jp1000539] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Aymeric Naômé
- Laboratoire de Physico-Chimie Informatique, Unité de Chimie Physique Théorique et Structurale, University of Namur (FUNDP), Namur, Belgium, and Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
| | - Patric Schyman
- Laboratoire de Physico-Chimie Informatique, Unité de Chimie Physique Théorique et Structurale, University of Namur (FUNDP), Namur, Belgium, and Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
| | - Aatto Laaksonen
- Laboratoire de Physico-Chimie Informatique, Unité de Chimie Physique Théorique et Structurale, University of Namur (FUNDP), Namur, Belgium, and Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
| | - Daniel P. Vercauteren
- Laboratoire de Physico-Chimie Informatique, Unité de Chimie Physique Théorique et Structurale, University of Namur (FUNDP), Namur, Belgium, and Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
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Temiz AN, Benos PV, Camacho CJ. Electrostatic hot spot on DNA-binding domains mediates phosphate desolvation and the pre-organization of specificity determinant side chains. Nucleic Acids Res 2010; 38:2134-44. [PMID: 20047959 PMCID: PMC2853105 DOI: 10.1093/nar/gkp1132] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A major obstacle towards elucidating the molecular basis of transcriptional regulation is the lack of a detailed understanding of the interplay between non-specific and specific protein–DNA interactions. Based on molecular dynamics simulations of C2H2 zinc fingers (ZFs) and engrailed homeodomain transcription factors (TFs), we show that each of the studied DNA-binding domains has a set of highly constrained side chains in preset configurations ready to form hydrogen bonds with the DNA backbone. Interestingly, those domains that bury their recognition helix into the major groove are found to have an electrostatic hot spot for Cl− ions located on the same binding cavity as the most buried DNA phosphate. The spot is characterized by three protein hydrogen bond donors, often including two basic side chains. If bound, Cl− ions, likely mimicking phosphates, steer side chains that end up forming specific contacts with bases into bound-like conformations. These findings are consistent with a multi-step DNA-binding mechanism in which a pre-organized set of TF side chains assist in the desolvation of phosphates into well defined sites, prompting the re-organization of specificity determining side chains into conformations suitable for the recognition of their cognate sequence.
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Affiliation(s)
- Alpay N Temiz
- Department of Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
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Furmanchuk A, Isayev O, Shishkin OV, Gorb L, Leszczynski J. Hydration of nucleic acid bases: a Car–Parrinello molecular dynamics approach. Phys Chem Chem Phys 2010; 12:3363-75. [DOI: 10.1039/b923930h] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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Acchione M, Lipschultz CA, DeSantis ME, Shanmuganathan A, Li M, Wlodawer A, Tarasov S, Smith-Gill SJ. Light chain somatic mutations change thermodynamics of binding and water coordination in the HyHEL-10 family of antibodies. Mol Immunol 2009; 47:457-64. [PMID: 19781789 DOI: 10.1016/j.molimm.2009.08.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Accepted: 08/28/2009] [Indexed: 01/14/2023]
Abstract
Thermodynamic and structural studies addressed the increased affinity due to L-chain somatic mutations in the HyHEL-10 family of affinity matured IgG antibodies, using ITC, SPR with van't Hoff analysis, and X-ray crystallography. When compared to the parental antibody H26L26, the H26L10 and H26L8 chimeras binding to lysozyme showed an increase in favorable DeltaG(o) of -1.2+/-0.1 kcal mol(-1) and -1.3+/-0.1 kcal mol(-1), respectively. Increase in affinity of the H26L10 chimera was due to a net increase in favorable enthalpy change with little difference in change in entropy compared to H26L26. The H26L8 chimera exhibited the greatest increase in favorable enthalpy but also showed an increase in unfavorable entropy change, with the result being that the affinities of both chimeras were essentially equivalent. Site-directed L-chain mutants identified the shared somatic mutation S30G as the dominant contributor to increasing affinity to lysozyme. This mutation was not influenced by H-chain somatic mutations. Residue 30L is at the periphery of the binding interface and S30G effects an increase in hydrophobicity and decrease in H-bonding ability and size, but does not make any new energetically important antigen contacts. A new 1.2-A structure of the H10L10-HEL complex showed changes in the pattern of both inter- and intra-molecular water bridging with no other significant structural alterations near the binding interface compared to the H26L26-HEL complex. These results highlight the necessity for investigating both the structure and the thermodynamics associated with introduced mutations, in order to better assess and understand their impact on binding. Furthermore, it provides an important example of how backbone flexibility and water-bridging may favorably influence the thermodynamics of an antibody-antigen interaction.
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Affiliation(s)
- Mauro Acchione
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
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40
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Bayden AS, Fornabaio M, Scarsdale JN, Kellogg GE. Web application for studying the free energy of binding and protonation states of protein-ligand complexes based on HINT. J Comput Aided Mol Des 2009; 23:621-32. [PMID: 19554265 DOI: 10.1007/s10822-009-9270-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2008] [Accepted: 01/22/2009] [Indexed: 10/20/2022]
Abstract
A public web server performing computational titration at the active site in a protein-ligand complex has been implemented. This calculation is based on the Hydropathic interaction noncovalent force field. From 3D coordinate data for the protein, ligand and bridging waters (if available), the server predicts the best combination of protonation states for each ionizable residue and/or ligand functional group as well as the Gibbs free energy of binding for the ionization-optimized protein-ligand complex. The 3D structure for the modified molecules is available as output. In addition, a graph depicting how this energy changes with acidity, i.e., as a function of added protons, can be obtained. This data may prove to be of use in preparing models for virtual screening and molecular docking. A few illustrative examples are presented. In beta secretase (2va7) computational titration flipped the amide groups of Gln12 and Asn37 and protonated a ligand amine yielding an improvement of 6.37 kcal mol(-1) in the protein-ligand binding score. Protonation of Glu139 in mutant HIV-1 reverse transcriptase (2opq) allows a water bridge between the protein and inhibitor that increases the protein-ligand interaction score by 0.16 kcal mol(-1). In human sialidase NEU2 complexed with an isobutyl ether mimetic inhibitor (2f11) computational titration suggested that protonating Glu218, deprotonating Arg237, flipping the amide bond on Tyr334, and optimizing the positions of several other polar protons would increase the protein-ligand interaction score by 0.71 kcal mol(-1).
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Affiliation(s)
- Alexander S Bayden
- Department of Medicinal Chemistry & Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23298-0540, USA
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41
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Amadasi A, Mozzarelli A, Meda C, Maggi A, Cozzini P. Identification of xenoestrogens in food additives by an integrated in silico and in vitro approach. Chem Res Toxicol 2009; 22:52-63. [PMID: 19063592 DOI: 10.1021/tx800048m] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In the search for xenoestrogens within food additives, we have analyzed the Joint FAO-WHO expert committee database, containing 1500 compounds, using an integrated in silico and in vitro approach. This analysis identified 31 potential estrogen receptor alpha ligands that were reduced to 13 upon applying a stringent filter based on ligand volume and binding mode. Among the 13 potential xenoestrogens, four were already known to exhibit an estrogenic activity, and the other nine were assayed in vitro, determining the binding affinity to the receptor and biological effects. Propyl gallate was found to act as an antagonist, and 4-hexylresorcinol was found to act as a potent transactivator; both ligands were active at nanomolar concentrations, as predicted by the in silico analysis. Some caution should be issued for the use of propyl gallate and 4-hexylresorcinol as food additives.
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Affiliation(s)
- Alessio Amadasi
- Department of Biochemistry and Molecular Biology, University of Parma, 43100 Parma, Italy
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Marabotti A, Spyrakis F, Facchiano A, Cozzini P, Alberti S, Kellogg GE, Mozzarelli A. Energy-based prediction of amino acid-nucleotide base recognition. J Comput Chem 2008; 29:1955-69. [PMID: 18366021 DOI: 10.1002/jcc.20954] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Despite decades of investigations, it is not yet clear whether there are rules dictating the specificity of the interaction between amino acids and nucleotide bases. This issue was addressed by determining, in a dataset consisting of 100 high-resolution protein-DNA structures, the frequency and energy of interaction between each amino acid and base, and the energetics of water-mediated interactions. The analysis was carried out using HINT, a non-Newtonian force field encoding both enthalpic and entropic contributions, and Rank, a geometry-based tool for evaluating hydrogen bond interactions. A frequency- and energy-based preferential interaction of Arg and Lys with G, Asp and Glu with C, and Asn and Gln with A was found. Not only favorable, but also unfavorable contacts were found to be conserved. Water-mediated interactions strongly increase the probability of Thr-A, Lys-A, and Lys-C contacts. The frequency, interaction energy, and water enhancement factors associated with each amino acid-base pair were used to predict the base triplet recognized by the helix motif in 45 zinc fingers, which represents an ideal case study for the analysis of one-to-one amino acid-base pair contacts. The model correctly predicted 70.4% of 135 amino acid-base pairs, and, by weighting the energetic relevance of each amino acid-base pair to the overall recognition energy, it yielded a prediction rate of 89.7%.
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Affiliation(s)
- Anna Marabotti
- Laboratory for Bioinformatics and Computational Biology, Institute of Food Science, National Research Council, Avellino, Italy.
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43
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Bandyopadhyay D, Mehler EL. Quantitative expression of protein heterogeneity: Response of amino acid side chains to their local environment. Proteins 2008; 72:646-59. [PMID: 18247345 DOI: 10.1002/prot.21958] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A general method has been developed to characterize the hydrophobicity or hydrophilicity of the microenvironment (MENV), in which a given amino acid side chain is immersed, by calculating a quantitative property descriptor (QPD) based on the relative (to water) hydrophobicity of the MENV. Values of the QPD were calculated for a test set of 733 proteins to analyze the modulating effects on amino acid residue properties by the MENV in which they are imbedded. The QPD values and solvent accessibility were used to derive a partitioning of residues based on the MENV hydrophobicities. From this partitioning, a new hydrophobicity scale was developed, entirely in the context of protein structure, where amino acid residues are immersed in one or more "MENVpockets." Thus, the partitioning is based on the residues "sampling" a large number of "solvents" (MENVs) that represent a very large range of hydrophobicity values. It was found that the hydrophobicity of around 80% of amino acid side chains and their MENV are complementary to each other, but for about 20%, the MENV and their imbedded residue can be considered as mismatched. Many of these mismatches could be rationalized in terms of the structural stability of the protein and/or the involvement of the imbedded residue in function. The analysis also indicated a remarkable conservation of local environments around highly conserved active site residues that have similar functions across protein families, but where members have relatively low sequence homology. Thus, quantitative evaluation of this QPD is suggested, here, as a tool for structure-function prediction, analysis, and parameter development for the calculation of properties in proteins.
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Affiliation(s)
- Debashree Bandyopadhyay
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, New York 10021, USA
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Amadasi A, Surface JA, Spyrakis F, Cozzini P, Mozzarelli A, Kellogg GE. Robust Classification of “Relevant” Water Molecules in Putative Protein Binding Sites. J Med Chem 2008; 51:1063-7. [DOI: 10.1021/jm701023h] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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45
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Amadasi A, Dall'asta C, Ingletto G, Pela R, Marchelli R, Cozzini P. Explaining cyclodextrin–mycotoxin interactions using a ‘natural’ force field. Bioorg Med Chem 2007; 15:4585-94. [PMID: 17449255 DOI: 10.1016/j.bmc.2007.04.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2006] [Revised: 04/03/2007] [Accepted: 04/05/2007] [Indexed: 11/19/2022]
Abstract
Docking techniques and the HINT (Hydropathic Interaction) program were used to explain interactions of aflatoxin B(1) and ochratoxin A with beta- and gamma-cyclodextrins. The work was aimed at designing a chemosensor to identify very low concentrations of these mycotoxins by exploiting the affinity of the cyclodextrin cavity for many small organic molecules. Actually, the inclusion of the fluorescent portion of these toxins into the cavity may lower the quenching effect of the solvent, thus enhancing the luminescence. HINT is a 'natural' force field, based on experimentally determined LogP(octanol/water) values, that is able to consider both enthalpic and entropic contributions to the binding free energy with an unified approach. HINT is normally applied to predict the DeltaG degrees of binding for protein-ligand, protein-protein, and protein-DNA interactions. The leading forces in biomolecular processes are the same as those involved in organic host-guest inclusion phenomena, therefore we applied this methodology for the first time to cyclodextrin complexes. The results allowed us to explain spectroscopic data in absence of available crystallographic or NMR structural data.
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Affiliation(s)
- Alessio Amadasi
- Department of Biochemistry and Molecular Biology, University of Parma, I-43100 Parma, Italy
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46
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Marabotti A, Colonna G, Facchiano A. New computational strategy to analyze the interactions of ERalpha and ERbeta with different ERE sequences. J Comput Chem 2007; 28:1031-41. [PMID: 17269124 DOI: 10.1002/jcc.20582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The importance of computational methods for the simulation and analysis of biological systems has increased during the last years. In particular, methods to predict binding energies are developing not only with the aim of ranking the affinities between two or more complexes, but also to quantify the contribution of different types of interaction. In this work, we present the application of HINT, a non Newtonian force field, to rank the affinities of complexes formed by estrogen receptors (ER) alpha and beta and different estrogen responsive elements (ERE) near the estrogen-regulated genes. We used the crystallographic coordinates of the DNA binding domain of ERalpha complexed to a consensus ERE as a starting point to simulate several complexes in which some nucleotides in the ERE sequence were mutated. Moreover, we used homology modeling methods to create the structure of the complexes between the DNA binding domain of ERbeta (for which no experimental structures are currently available) and the same ERE sequences. Our results show that HINT is able to rank the affinities of ERalpha and ERbeta for different ERE sequences, and to correctly identify the positions on the DNA sequence that are most important for binding affinity. Moreover, the HINT output gives us the opportunity to identify and quantify the role played by each single atom of amino acids and nucleotides in the binding event, as well as to predict the effect on the binding affinity for other nucleotide mutations.
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Affiliation(s)
- Anna Marabotti
- Laboratory of Bioinformatics and Computational Biology, Institute of Food Science, National Research Council, Avellino, Italy.
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