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Wei X, Chen C, Popov AV, Bathe M, Hernandez R. Binding Site Programmable Self-Assembly of 3D Hierarchical DNA Origami Nanostructures. J Phys Chem A 2024; 128:4999-5008. [PMID: 38875485 DOI: 10.1021/acs.jpca.4c02603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2024]
Abstract
DNA nanotechnology has broad applications in biomedical drug delivery and programmable materials. Characterization of the self-assembly of DNA origami and quantum dots (QDs) is necessary for the development of new DNA-based nanostructures. We use computation and experiment to show that the self-assembly of 3D hierarchical nanostructures can be controlled by programming the binding site number and their positions on DNA origami. Using biotinylated pentagonal pyramid wireframe DNA origamis and streptavidin capped QDs, we demonstrate that DNA origami with 1 binding site at the outer vertex can assemble multimeric origamis with up to 6 DNA origamis on 1 QD, and DNA origami with 1 binding site at the inner center can only assemble monomeric and dimeric origamis. Meanwhile, the yield percentages of different multimeric origamis are controlled by the QD:DNA-origami stoichiometric mixing ratio. DNA origamis with 2 binding sites at the αγ positions (of the pentagon) make larger nanostructures than those with binding sites at the αβ positions. In general, increasing the number of binding sites leads to increases in the nanostructure size. At high DNA origami concentration, the QD number in each cluster becomes the limiting factor for the growth of nanostructures. We find that reducing the QD size can also affect the self-assembly because of the reduced access to the binding sites from more densely packed origamis.
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Affiliation(s)
- Xingfei Wei
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Chi Chen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Alexander V Popov
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Rigoberto Hernandez
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
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Mao XR, Wang Q, Zhuo SP, Xu LP. Reactivity and Selectivity of the Diels-Alder Reaction of Anthracene in [Pd 6L 4] 12+ Supramolecular Cages: A Computational Study. Inorg Chem 2023; 62:4330-4340. [PMID: 36863004 DOI: 10.1021/acs.inorgchem.3c00005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
The field of supramolecular metal-organic cage catalysis has grown rapidly in recent years. However, theoretical studies regarding the reaction mechanism and reactivity and selectivity controlling factors for supramolecular catalysis are still underdeveloped. Herein, we demonstrate a detailed density functional theory study on the mechanism, catalytic efficiency, and regioselectivity of the Diels-Alder reaction in bulk solution and within two [Pd6L4]12+ supramolecular cages. Our calculations are consistent with experiments. The origins of the catalytic efficiency of the bowl-shaped cage 1 have been elucidated to be the host-guest stabilization of the transition states and the favorable entropy effect. The reasons for the switch of the regioselectivity from 9,10-addition to 1,4-addition within the octahedral cage 2 were attributed to the confinement effect and the noncovalent interactions. This work would shed light on the understanding of [Pd6L4]12+ metallocage-catalyzed reactions and provide a detailed mechanistic profile otherwise difficult to obtain from experiments. The findings of this study could also aid to the improvement and development of more efficient and selective supramolecular catalysis.
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Affiliation(s)
- Xin-Rui Mao
- School of Chemistry and Chemical Engineering, Shandong University of Technology, Zibo 255049, China
| | - Qian Wang
- School of Chemistry and Chemical Engineering, Shandong University of Technology, Zibo 255049, China
| | - Shu-Ping Zhuo
- School of Chemistry and Chemical Engineering, Shandong University of Technology, Zibo 255049, China
| | - Li-Ping Xu
- School of Chemistry and Chemical Engineering, Shandong University of Technology, Zibo 255049, China
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Dutkiewicz Z. Computational methods for calculation of protein-ligand binding affinities in structure-based drug design. PHYSICAL SCIENCES REVIEWS 2022. [DOI: 10.1515/psr-2020-0034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Abstract
Drug design is an expensive and time-consuming process. Any method that allows reducing the time the costs of the drug development project can have great practical value for the pharmaceutical industry. In structure-based drug design, affinity prediction methods are of great importance. The majority of methods used to predict binding free energy in protein-ligand complexes use molecular mechanics methods. However, many limitations of these methods in describing interactions exist. An attempt to go beyond these limits is the application of quantum-mechanical description for all or only part of the analyzed system. However, the extensive use of quantum mechanical (QM) approaches in drug discovery is still a demanding challenge. This chapter briefly reviews selected methods used to calculate protein-ligand binding affinity applied in virtual screening (VS), rescoring of docked poses, and lead optimization stage, including QM methods based on molecular simulations.
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Affiliation(s)
- Zbigniew Dutkiewicz
- Department of Chemical Technology of Drugs , Poznan University of Medical Sciences , ul. Grunwaldzka 6 , 60-780 Poznań , Poznan , 60-780, Poland
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Suriya U, Mahalapbutr P, Rungrotmongkol T. Integration of In Silico Strategies for Drug Repositioning towards P38α Mitogen-Activated Protein Kinase (MAPK) at the Allosteric Site. Pharmaceutics 2022; 14:pharmaceutics14071461. [PMID: 35890356 PMCID: PMC9321129 DOI: 10.3390/pharmaceutics14071461] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/05/2022] [Accepted: 07/10/2022] [Indexed: 02/05/2023] Open
Abstract
P38α mitogen-activated protein kinase (p38α MAPK), one of the p38 MAPK isoforms participating in a signaling cascade, has been identified for its pivotal role in the regulation of physiological processes such as cell proliferation, differentiation, survival, and death. Herein, by shedding light on docking- and 100-ns dynamic-based screening from 3210 FDA-approved drugs, we found that lomitapide (a lipid-lowering agent) and nilotinib (a Bcr-Abl fusion protein inhibitor) could alternatively inhibit phosphorylation of p38α MAPK at the allosteric site. All-atom molecular dynamics simulations and free energy calculations including end-point and QM-based ONIOM methods revealed that the binding affinity of the two screened drugs exhibited a comparable level as the known p38α MAPK inhibitor (BIRB796), suggesting the high potential of being a novel p38α MAPK inhibitor. In addition, noncovalent contacts and the number of hydrogen bonds were found to be corresponding with the great binding recognition. Key influential amino acids were mostly hydrophobic residues, while the two charged residues including E71 and D168 were considered crucial ones due to their ability to form very strong H-bonds with the focused drugs. Altogether, our contributions obtained here could be theoretical guidance for further conducting experimental-based preclinical studies necessary for developing therapeutic agents targeting p38α MAPK.
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Affiliation(s)
- Utid Suriya
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Panupong Mahalapbutr
- Department of Biochemistry, Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khan Kaen 40002, Thailand;
| | - Thanyada Rungrotmongkol
- Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Chulalongkorn University, Bangkok 10330, Thailand
- Ph.D. Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
- Correspondence:
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Dushanan R, Weerasinghe S, Dissanayake DP, Senthilinithy R. Implication of Ab Initio, QM/MM, and molecular dynamics calculations on the prediction of the therapeutic potential of some selected HDAC inhibitors. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2097672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Ramachandren Dushanan
- Department of Chemistry, Faculty of Natural Sciences, The Open University of Sri Lanka, Nugegoda, Sri Lanka
| | - Samantha Weerasinghe
- Department of Chemistry, Faculty of Science, University of Colombo, Colombo, Sri Lanka
| | | | - Rajendram Senthilinithy
- Department of Chemistry, Faculty of Natural Sciences, The Open University of Sri Lanka, Nugegoda, Sri Lanka
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Jović O, Šmuc T. Combined Machine Learning and Molecular Modelling Workflow for the Recognition of Potentially Novel Fungicides. Molecules 2020; 25:molecules25092198. [PMID: 32397151 PMCID: PMC7249108 DOI: 10.3390/molecules25092198] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/02/2020] [Accepted: 05/06/2020] [Indexed: 12/31/2022] Open
Abstract
Novel machine learning and molecular modelling filtering procedures for drug repurposing have been carried out for the recognition of the novel fungicide targets of Cyp51 and Erg2. Classification and regression approaches on molecular descriptors have been performed using stepwise multilinear regression (FS-MLR), uninformative-variable elimination partial-least square regression, and a non-linear method called Forward Stepwise Limited Correlation Random Forest (FS-LM-RF). Altogether, 112 prediction models from two different approaches have been built for the descriptor recognition of fungicide hit compounds. Aiming at the fungal targets of sterol biosynthesis in membranes, antifungal hit compounds have been selected for docking experiments from the Drugbank database using the Autodock4 molecular docking program. The results were verified by Gold Protein-Ligand Docking Software. The best-docked conformation, for each high-scored ligand considered, was submitted to quantum mechanics/molecular mechanics (QM/MM) gradient optimization with final single point calculations taking into account both the basis set superposition error and thermal corrections (with frequency calculations). Finally, seven Drugbank lead compounds were selected based on their high QM/MM scores for the Cyp51 target, and three were selected for the Erg2 target. These lead compounds could be recommended for further in vitro studies.
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Maurer M, Oostenbrink C. Water in protein hydration and ligand recognition. J Mol Recognit 2019; 32:e2810. [PMID: 31456282 PMCID: PMC6899928 DOI: 10.1002/jmr.2810] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/31/2019] [Accepted: 08/01/2019] [Indexed: 12/16/2022]
Abstract
This review describes selected basics of water in biomolecular recognition. We focus on a qualitative understanding of the most important physical aspects, how these change in magnitude between bulk water and protein environment, and how the roles that water plays for proteins arise from them. These roles include mechanical support, thermal coupling, dielectric screening, mass and charge transport, and the competition with a ligand for the occupation of a binding site. The presence or absence of water has ramifications that range from the thermodynamic binding signature of a single ligand up to cellular survival. The large inhomogeneity in water density, polarity and mobility around a solute is hard to assess in experiment. This is a source of many difficulties in the solvation of protein models and computational studies that attempt to elucidate or predict ligand recognition. The influence of water in a protein binding site on the experimental enthalpic and entropic signature of ligand binding is still a point of much debate. The strong water‐water interaction in enthalpic terms is counteracted by a water molecule's high mobility in entropic terms. The complete arrest of a water molecule's mobility sets a limit on the entropic contribution of a water displacement process, while the solvent environment sets limits on ligand reactivity.
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Affiliation(s)
- Manuela Maurer
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria
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Jalili S, Maddah M, Schofield J. Molecular dynamics simulation and free energy analysis of the interaction of platinum-based anti-cancer drugs with DNA. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2016. [DOI: 10.1142/s0219633616500541] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Cisplatin and oxaliplatin are two widely-used anti-cancer drugs which covalently bind to a same location in DNA strands. Platinum agents make intrastrand and interstrand cross-links with the N7 atoms of guanine nucleotides which prevent DNA from polymerization by causing a distortion in the double helix. Molecular dynamics simulations and free energy calculations were carried out to investigate the binding of two platinum-based anti-cancer drugs with DNA. We compared the binding of these drugs which differ in their carrier ligands, and hence their potential interactions with DNA. When a platinum agent binds to nucleotides, it causes a high amount of deformation in DNA structure. To find the extent of deformation, torsion angles and base pair and groove parameters of DNA were considered. These parameters were compared with normal B-DNA which was considered as the undamaged DNA. The formation of hydrogen bonds between drugs and DNA nucleotides was examined in solution. It was shown that oxaliplatin forms more hydrogen bonds than cisplatin. Our results confirm that the structure of the platinated DNA rearranges significantly and cisplatin tries to deform DNA more than oxaliplatin. The binding free energies were also investigated to understand the affinities, types and the contributions of interactions between drugs and DNA. It was concluded that oxaliplatin tendency for binding to DNA is more than cisplatin in solvent environment. The binding free energy was calculated based on the MM/PBSA and MM/GBSA methods and the results of QM/MM calculations verified them.
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Affiliation(s)
- Seifollah Jalili
- Department of Chemistry, K. N. Toosi University of Technology, P. O. Box 15875-4416, Tehran, Iran
- Computational Physical Sciences Research Laboratory, School of Nano-Science, Institute for Research in Fundamental Sciences (IPM), P. O. Box 19395-5531 Tehran, Iran
| | - Mina Maddah
- Department of Chemistry, K. N. Toosi University of Technology, P. O. Box 15875-4416, Tehran, Iran
| | - Jeremy Schofield
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Ontario M5S 3H6, Canada
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Omelyan I, Kovalenko A. MTS-MD of Biomolecules Steered with 3D-RISM-KH Mean Solvation Forces Accelerated with Generalized Solvation Force Extrapolation. J Chem Theory Comput 2016; 11:1875-95. [PMID: 26574393 DOI: 10.1021/ct5010438] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We developed a generalized solvation force extrapolation (GSFE) approach to speed up multiple time step molecular dynamics (MTS-MD) of biomolecules steered with mean solvation forces obtained from the 3D-RISM-KH molecular theory of solvation (three-dimensional reference interaction site model with the Kovalenko-Hirata closure). GSFE is based on a set of techniques including the non-Eckart-like transformation of coordinate space separately for each solute atom, extension of the force-coordinate pair basis set followed by selection of the best subset, balancing the normal equations by modified least-squares minimization of deviations, and incremental increase of outer time step in motion integration. Mean solvation forces acting on the biomolecule atoms in conformations at successive inner time steps are extrapolated using a relatively small number of best (closest) solute atomic coordinates and corresponding mean solvation forces obtained at previous outer time steps by converging the 3D-RISM-KH integral equations. The MTS-MD evolution steered with GSFE of 3D-RISM-KH mean solvation forces is efficiently stabilized with our optimized isokinetic Nosé-Hoover chain (OIN) thermostat. We validated the hybrid MTS-MD/OIN/GSFE/3D-RISM-KH integrator on solvated organic and biomolecules of different stiffness and complexity: asphaltene dimer in toluene solvent, hydrated alanine dipeptide, miniprotein 1L2Y, and protein G. The GSFE accuracy and the OIN efficiency allowed us to enlarge outer time steps up to huge values of 1-4 ps while accurately reproducing conformational properties. Quasidynamics steered with 3D-RISM-KH mean solvation forces achieves time scale compression of conformational changes coupled with solvent exchange, resulting in further significant acceleration of protein conformational sampling with respect to real time dynamics. Overall, this provided a 50- to 1000-fold effective speedup of conformational sampling for these systems, compared to conventional MD with explicit solvent. We have been able to fold the miniprotein from a fully denatured, extended state in about 60 ns of quasidynamics steered with 3D-RISM-KH mean solvation forces, compared to the average physical folding time of 4-9 μs observed in experiment.
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Affiliation(s)
- Igor Omelyan
- Department of Mechanical Engineering, University of Alberta , Mechanical Engineering Building 4-9, Edmonton, Alberta T6G 2G8, Canada.,National Institute for Nanotechnology, 11421 Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada.,Institute for Condensed Matter Physics, National Academy of Sciences of Ukraine , 1 Svientsitskii Street, Lviv 79011, Ukraine
| | - Andriy Kovalenko
- Department of Mechanical Engineering, University of Alberta , Mechanical Engineering Building 4-9, Edmonton, Alberta T6G 2G8, Canada.,National Institute for Nanotechnology, 11421 Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
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10
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Ryde U, Söderhjelm P. Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods. Chem Rev 2016; 116:5520-66. [DOI: 10.1021/acs.chemrev.5b00630] [Citation(s) in RCA: 175] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ulf Ryde
- Department of Theoretical
Chemistry and ‡Department of Biophysical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Pär Söderhjelm
- Department of Theoretical
Chemistry and ‡Department of Biophysical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
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11
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van den Hurk R, Evoy S. A Review of Membrane-Based Biosensors for Pathogen Detection. SENSORS 2015; 15:14045-78. [PMID: 26083229 PMCID: PMC4507637 DOI: 10.3390/s150614045] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 05/29/2015] [Accepted: 06/05/2015] [Indexed: 01/14/2023]
Abstract
Biosensors are of increasing interest for the detection of bacterial pathogens in many applications such as human, animal and plant health, as well as food and water safety. Membranes and membrane-like structures have been integral part of several pathogen detection platforms. Such structures may serve as simple mechanical support, function as a part of the transduction mechanism, may be used to filter out or concentrate pathogens, and may be engineered to specifically house active proteins. This review focuses on membrane materials, their associated biosensing applications, chemical linking procedures, and transduction mechanisms. The sensitivity of membrane biosensors is discussed, and the state of the field is evaluated and summarized.
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Affiliation(s)
- Remko van den Hurk
- Department of Electrical and Computer Engineering, University of Alberta Edmonton, Alberta, AB T6G 2V4, Canada.
| | - Stephane Evoy
- Department of Electrical and Computer Engineering, University of Alberta Edmonton, Alberta, AB T6G 2V4, Canada.
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12
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Chung LW, Sameera WMC, Ramozzi R, Page AJ, Hatanaka M, Petrova GP, Harris TV, Li X, Ke Z, Liu F, Li HB, Ding L, Morokuma K. The ONIOM Method and Its Applications. Chem Rev 2015; 115:5678-796. [PMID: 25853797 DOI: 10.1021/cr5004419] [Citation(s) in RCA: 734] [Impact Index Per Article: 81.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Lung Wa Chung
- †Department of Chemistry, South University of Science and Technology of China, Shenzhen 518055, China
| | - W M C Sameera
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Romain Ramozzi
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Alister J Page
- §Newcastle Institute for Energy and Resources, The University of Newcastle, Callaghan 2308, Australia
| | - Miho Hatanaka
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Galina P Petrova
- ∥Faculty of Chemistry and Pharmacy, University of Sofia, Bulgaria Boulevard James Bourchier 1, 1164 Sofia, Bulgaria
| | - Travis V Harris
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan.,⊥Department of Chemistry, State University of New York at Oswego, Oswego, New York 13126, United States
| | - Xin Li
- #State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhuofeng Ke
- ∇School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Fengyi Liu
- ○Key Laboratory of Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Hai-Bei Li
- ■School of Ocean, Shandong University, Weihai 264209, China
| | - Lina Ding
- ▲School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Keiji Morokuma
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
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Fedotova MV, Dmitrieva OA. Characterization of selective binding of biologically relevant inorganic ions with the proline zwitterion by 3D-RISM theory. NEW J CHEM 2015. [DOI: 10.1039/c5nj01559f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The features of selective binding of several biologically relevant mono- and divalent inorganic ions with the proline zwitterion were studied over a wide range of electrolyte concentrations.
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Affiliation(s)
- Marina V. Fedotova
- G.A. Krestov Institute of Solution Chemistry
- Russian Academy of Sciences
- Ivanovo 153045
- Russia
| | - Olga A. Dmitrieva
- G.A. Krestov Institute of Solution Chemistry
- Russian Academy of Sciences
- Ivanovo 153045
- Russia
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Sakulsombat M, Vongvilai P, Ramström O. Efficient asymmetric synthesis of 1-cyano-tetrahydroisoquinolines from lipase dual activity and opposite enantioselectivities in α-Aminonitrile resolution. Chemistry 2014; 20:11322-5. [PMID: 25055970 PMCID: PMC4497319 DOI: 10.1002/chem.201402615] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Indexed: 01/15/2023]
Abstract
Dual promiscuous racemization/amidation activities of lipases leading to efficient dynamic kinetic resolution protocols of racemic α-aminonitrile compounds are described. α-Amidonitrile products of high enantiomeric purity could be formed in high yields. Several lipases from different sources were shown to exhibit the dual catalytic activities, where opposite enantioselectivities could be recorded for certain substrates.
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Affiliation(s)
- Morakot Sakulsombat
- KTH Royal Institute of Technology Department of ChemistryTeknikringen 30, 10044 Stockholm (Sweden)
| | - Pornrapee Vongvilai
- KTH Royal Institute of Technology Department of ChemistryTeknikringen 30, 10044 Stockholm (Sweden)
- BioNet-Asia Co., Ltd. 19 Soi Udomsuk 37, Sukhumvit 103 road, Bangkok 10260 (Thailand)
| | - Olof Ramström
- KTH Royal Institute of Technology Department of ChemistryTeknikringen 30, 10044 Stockholm (Sweden)
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15
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Fedotova MV, Kruchinin SE. Ion-binding of glycine zwitterion with inorganic ions in biologically relevant aqueous electrolyte solutions. Biophys Chem 2014; 190-191:25-31. [DOI: 10.1016/j.bpc.2014.04.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 04/02/2014] [Accepted: 04/02/2014] [Indexed: 11/29/2022]
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Abstract
AbstractAbstract Experimentally-known sulfur-sulfur distances shorter than the sum of van der Waals radii and involving two chemically-identical sulfur atoms are examined at several levels of theory (BP86/6-31G** to CCSD(T)/6-311+G**). None of the theoretical methods predict an attractive interaction from an energetic point of view, even though molecular orbitals stretching between the two sulfur atoms have been identified. Most likely, if there is indeed an attractive interaction force between chemically identical sulfur atoms, its value is comparable to the accuracy of the methods employed here — implying an attractive interaction below 1 kcal/mol. The investigation includes some simple models of 1,6,12,17-tetrathiacyclodocosa-2,4,13,15-tetrayne which was previously shown to have an S—S interaction involving two chemically-identical atoms. Attractive interactions calculated for these latter models are shown to arise from S—HC weak bonding, with the S—S interaction being again repulsive. Graphical abstract
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17
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Deng L, Kitova EN, Klassen JS. Dissociation kinetics of the streptavidin-biotin interaction measured using direct electrospray ionization mass spectrometry analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:49-56. [PMID: 23247970 DOI: 10.1007/s13361-012-0533-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Revised: 10/31/2012] [Accepted: 11/02/2012] [Indexed: 06/01/2023]
Abstract
Dissociation rate constants (k (off)) for the model high affinity interaction between biotin (B) and the homotetramer of natural core streptavidin (S(4)) were measured at pH 7 and temperatures ranging from 15 to 45 °C using electrospray ionization mass spectrometry (ESI-MS). Two different approaches to data analysis were employed, one based on the initial rate of dissociation of the (S(4) + 4B) complex, the other involving nonlinear fitting of the time-dependent relative abundances of the (S(4) + iB) species. The two methods were found to yield k (off) values that are in good agreement, within a factor of two. The Arrhenius parameters for the dissociation of the biotin-streptavidin interaction in solution were established from the k (off) values determined by ESI-MS and compared with values measured using a radiolabeled biotin assay. Importantly, the dissociation activation energies determined by ESI-MS agree, within 1 kcal mol(-1), with the reported value. In addition to providing a quantitative measure of k (off), the results of the ESI-MS measurements revealed that the apparent cooperative distribution of (S(4) + iB) species observed at short reaction times is of kinetic origin and that sequential binding of B to S(4) occurs in a noncooperative fashion with the four ligand binding sites being kinetically and thermodynamically equivalent and independent.
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Affiliation(s)
- Lu Deng
- Department of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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18
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Kinetic Stability of the Streptavidin–Biotin Interaction Enhanced in the Gas Phase. J Am Chem Soc 2012; 134:16586-96. [DOI: 10.1021/ja305213z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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da Costa LM, Hayaki S, Stoyanov SR, Gusarov S, Tan X, Gray MR, Stryker JM, Tykwinski R, Carneiro JWDM, Sato H, Seidl PR, Kovalenko A. 3D-RISM-KH molecular theory of solvation and density functional theory investigation of the role of water in the aggregation of model asphaltenes. Phys Chem Chem Phys 2012; 14:3922-34. [DOI: 10.1039/c2cp23131j] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Le Trong I, Wang Z, Hyre DE, Lybrand TP, Stayton PS, Stenkamp RE. Streptavidin and its biotin complex at atomic resolution. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2011; 67:813-21. [PMID: 21904034 PMCID: PMC3169315 DOI: 10.1107/s0907444911027806] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Accepted: 07/11/2011] [Indexed: 11/10/2022]
Abstract
Atomic resolution crystallographic studies of streptavidin and its biotin complex have been carried out at 1.03 and 0.95 Å, respectively. The wild-type protein crystallized with a tetramer in the asymmetric unit, while the crystals of the biotin complex contained two subunits in the asymmetric unit. Comparison of the six subunits shows the various ways in which the protein accommodates ligand binding and different crystal-packing environments. Conformational variation is found in each of the polypeptide loops connecting the eight strands in the β-sandwich subunit, but the largest differences are found in the flexible binding loop (residues 45-52). In three of the unliganded subunits the loop is in an `open' conformation, while in the two subunits binding biotin, as well as in one of the unliganded subunits, this loop `closes' over the biotin-binding site. The `closed' loop contributes to the protein's high affinity for biotin. Analysis of the anisotropic displacement parameters included in the crystallographic models is consistent with the variation found in the loop structures and the view that the dynamic nature of the protein structure contributes to the ability of the protein to bind biotin so tightly.
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Affiliation(s)
- Isolde Le Trong
- Department of Biological Structure, University of Washington, Box 35742, Seattle, WA 98195-7420, USA
- Biomolecular Structure Center, University of Washington, Box 357742, Seattle, WA 98195-7742, USA
| | - Zhizhi Wang
- Department of Biological Structure, University of Washington, Box 35742, Seattle, WA 98195-7420, USA
| | - David E. Hyre
- Department of Bioengineering, University of Washington, Box 355061, Seattle, WA 98195-5061, USA
| | - Terry P. Lybrand
- Center for Structural Biology, Department of Chemistry, Vanderbilt University, 5142 Medical Research Building III, 465 21st Avenue South, Nashville, TN 37232-8725, USA
| | - Patrick S. Stayton
- Department of Bioengineering, University of Washington, Box 355061, Seattle, WA 98195-5061, USA
| | - Ronald E. Stenkamp
- Department of Biological Structure, University of Washington, Box 35742, Seattle, WA 98195-7420, USA
- Biomolecular Structure Center, University of Washington, Box 357742, Seattle, WA 98195-7742, USA
- Department of Biochemistry, University of Washington, Box 357430, Seattle, WA 98195-7430, USA
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Genheden S, Mikulskis P, Hu L, Kongsted J, Söderhjelm P, Ryde U. Accurate Predictions of Nonpolar Solvation Free Energies Require Explicit Consideration of Binding-Site Hydration. J Am Chem Soc 2011; 133:13081-92. [DOI: 10.1021/ja202972m] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Samuel Genheden
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Paulius Mikulskis
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - LiHong Hu
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
- School of Computer Science and Information Technology, Northeast Normal University, Changchun, 130024, People's Republic of China
| | - Jacob Kongsted
- Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Pär Söderhjelm
- Department of Chemistry and Applied Biosciences—Computational Science, ETH Zürich, Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
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How the biotin-streptavidin interaction was made even stronger: investigation via crystallography and a chimaeric tetramer. Biochem J 2011; 435:55-63. [PMID: 21241253 PMCID: PMC3062853 DOI: 10.1042/bj20101593] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The interaction between SA (streptavidin) and biotin is one of the strongest non-covalent interactions in Nature. SA is a widely used tool and a paradigm for protein–ligand interactions. We previously developed a SA mutant, termed Tr (traptavidin), possessing a 10-fold lower off-rate for biotin, with increased mechanical and thermal stability. In the present study, we determined the crystal structures of apo-Tr and biotin–Tr at 1.5 Å resolution. In apo-SA the loop (L3/4), near biotin's valeryl tail, is typically disordered and open, but closes upon biotin binding. In contrast, L3/4 was shut in both apo-Tr and biotin–Tr. The reduced flexibility of L3/4 and decreased conformational change on biotin binding provide an explanation for Tr's reduced biotin off- and on-rates. L3/4 includes Ser45, which forms a hydrogen bond to biotin consistently in Tr, but erratically in SA. Reduced breakage of the biotin–Ser45 hydrogen bond in Tr is likely to inhibit the initiating event in biotin's dissociation pathway. We generated a Tr with a single biotin-binding site rather than four, which showed a simi-larly low off-rate, demonstrating that Tr's low off-rate was governed by intrasubunit effects. Understanding the structural features of this tenacious interaction may assist the design of even stronger affinity tags and inhibitors.
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Stoyanov SR, Yin CX, Gray MR, Stryker JM, Gusarov S, Kovalenko A. Computational and experimental study of the structure, binding preferences, and spectroscopy of nickel(II) and vanadyl porphyrins in petroleum. J Phys Chem B 2010; 114:2180-8. [PMID: 20099931 DOI: 10.1021/jp908641t] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a computational exploration of five- and six-coordinate Ni(II) and vanadyl porphyrins, including prediction of UV-vis spectroscopic behavior and metalloporphyrin structure as well as determination of a binding energy threshold between strongly bound complexes that have been isolated as single crystals and weakly bound ones that we detect by visible absorption spectroscopy. The excited states are calculated using the tandem of the time-dependent density functional theory (TD-DFT) and the conductor-like polarizable continuum model (CPCM). The excited-state energies in chloroform solvent obtained by using two density functionals are found to correlate linearly with the experimental Soret and alpha-band energies for a known series of five-coordinate vanadyl porphyrins. The established linear correction allows simulation of the excited states for labile octahedral vanadyl porphyrins that have not been isolated and yields Soret and alpha-band bathochromic shifts that are in agreement with our UV-vis spectroscopic results. The PBE0 and PW91 functionals in combination with DNP basis set perform best for both structure and binding energy prediction. The reactivity preferences of Ni(II) and vanadyl porphyrins toward aromatic fragments of large petroleum molecules are explored by using the density functional theory (DFT). Analysis of electrostatic potentials and Fukui functions matching shows that axial coordination and hydrogen bonding are the preferred aggregation modes between vanadyl porphyrins and nitrogen-containing heterocycle fragments. This investigation improves our understanding on the cause for broadening of the Ni and V porphyrin Soret band in heavy oils. Our findings can be useful for the development of metals removal methods for heavy oil upgrading.
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Affiliation(s)
- Stanislav R Stoyanov
- National Institute for Nanotechnology, National Research Council of Canada, 11421 Saskatchewan Drive, Edmonton, AB, T6G 2M9, Canada
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