1
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Rezaul Islam M, Akash S, Murshedul Islam M, Sarkar N, Kumer A, Chakraborty S, Dhama K, Ahmed Al-Shaeri M, Anwar Y, Wilairatana P, Rauf A, Halawani IF, Alzahrani FM, Khan H. Alkaloids as drug leads in Alzheimer's treatment: Mechanistic and therapeutic insights. Brain Res 2024; 1834:148886. [PMID: 38582413 DOI: 10.1016/j.brainres.2024.148886] [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: 02/10/2024] [Revised: 03/22/2024] [Accepted: 03/23/2024] [Indexed: 04/08/2024]
Abstract
Alzheimer's disease (AD) has few effective treatment options and continues to be a major global health concern. AD is a neurodegenerative disease that typically affects elderly people. Alkaloids have potential sources for novel drug discovery due to their diverse chemical structures and pharmacological activities. Alkaloids, natural products with heterocyclic nitrogen-containing structures, are considered potential treatments for AD. This review explores the neuroprotective properties of alkaloids in AD, focusing on their ability to regulate pathways such as amyloid-beta aggregation, oxidative stress, synaptic dysfunction, tau hyperphosphorylation, and neuroinflammation. The FDA has approved alkaloids such as acetylcholinesterase inhibitors like galantamine and rivastigmine. This article explores AD's origins, current market medications, and clinical applications of alkaloids in AD therapy. This review explores the development of alkaloid-based drugs for AD, focusing on pharmacokinetics, blood-brain barrier penetration, and potential adverse effects. Future research should focus on the clinical evaluation of promising alkaloids, developing recently discovered alkaloids, and the ongoing search for novel alkaloids for medical treatment. A pharmaceutical option containing an alkaloid may potentially slow down the progression of AD while enhancing its symptoms. This review highlights the potential of alkaloids as valuable drug leads in treating AD, providing a comprehensive understanding of their mechanisms of action and therapeutic implications.
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Affiliation(s)
- Md Rezaul Islam
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Daffodil Smart City, Birulia, Savar, Dhaka 1216, Bangladesh
| | - Shopnil Akash
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Daffodil Smart City, Birulia, Savar, Dhaka 1216, Bangladesh
| | - Mohammed Murshedul Islam
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Daffodil Smart City, Birulia, Savar, Dhaka 1216, Bangladesh
| | - Nadia Sarkar
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Daffodil Smart City, Birulia, Savar, Dhaka 1216, Bangladesh
| | - Ajoy Kumer
- Laboratory of Computational Research for Drug Design and Material Science, Department of Chemistry, College of Arts and Sciences IUBAT-International University of Business Agriculture and Technology, 4 Embankment Drive Road, Sector 10, Uttara Model Town, Dhaka 1230, Bangladesh; Center for Global Health Research, Saveetha Medical College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
| | - Sandip Chakraborty
- State Disease Investigation Laboratory, ARDD, Abhoynagar, Agartala, West Tripura, Pin-799005, India
| | - Kuldeep Dhama
- Division of Pathology, Indian Veterinary Research Institute (IVRI) Izatnagar-243 122, Bareilly, Uttar Pradesh, India
| | - Majed Ahmed Al-Shaeri
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21441, Kingdom of Saudi Arabia
| | - Yasir Anwar
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21441, Kingdom of Saudi Arabia
| | - Polrat Wilairatana
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Abdur Rauf
- Department of Chemistry, University of Swabi, Anbar 23561, Khyber Pakhtunkhwa, Pakistan
| | - Ibrahim F Halawani
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Fuad M Alzahrani
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Haroon Khan
- Department of Pharmacy, Abdul Wali Khan University Mardan, 23200 Mardan, Pakistan.
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2
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Richmond V, Falcone BN, Maier MS, Arroyo Máñez P. Putting the Puzzle Together To Get the Whole Picture: Molecular Basis of the Affinity of Two Steroid Derivatives to Acetylcholinesterase. ACS OMEGA 2023; 8:25610-25622. [PMID: 37483177 PMCID: PMC10357547 DOI: 10.1021/acsomega.3c03749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 06/14/2023] [Indexed: 07/25/2023]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder that has no cure because its etiology is still unknown, and its main treatment is the administration of acetylcholinesterase (AChE) inhibitors. The study of the mechanism of action of this family of compounds is critical for the design of new more potent and specific inhibitors. In this work, we study the molecular basis of an uncompetitive inhibitor (compound 1, 2β, 3α-dihydroxy-5α-cholestan-6-one disulfate), which we have proved to be a peripheral anionic site (PAS)-binding AChE inhibitor. The pipeline designed in this work is key to the development of other PAS inhibitors that not only inhibit the esterase action of the enzyme but could also modulate the non-cholinergic functions of AChE linked to the process of amylogenesis. Our studies showed that 1 inhibits the enzyme not simply by blocking the main gate but by an allosteric mechanism. A detailed and careful analysis of the ligand binding position and the protein dynamics, particularly regarding their secondary gates and active site, was necessary to conclude this. The same analysis was executed with an inactive analogue (compound 2, 2β, 3α-dihydroxy-5α-cholestan-6-one). Our first computational results showed no differences in affinity to AChE between both steroids, making further analysis necessary. This work highlights the variables to be considered and develops a refined methodology, for the successful design of new potent dual-action drugs for AD, particularly PAS inhibitors, an attractive strategy to combat AD.
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Affiliation(s)
- Victoria Richmond
- Facultad
de Ciencias Exactas y Naturales, Departamento de Química Orgánica, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
- Unidad
de Microanálisis y Métodos Físicos aplicados
a la Química Orgánica (UMYMFOR), CONICET-Universidad de Buenos Aires, Pabellón 2 de Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
| | - Bruno N. Falcone
- Facultad
de Ciencias Exactas y Naturales, Departamento de Química Orgánica, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
- Unidad
de Microanálisis y Métodos Físicos aplicados
a la Química Orgánica (UMYMFOR), CONICET-Universidad de Buenos Aires, Pabellón 2 de Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
| | - Marta S. Maier
- Facultad
de Ciencias Exactas y Naturales, Departamento de Química Orgánica, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
- Unidad
de Microanálisis y Métodos Físicos aplicados
a la Química Orgánica (UMYMFOR), CONICET-Universidad de Buenos Aires, Pabellón 2 de Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
| | - Pau Arroyo Máñez
- Instituto
Interuniversitario de Investigación de Reconocimiento Molecular
y Desarrollo Tecnológico (IDM), Universitat
Politècnica de València, Universitat de València, Doctor Moliner 50, Burjassot, Valencia 46100, Spain
- Departamento
de Química Orgánica, Universitat
de València, Doctor Moliner 50, Burjassot, Valencia 46100, Spain
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3
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Diffusion control in biochemical specificity. Biophys J 2022; 121:1541-1548. [PMID: 35278424 PMCID: PMC9072584 DOI: 10.1016/j.bpj.2022.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/28/2021] [Accepted: 03/04/2022] [Indexed: 11/20/2022] Open
Abstract
Biochemical specificity is critical in enzyme function, evolution, and engineering. Here we employ an established kinetic model to dissect the effects of reactant geometry and diffusion on product formation speed and accuracy in the presence of cognate (correct) and near-cognate (incorrect) substrates. Using this steady-state model for spherical geometries, we find that, for distinct kinetic regimes, the speed and accuracy of the reactions are optimized on different regions of the geometric landscape. From this model we deduce that accuracy can be strongly dependent on reactant geometric properties even for chemically limited reactions. Notably, substrates with a specific geometry and reactivity can be discriminated by the enzyme with higher efficacy than others through purely diffusive effects. For similar cognate and near-cognate substrate geometries (as is the case for polymerases or the ribosome), we observe that speed and accuracy are maximized in opposing regions of the geometric landscape. We also show that, in relevant environments, diffusive effects on accuracy can be substantial even far from extreme kinetic conditions. Finally, we find how reactant chemical discrimination and diffusion can be related to simultaneously optimize steady-state flux and accuracy. These results highlight how diffusion and geometry can be employed to enhance reaction speed and discrimination, and similarly how they impose fundamental restraints on these quantities.
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4
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Gisriel CJ, Wang J, Liu J, Flesher DA, Reiss KM, Huang HL, Yang KR, Armstrong WH, Gunner MR, Batista VS, Debus RJ, Brudvig GW. High-resolution cryo-electron microscopy structure of photosystem II from the mesophilic cyanobacterium, Synechocystis sp. PCC 6803. Proc Natl Acad Sci U S A 2022; 119:e2116765118. [PMID: 34937700 PMCID: PMC8740770 DOI: 10.1073/pnas.2116765118] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2021] [Indexed: 12/15/2022] Open
Abstract
Photosystem II (PSII) enables global-scale, light-driven water oxidation. Genetic manipulation of PSII from the mesophilic cyanobacterium Synechocystis sp. PCC 6803 has provided insights into the mechanism of water oxidation; however, the lack of a high-resolution structure of oxygen-evolving PSII from this organism has limited the interpretation of biophysical data to models based on structures of thermophilic cyanobacterial PSII. Here, we report the cryo-electron microscopy structure of PSII from Synechocystis sp. PCC 6803 at 1.93-Å resolution. A number of differences are observed relative to thermophilic PSII structures, including the following: the extrinsic subunit PsbQ is maintained, the C terminus of the D1 subunit is flexible, some waters near the active site are partially occupied, and differences in the PsbV subunit block the Large (O1) water channel. These features strongly influence the structural picture of PSII, especially as it pertains to the mechanism of water oxidation.
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Affiliation(s)
| | - Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - Jinchan Liu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - David A Flesher
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - Krystle M Reiss
- Department of Chemistry, Yale University, New Haven, CT 06520
| | - Hao-Li Huang
- Department of Chemistry, Yale University, New Haven, CT 06520
| | - Ke R Yang
- Department of Chemistry, Yale University, New Haven, CT 06520
| | | | - M R Gunner
- Department of Physics, City College of New York, New York, NY 100031
| | | | - Richard J Debus
- Department of Biochemistry, University of California, Riverside, CA 92521
| | - Gary W Brudvig
- Department of Chemistry, Yale University, New Haven, CT 06520;
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
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5
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Sadiq SK, Muñiz Chicharro A, Friedrich P, Wade RC. Multiscale Approach for Computing Gated Ligand Binding from Molecular Dynamics and Brownian Dynamics Simulations. J Chem Theory Comput 2021; 17:7912-7929. [PMID: 34739248 DOI: 10.1021/acs.jctc.1c00673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We develop an approach to characterize the effects of gating by a multiconformation protein consisting of macrostate conformations that are either accessible or inaccessible to ligand binding. We first construct a Markov state model of the apo-protein from atomistic molecular dynamics simulations from which we identify macrostates and their conformations, compute their relative macrostate populations and interchange kinetics, and structurally characterize them in terms of ligand accessibility. We insert the calculated first-order rate constants for conformational transitions into a multistate gating theory from which we derive a gating factor γ that quantifies the degree of conformational gating. Applied to HIV-1 protease, our approach yields a kinetic network of three accessible (semi-open, open, and wide-open) and two inaccessible (closed and a newly identified, "parted") macrostate conformations. The parted conformation sterically partitions the active site, suggesting a possible role in product release. We find that the binding kinetics of drugs and drug-like inhibitors to HIV-1 protease falls in the slow gating regime. However, because γ = 0.75, conformational gating only modestly slows ligand binding. Brownian dynamics simulations of the diffusional association of eight inhibitors to the protease─having a wide range of experimental association constants (∼104-1010 M-1 s-1)─yields gated rate constants in the range of ∼0.5-5.7 × 108 M-1 s-1. This indicates that, whereas the association rate of some inhibitors could be described by the model, for many inhibitors either subsequent conformational transitions or alternate binding mechanisms may be rate-limiting. For systems known to be modulated by conformational gating, the approach could be scaled computationally efficiently to screen association kinetics for a large number of ligands.
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Affiliation(s)
- S Kashif Sadiq
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.,Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.,Infection Biology Unit, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), C/Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Abraham Muñiz Chicharro
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Im Neuenheimer Feld 234, 69120 Heidelberg, Germany
| | - Patrick Friedrich
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.,Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.,Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
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6
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Lawing AM, McCoy M, Reinke BA, Sarkar SK, Smith FA, Wright D. A Framework for Investigating Rules of Life by Establishing Zones of Influence. Integr Comp Biol 2021; 61:2095-2108. [PMID: 34297089 DOI: 10.1093/icb/icab169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/26/2021] [Accepted: 07/20/2021] [Indexed: 12/18/2022] Open
Abstract
The incredible complexity of biological processes across temporal and spatial scales hampers defining common underlying mechanisms driving the patterns of life. However, recent advances in sequencing, big data analysis, machine learning, and molecular dynamics simulation have renewed the hope and urgency of finding potential hidden rules of life. There currently exists no framework to develop such synoptic investigations. Some efforts aim to identify unifying rules of life across hierarchical levels of time, space, and biological organization, but not all phenomena occur across all the levels of these hierarchies. Instead of identifying the same parameters and rules across levels, we posit that each level of a temporal and spatial scale and each level of biological organization has unique parameters and rules that may or may not predict outcomes in neighboring levels. We define this neighborhood, or the set of levels, across which a rule functions as the zone of influence. Here, we introduce the zone of influence framework and explain using three examples: (Smocovitis, 1992) randomness in biology, where we use a Poisson process to describe processes from protein dynamics to DNA mutations to gene expressions, (Leroi, 2014) island biogeography, and (Gropp, 2016) animal coloration. The zone of influence framework may enable researchers to identify which levels are worth investigating for a particular phenomenon and reframe the narrative of searching for a unifying rule of life to the investigation of how, when, and where various rules of life operate.
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Affiliation(s)
| | - Michael McCoy
- Department of Biology, East Carolina University, NC, USA
| | - Beth A Reinke
- Department of Biology, Northeastern Illinois University, IL, USA
| | | | - Felisa A Smith
- Department of Biology, University of New Mexico, NM, USA
| | - Derek Wright
- Department of Physics, Colorado School of Mines, CO, USA
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7
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Bagri K, Kumar A, Manisha, Kumar P. Computational Studies on Acetylcholinesterase Inhibitors: From Biochemistry to Chemistry. Mini Rev Med Chem 2021; 20:1403-1435. [PMID: 31884928 DOI: 10.2174/1389557520666191224144346] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/23/2019] [Accepted: 10/28/2019] [Indexed: 11/22/2022]
Abstract
Acetylcholinesterase inhibitors are the most promising therapeutics for Alzheimer's disease treatment as these prevent the loss of acetylcholine and slows the progression of the disease. The drugs approved for the management of Alzheimer's disease by the FDA are acetylcholinesterase inhibitors but are associated with side effects. Consistent and stringent efforts by the researchers with the help of computational methods opened new ways of developing novel molecules with good acetylcholinesterase inhibitory activity. In this manuscript, we reviewed the studies that identified the essential structural features of acetylcholinesterase inhibitors at the molecular level as well as the techniques like molecular docking, molecular dynamics, quantitative structure-activity relationship, virtual screening, and pharmacophore modelling that were used in designing these inhibitors.
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Affiliation(s)
- Kiran Bagri
- Department of Pharmaceutical Sciences, Guru Jambheshwar University of Science & Technology, Hisar 125001, India
| | - Ashwani Kumar
- Department of Pharmaceutical Sciences, Guru Jambheshwar University of Science & Technology, Hisar 125001, India
| | - Manisha
- Department of Pharmaceutical Sciences, Guru Jambheshwar University of Science & Technology, Hisar 125001, India
| | - Parvin Kumar
- Department of Chemistry, Kurukshetra University, Kurukshetra, India
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8
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Selivanovitch E, LaFrance B, Douglas T. Molecular exclusion limits for diffusion across a porous capsid. Nat Commun 2021; 12:2903. [PMID: 34006828 PMCID: PMC8131759 DOI: 10.1038/s41467-021-23200-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 04/01/2021] [Indexed: 12/19/2022] Open
Abstract
Molecular communication across physical barriers requires pores to connect the environments on either side and discriminate between the diffusants. Here we use porous virus-like particles (VLPs) derived from bacteriophage P22 to investigate the range of molecule sizes able to gain access to its interior. Although there are cryo-EM models of the VLP, they may not accurately depict the parameters of the molecules able to pass across the pores due to the dynamic nature of the P22 particles in the solution. After encapsulating the enzyme AdhD within the P22 VLPs, we use a redox reaction involving PAMAM dendrimer modified NADH/NAD+ to examine the size and charge limitations of molecules entering P22. Utilizing the three different accessible morphologies of the P22 particles, we determine the effective pore sizes of each and demonstrate that negatively charged substrates diffuse across more readily when compared to those that are neutral, despite the negatively charge exterior of the particles.
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Affiliation(s)
| | - Benjamin LaFrance
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Trevor Douglas
- Department of Chemistry, Indiana University, Bloomington, IN, USA.
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9
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De Boer D, Nguyen N, Mao J, Moore J, Sorin EJ. A Comprehensive Review of Cholinesterase Modeling and Simulation. Biomolecules 2021; 11:580. [PMID: 33920972 PMCID: PMC8071298 DOI: 10.3390/biom11040580] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/08/2021] [Accepted: 04/11/2021] [Indexed: 01/18/2023] Open
Abstract
The present article reviews published efforts to study acetylcholinesterase and butyrylcholinesterase structure and function using computer-based modeling and simulation techniques. Structures and models of both enzymes from various organisms, including rays, mice, and humans, are discussed to highlight key structural similarities in the active site gorges of the two enzymes, such as flexibility, binding site location, and function, as well as differences, such as gorge volume and binding site residue composition. Catalytic studies are also described, with an emphasis on the mechanism of acetylcholine hydrolysis by each enzyme and novel mutants that increase catalytic efficiency. The inhibitory activities of myriad compounds have been computationally assessed, primarily through Monte Carlo-based docking calculations and molecular dynamics simulations. Pharmaceutical compounds examined herein include FDA-approved therapeutics and their derivatives, as well as several other prescription drug derivatives. Cholinesterase interactions with both narcotics and organophosphate compounds are discussed, with the latter focusing primarily on molecular recognition studies of potential therapeutic value and on improving our understanding of the reactivation of cholinesterases that are bound to toxins. This review also explores the inhibitory properties of several other organic and biological moieties, as well as advancements in virtual screening methodologies with respect to these enzymes.
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Affiliation(s)
- Danna De Boer
- Department of Chemistry & Biochemistry, California State University, Long Beach, CA 90840, USA;
| | - Nguyet Nguyen
- Department of Chemical Engineering, California State University, Long Beach, CA 90840, USA; (N.N.); (J.M.)
| | - Jia Mao
- Department of Chemical Engineering, California State University, Long Beach, CA 90840, USA; (N.N.); (J.M.)
| | - Jessica Moore
- Department of Biomedical Engineering, California State University, Long Beach, CA 90840, USA;
| | - Eric J. Sorin
- Department of Chemistry & Biochemistry, California State University, Long Beach, CA 90840, USA;
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10
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Kumawat A, Raheem S, Ali F, Dar TA, Chakrabarty S, Rizvi MA. Organoselenium Compounds as Acetylcholinesterase Inhibitors: Evidence and Mechanism of Mixed Inhibition. J Phys Chem B 2021; 125:1531-1541. [PMID: 33538163 DOI: 10.1021/acs.jpcb.0c08111] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Acetylcholinesterase (AChE) inhibitors are actively used for the effective treatment of Alzheimer's disease. In recent years, the neuroprotective effects of organoselenium compounds such as ebselen and diselenides on the AChE activity have been investigated as potential therapeutic agents. In this work, we have carried out systematic kinetic and intrinsic fluorescence assays in combination with docking and molecular dynamics (MD) simulations to elucidate the molecular mechanism of the mixed inhibition of AChE by ebselen and diphenyl diselenide (DPDSe) molecules. Our MD simulations demonstrate significant heterogeneity in the binding modes and allosteric hotspots for DPDSe on AChE due to non-specific interactions. We have further identified that both ebselen and DPDSe can strongly bind around the peripheral anionic site (PAS), leading to non-competitive inhibition similar to other PAS-binding inhibitors. We also illustrate the entry of the DPDSe molecule into the gorge through a "side door", which offers an alternate entry point for AChE inhibitors as compared to the usual substrate entry point of the gorge. Together with results from experiments, these simulations provide mechanistic insights into the mixed type of inhibition for AChE using DPDSe as a promising inhibitor for AChE.
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Affiliation(s)
- Amit Kumawat
- Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata 700106, India
| | - Shabnam Raheem
- Department of Chemistry, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India
| | - Fasil Ali
- Department of Clinical Bio-Chemistry, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India
| | - Tanveer Ali Dar
- Department of Clinical Bio-Chemistry, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India
| | - Suman Chakrabarty
- Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata 700106, India
| | - Masood Ahmad Rizvi
- Department of Chemistry, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India
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11
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Vitorović-Todorović M, Cvijetić I, Zloh M, Perdih A. Molecular recognition of acetylcholinesterase and its subnanomolar reversible inhibitor: a molecular simulations study. J Biomol Struct Dyn 2020; 40:1671-1691. [DOI: 10.1080/07391102.2020.1831960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
| | - Ilija Cvijetić
- Innovation Center of the Faculty of Chemistry, University of Belgrade, Serbia
| | - Mire Zloh
- Faculty of Pharmacy, University Business Academy, Novi Sad, Serbia
- Nanopuzzle Medicines Design Ltd, Stevenage, UK
| | - Andrej Perdih
- National Institute of Chemistry, Ljubljana, Slovenia
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12
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Rahmaninejad H, Pace T, Bhatt S, Sun B, Kekenes-Huskey P. Co-localization and confinement of ecto-nucleotidases modulate extracellular adenosine nucleotide distributions. PLoS Comput Biol 2020; 16:e1007903. [PMID: 32584811 PMCID: PMC7316229 DOI: 10.1371/journal.pcbi.1007903] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 04/22/2020] [Indexed: 12/30/2022] Open
Abstract
Nucleotides comprise small molecules that perform critical signaling roles in biological systems. Adenosine-based nucleotides, including adenosine tri-, di-, and mono-phosphate, are controlled through their rapid degradation by diphosphohydrolases and ecto-nucleotidases (NDAs). The interplay between nucleotide signaling and degradation is especially important in synapses formed between cells, which create signaling 'nanodomains'. Within these 'nanodomains', charged nucleotides interact with densely-packed membranes and biomolecules. While the contributions of electrostatic and steric interactions within such nanodomains are known to shape diffusion-limited reaction rates, less is understood about how these factors control the kinetics of nucleotidase activity. To quantify these factors, we utilized reaction-diffusion numerical simulations of 1) adenosine triphosphate (ATP) hydrolysis into adenosine monophosphate (AMP) and 2) AMP into adenosine (Ado) via two representative nucleotidases, CD39 and CD73. We evaluate these sequentially-coupled reactions in nanodomain geometries representative of extracellular synapses, within which we localize the nucleotidases. With this model, we find that 1) nucleotidase confinement reduces reaction rates relative to an open (bulk) system, 2) the rates of AMP and ADO formation are accelerated by restricting the diffusion of substrates away from the enzymes, and 3) nucleotidase co-localization and the presence of complementary (positive) charges to ATP enhance reaction rates, though the impact of these contributions on nucleotide pools depends on the degree to which the membrane competes for substrates. As a result, these contributions integratively control the relative concentrations and distributions of ATP and its metabolites within the junctional space. Altogether, our studies suggest that CD39 and CD73 nucleotidase activity within junctional spaces can exploit their confinement and favorable electrostatic interactions to finely control nucleotide signaling.
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Affiliation(s)
- Hadi Rahmaninejad
- Department of Physics and Astronomy, University of Kentucky, Lexington, Kentucky, United States of America
| | - Tom Pace
- Department of Physics and Astronomy, University of Kentucky, Lexington, Kentucky, United States of America
| | - Shashank Bhatt
- Paul Laurence Dunbar High School, Lexington, Kentucky, United States of America
| | - Bin Sun
- Department of Chemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Peter Kekenes-Huskey
- Department of Cell & Molecular Physiology, Loyola University Chicago, Chicago, Illinois, United States of America
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13
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Uzdensky AB. Multifunctional Proteins. Biophysics (Nagoya-shi) 2020. [DOI: 10.1134/s0006350920030227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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14
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Akine S, Sakata Y. Control of Guest Binding Kinetics in Macrocycles and Molecular Cages. CHEM LETT 2020. [DOI: 10.1246/cl.200017] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Shigehisa Akine
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Yoko Sakata
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
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15
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Lambrughi M, Sanader Maršić Ž, Saez-Jimenez V, Mapelli V, Olsson L, Papaleo E. Conformational gating in ammonia lyases. Biochim Biophys Acta Gen Subj 2020; 1864:129605. [PMID: 32222547 DOI: 10.1016/j.bbagen.2020.129605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 03/11/2020] [Accepted: 03/23/2020] [Indexed: 11/17/2022]
Abstract
BACKGROUND Ammonia lyases are enzymes of industrial and biomedical interest. Knowledge of structure-dynamics-function relationship in ammonia lyases is instrumental for exploiting the potential of these enzymes in industrial or biomedical applications. METHODS We investigated the conformational changes in the proximity of the catalytic pocket of a 3-methylaspartate ammonia lyase (MAL) as a model system. At this scope, we used microsecond all-atom molecular dynamics simulations, analyzed with dimensionality reduction techniques, as well as in terms of contact networks and correlated motions. RESULTS We identify two regulatory elements in the MAL structure, i.e., the β5-α2 loop and the helix-hairpin-loop subdomain. These regulatory elements undergo conformational changes switching from 'occluded' to 'open' states. The rearrangements are coupled to changes in the accessibility of the active site. The β5-α2 loop and the helix-hairpin-loop subdomain modulate the formation of tunnels from the protein surface to the catalytic site, making the active site more accessible to the substrate when they are in an open state. CONCLUSIONS Our work pinpoints a sequential mechanism, in which the helix-hairpin-loop subdomain of MAL needs to break a subset of intramolecular interactions first to favor the displacement of the β5-α2 loop. The coupled conformational changes of these two elements contribute to modulate the accessibility of the catalytic site. GENERAL SIGNIFICANCE Similar molecular mechanisms can have broad relevance in other ammonia lyases with similar regulatory loops. Our results also imply that it is important to account for protein dynamics in the design of variants of ammonia lyases for industrial and biomedical applications.
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Affiliation(s)
- Matteo Lambrughi
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Željka Sanader Maršić
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Veronica Saez-Jimenez
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Valeria Mapelli
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Lisbeth Olsson
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Elena Papaleo
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark; Translational Disease Systems Biology, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research University of Copenhagen, Copenhagen, Denmark.
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16
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Dasgupta S, Mukherjee S, Sekar K, Mukhopadhyay BP. The conformational dynamics of wing gates Ile199 and Phe103 on the binding of dopamine and benzylamine substrates in human monoamine Oxidase B. J Biomol Struct Dyn 2020; 39:1879-1886. [PMID: 32093545 DOI: 10.1080/07391102.2020.1734483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Subrata Dasgupta
- Department of Chemistry, National Institute of Technology-Durgapur, West Bengal, Durgapur, India
| | - Soumita Mukherjee
- Department of Chemistry, National Institute of Technology-Durgapur, West Bengal, Durgapur, India
| | - Kanakaraj Sekar
- Laboratory for Structural Biology and Bio-Computing, Department of Computational and Data Sciences, Indian Institute of Science Bangalore, India
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17
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Escalante DE, Aksan A. Role of Water Hydrogen Bonding on Transport of Small Molecules inside Hydrophobic Channels. J Phys Chem B 2019; 123:6673-6685. [PMID: 31310534 DOI: 10.1021/acs.jpcb.9b03060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We conducted a systematic analysis of water networking inside smooth hyperboloid hydrophobic structures (cylindrical, barrel, and hourglass shapes) to elucidate the role of water hydrogen bonding on the transport of small hydrophobic molecules (ligands). Through a series of molecular dynamics simulations, we established that a hydrogen-bonded network forming along the centerline resulted in a water exclusion zone adjacent to the walls. The size of the exclusion zone is a function of the geometry and the nonbonded interaction strength, defining the effective hydrophobicity of the structure. Exclusion of water molecules from this zone results in lower apparent viscosity, leading to acceleration of ligand transport up to 7 times faster than that measured in the bulk. Transport of ligands into and out of the hydrophobic structures was shown to be controlled by a single water molecule that capped the narrow regions in the structure. This mechanism provides physical insights into the behavior and role of water in the bottleneck regions of hydrophobic enzyme channels. These findings were then used in a sister publication [ Escalante , D. E. , Comput. Struct. Biotechnol. J. 2019 17 757 760 ] to develop a model that can accurately predict the transport of ligands along nanochannels of broad-substrate specificity enzymes.
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Affiliation(s)
- Diego E Escalante
- Department of Mechanical Engineering , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Alptekin Aksan
- Department of Mechanical Engineering , University of Minnesota , Minneapolis , Minnesota 55455 , United States.,BioTechnology Institute , University of Minnesota , St. Paul , Minnesota 55108 , United States
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18
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Alvarado W, Bremer PL, Choy A, Dinh HN, Eung A, Gonzalez J, Ly P, Tran T, Nakayama K, Schwans JP, Sorin EJ. Understanding the enzyme-ligand complex: insights from all-atom simulations of butyrylcholinesterase inhibition. J Biomol Struct Dyn 2019; 38:1028-1041. [PMID: 30909811 DOI: 10.1080/07391102.2019.1596836] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
All-atom molecular dynamics simulations of butyrylcholinesterase (BChE) sans inhibitor and in complex with each of 15 dialkyl phenyl phosphate derivatives were conducted to characterize inhibitor binding modes and strengths. Each system was sampled on the 250 ns timescale in explicit ionic solvent, for a total of over 4 μs of simulation time. A K-means algorithm was used to cluster the resulting structures into distinct binding modes, which were further characterized based on atomic-level contacts between inhibitor chemical groups and active site residues. Comparison of experimentally observed inhibition constants (KI) with the resulting contact tables provides structural explanations for relative binding coefficients and highlights several notable interaction motifs. These include ubiquitous contact between glycines in the oxyanion hole and the inhibitor phosphate group; a sterically driven binding preference for positional isomers that extend aromaticity; a stereochemical binding preference for choline-containing inhibitors, which mimic natural BChE substrates; and the mechanically induced opening of the omega loop region to fully expose the active site gorge in the presence of choline-containing inhibitors. Taken together, these observations can greatly inform future design of BChE inhibitors, and the approach reported herein is generalizable to other enzyme-inhibitor systems and similar complexes that depend on non-covalent molecular recognition.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Walter Alvarado
- Department of Physics & Astronomy, California State University Long Beach, Long Beach, CA, USA
| | - Parker Ladd Bremer
- Department of Chemistry & Biochemistry, California State University Long Beach, Long Beach, CA, USA
| | - Angela Choy
- Department of Chemical Engineering, California State University Long Beach, Long Beach, CA, USA
| | - Helen N Dinh
- Department of Chemistry & Biochemistry, California State University Long Beach, Long Beach, CA, USA
| | - Aingty Eung
- Department of Computer Engineering & Computer Science, California State University Long Beach, Long Beach, CA, USA
| | - Jeannette Gonzalez
- Department of Biological Sciences, California State University Long Beach, Long Beach, CA, USA
| | - Phillippe Ly
- Department of Chemistry & Biochemistry, California State University Long Beach, Long Beach, CA, USA
| | - Trina Tran
- Department of Chemistry & Biochemistry, California State University Long Beach, Long Beach, CA, USA
| | - Kensaku Nakayama
- Department of Chemistry & Biochemistry, California State University Long Beach, Long Beach, CA, USA
| | - Jason P Schwans
- Department of Chemistry & Biochemistry, California State University Long Beach, Long Beach, CA, USA
| | - Eric J Sorin
- Department of Chemistry & Biochemistry, California State University Long Beach, Long Beach, CA, USA
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19
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Sun B, Cook EC, Creamer TP, Kekenes-Huskey PM. Electrostatic control of calcineurin's intrinsically-disordered regulatory domain binding to calmodulin. Biochim Biophys Acta Gen Subj 2018; 1862:2651-2659. [PMID: 30071273 PMCID: PMC6317854 DOI: 10.1016/j.bbagen.2018.07.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 07/13/2018] [Accepted: 07/24/2018] [Indexed: 12/26/2022]
Abstract
Calcineurin (CaN) is a serine/threonine phosphatase that regulates a variety of physiological and pathophysiological processes in mammalian tissue. The calcineurin (CaN) regulatory domain (RD) is responsible for regulating the enzyme's phosphatase activity, and is believed to be highly-disordered when inhibiting CaN, but undergoes a disorder-to-order transition upon diffusion-limited binding with the regulatory protein calmodulin (CaM). The prevalence of polar and charged amino acids in the regulatory domain (RD) suggests electrostatic interactions are involved in mediating calmodulin (CaM) binding, yet the lack of atomistic-resolution data for the bound complex has stymied efforts to probe how the RD sequence controls its conformational ensemble and long-range attractions contribute to target protein binding. In the present study, we investigated via computational modeling the extent to which electrostatics and structural disorder facilitate CaM/CaN association kinetics. Specifically, we examined several RD constructs that contain the CaM binding region (CAMBR) to characterize the roles of electrostatics versus conformational diversity in controlling diffusion-limited association rates, via microsecond-scale molecular dynamics (MD) and Brownian dynamic (BD) simulations. Our results indicate that the RD amino acid composition and sequence length influence both the dynamic availability of conformations amenable to CaM binding, as well as long-range electrostatic interactions to steer association. These findings provide intriguing insight into the interplay between conformational diversity and electrostatically-driven protein-protein association involving CaN, which are likely to extend to wide-ranging diffusion-limited processes regulated by intrinsically-disordered proteins.
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Affiliation(s)
- Bin Sun
- Department of Chemistry, University of Kentucky, 505 Rose St., Chemistry-Physics Building, Lexington, KY, USA 40506
| | - Erik C Cook
- Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, St. Lexington, KY, USA 40536
| | - Trevor P Creamer
- Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, St. Lexington, KY, USA 40536
| | - Peter M Kekenes-Huskey
- Department of Chemistry, University of Kentucky, 505 Rose St., Chemistry-Physics Building, Lexington, KY, USA 40506.
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20
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Barletta GP, Fernandez-Alberti S. Protein Fluctuations and Cavity Changes Relationship. J Chem Theory Comput 2018; 14:998-1008. [PMID: 29262685 DOI: 10.1021/acs.jctc.7b00744] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein cavities and tunnels are critical for function. Ligand recognition and binding, transport, and enzyme catalysis require cavities rearrangements. Therefore, the flexibility of cavities should be guaranteed by protein vibrational dynamics. Molecular dynamics simulations provide a framework to explore conformational plasticity of protein cavities. Herein, we present a novel procedure to characterize the dynamics of protein cavities in terms of their volume gradient vector. For this purpose, we make use of algorithms for calculation of the cavity volume that result robust for numerical differentiations. Volume gradient vector is expressed in terms of principal component analysis obtained from equilibrated molecular dynamics simulations. We analyze contributions of principal component modes to the volume gradient vector according to their frequency and degree of delocalization. In all our test cases, we find that low frequency modes play a critical role together with minor contributions of high frequency modes. These modes involve concerted motions of significant fractions of the total residues lining the cavities. We make use of variations of the potential energy of a protein in the direction of the volume gradient vector as a measure of flexibility of the cavity. We show that proteins whose collective low frequency fluctuations contribute the most to changes of cavity volume exhibit more flexible cavities.
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Affiliation(s)
- German P Barletta
- Universidad Nacional de Quilmes/CONICET , Roque Saenz Peña 352, B1876BXD Bernal, Argentina
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21
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Hasenahuer MA, Barletta GP, Fernandez-Alberti S, Parisi G, Fornasari MS. Pockets as structural descriptors of EGFR kinase conformations. PLoS One 2017; 12:e0189147. [PMID: 29228029 PMCID: PMC5724837 DOI: 10.1371/journal.pone.0189147] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/20/2017] [Indexed: 12/19/2022] Open
Abstract
Epidermal Growth Factor Receptor (EGFR), a tyrosine kinase receptor, is one of the main tumor markers in different types of cancers. The kinase native state is mainly composed of two populations of conformers: active and inactive. Several sequence variations in EGFR kinase region promote the differential enrichment of conformers with higher activity. Some structural characteristics have been proposed to differentiate kinase conformations, but these considerations could lead to ambiguous classifications. We present a structural characterisation of EGFR kinase conformers, focused on active site pocket comparisons, and the mapping of known pathological sequence variations. A structural based clustering of this pocket accurately discriminates active from inactive, well-characterised conformations. Furthermore, this main pocket contains, or is in close contact with, ≈65% of cancer-related variation positions. Although the relevance of protein dynamics to explain biological function has been extensively recognised, the usage of the ensemble of conformations in dynamic equilibrium to represent the functional state of proteins and the importance of pockets, cavities and/or tunnels was often neglected in previous studies. These functional structures and the equilibrium between them could be structurally analysed in wild type as well as in sequence variants. Our results indicate that biologically important pockets, as well as their shape and dynamics, are central to understanding protein function in wild-type, polymorphic or disease-related variations.
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Affiliation(s)
- Marcia Anahi Hasenahuer
- Departamento de Ciencia Y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina
| | - German Patricio Barletta
- Departamento de Ciencia Y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina
| | | | - Gustavo Parisi
- Departamento de Ciencia Y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina
| | - María Silvina Fornasari
- Departamento de Ciencia Y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina
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22
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Monzon AM, Zea DJ, Marino-Buslje C, Parisi G. Homology modeling in a dynamical world. Protein Sci 2017; 26:2195-2206. [PMID: 28815769 DOI: 10.1002/pro.3274] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 08/09/2017] [Accepted: 08/09/2017] [Indexed: 12/31/2022]
Abstract
A key concept in template-based modeling (TBM) is the high correlation between sequence and structural divergence, with the practical consequence that homologous proteins that are similar at the sequence level will also be similar at the structural level. However, conformational diversity of the native state will reduce the correlation between structural and sequence divergence, because structural variation can appear without sequence diversity. In this work, we explore the impact that conformational diversity has on the relationship between structural and sequence divergence. We find that the extent of conformational diversity can be as high as the maximum structural divergence among families. Also, as expected, conformational diversity impairs the well-established correlation between sequence and structural divergence, which is nosier than previously suggested. However, we found that this noise can be resolved using a priori information coming from the structure-function relationship. We show that protein families with low conformational diversity show a well-correlated relationship between sequence and structural divergence, which is severely reduced in proteins with larger conformational diversity. This lack of correlation could impair TBM results in highly dynamical proteins. Finally, we also find that the presence of order/disorder can provide useful beforehand information for better TBM performance.
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Affiliation(s)
- Alexander Miguel Monzon
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, CONICET, B1876BXD, Bernal, Argentina
| | - Diego Javier Zea
- Structural Bioinformatics Unit, Fundación Instituto Leloir, CONICET, C1405BWE Ciudad Autónoma de Buenos Aires, Argentina
| | - Cristina Marino-Buslje
- Structural Bioinformatics Unit, Fundación Instituto Leloir, CONICET, C1405BWE Ciudad Autónoma de Buenos Aires, Argentina
| | - Gustavo Parisi
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, CONICET, B1876BXD, Bernal, Argentina
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23
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Xiao J, Melvin RL, Salsbury FR. Mechanistic insights into thrombin's switch between "slow" and "fast" forms. Phys Chem Chem Phys 2017; 19:24522-24533. [PMID: 28849814 PMCID: PMC5719506 DOI: 10.1039/c7cp03671j] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Thrombin is a multifunctional enzyme that plays an important role in blood coagulation, cell growth, and metastasis. Depending upon the binding of sodium ions, thrombin presents significantly different enzymatic activities. In the environment with sodium ions, thrombin is highly active in cleaving the coagulated substrates and this is referred to as the "fast" form; in the environment without sodium ions, thrombin turns catalytically less active and is in the "slow" form. Although many experimental studies over the last two decades have attempted to reveal the structural and kinetic differences between these two forms, it remains vague and disputed how the functional switch between the "fast" and "slow" forms is mediated by Na+ cations. In this work, we employ microsecond-scale all-atom molecular dynamics simulations to investigate the differences in the structural ensembles in sodium-bound/unbound and potassium-bound/unbound thrombin. Our calculations indicate that the regulatory regions, including the 60s, γ loops, and exosite I and II, are primarily affected by both the bound and unbound cations. Conformational free energy surfaces, estimated from principal component analysis, further reveal the existence of multiple conformational states. The binding of a cation introduces changes in the distribution of these states. Through comparisons with potassium-binding, the binding of sodium ions appears to shift the population toward conformational states that might be catalytically favorable. Our study of thrombin in the presence of sodium/potassium ions suggests Na+-mediated generalized allostery is the mechanism of thrombin's functional switch between the "fast" and "slow" forms.
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Affiliation(s)
- Jiajie Xiao
- Department of Physics, Wake Forest University, Winston Salem, NC, USA.
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24
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Zhang S, Geryak R, Geldmeier J, Kim S, Tsukruk VV. Synthesis, Assembly, and Applications of Hybrid Nanostructures for Biosensing. Chem Rev 2017; 117:12942-13038. [DOI: 10.1021/acs.chemrev.7b00088] [Citation(s) in RCA: 206] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Shuaidi Zhang
- School of Materials Science
and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, United States
| | - Ren Geryak
- School of Materials Science
and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, United States
| | - Jeffrey Geldmeier
- School of Materials Science
and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, United States
| | - Sunghan Kim
- School of Materials Science
and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, United States
| | - Vladimir V. Tsukruk
- School of Materials Science
and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, United States
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25
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Xu Y, Cheng S, Sussman JL, Silman I, Jiang H. Computational Studies on Acetylcholinesterases. Molecules 2017; 22:molecules22081324. [PMID: 28796192 PMCID: PMC6152020 DOI: 10.3390/molecules22081324] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 08/07/2017] [Accepted: 08/07/2017] [Indexed: 01/18/2023] Open
Abstract
Functions of biomolecules, in particular enzymes, are usually modulated by structural fluctuations. This is especially the case in a gated diffusion-controlled reaction catalyzed by an enzyme such as acetylcholinesterase. The catalytic triad of acetylcholinesterase is located at the bottom of a long and narrow gorge, but it catalyzes the extremely rapid hydrolysis of the neurotransmitter, acetylcholine, with a reaction rate close to the diffusion-controlled limit. Computational modeling and simulation have produced considerable advances in exploring the dynamical and conformational properties of biomolecules, not only aiding in interpreting the experimental data, but also providing insights into the internal motions of the biomolecule at the atomic level. Given the remarkably high catalytic efficiency and the importance of acetylcholinesterase in drug development, great efforts have been made to understand the dynamics associated with its functions by use of various computational methods. Here, we present a comprehensive overview of recent computational studies on acetylcholinesterase, expanding our views of the enzyme from a microstate of a single structure to conformational ensembles, strengthening our understanding of the integration of structure, dynamics and function associated with the enzyme, and promoting the structure-based and/or mechanism-based design of new inhibitors for it.
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Affiliation(s)
- Yechun Xu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai 201203, China.
| | - Shanmei Cheng
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai 201203, China.
| | - Joel L Sussman
- Israel Structural Proteomics Center, Weizmann Institute of Science, Rehovot 76100, Israel.
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Israel Silman
- Department of Neurobiology, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Hualiang Jiang
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai 201203, China.
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26
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Gorge Motions of Acetylcholinesterase Revealed by Microsecond Molecular Dynamics Simulations. Sci Rep 2017; 7:3219. [PMID: 28607438 PMCID: PMC5468367 DOI: 10.1038/s41598-017-03088-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 04/11/2017] [Indexed: 11/27/2022] Open
Abstract
Acetylcholinesterase, with a deep, narrow active-site gorge, attracts enormous interest due to its particularly high catalytic efficiency and its inhibitors used for treatment of Alzheimer’s disease. To facilitate the massive pass-through of the substrate and inhibitors, “breathing” motions to modulate the size of the gorge are an important prerequisite. However, the molecular mechanism that governs such motions is not well explored. Here, to systematically investigate intrinsic motions of the enzyme, we performed microsecond molecular dynamics simulations on the monomer and dimer of Torpedo californica acetylcholinesterase (TcAChE) as well as the complex of TcAChE bound with the drug E2020. It has been revealed that protein-ligand interactions and dimerization both keep the gorge in bulk, and opening events of the gorge increase dramatically compared to the monomer. Dynamics of three subdomains, S3, S4 and the Ω-loop, are tightly associated with variations of the gorge size while the dynamics can be changed by ligand binding or protein dimerization. Moreover, high correlations among these subdomains provide a basis for remote residues allosterically modulating the gorge motions. These observations are propitious to expand our understanding of protein structure and function as well as providing clues for performing structure-based drug design.
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27
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Ouedraogo D, Souffrant M, Vasquez S, Hamelberg D, Gadda G. Importance of Loop L1 Dynamics for Substrate Capture and Catalysis in Pseudomonas aeruginosa d-Arginine Dehydrogenase. Biochemistry 2017; 56:2477-2487. [DOI: 10.1021/acs.biochem.7b00098] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Daniel Ouedraogo
- Department
of Chemistry, ‡Department of Biology, §Center for Diagnostics and Therapeutics, and ∥Center for Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
| | - Michael Souffrant
- Department
of Chemistry, ‡Department of Biology, §Center for Diagnostics and Therapeutics, and ∥Center for Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
| | - Sheena Vasquez
- Department
of Chemistry, ‡Department of Biology, §Center for Diagnostics and Therapeutics, and ∥Center for Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
| | - Donald Hamelberg
- Department
of Chemistry, ‡Department of Biology, §Center for Diagnostics and Therapeutics, and ∥Center for Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
| | - Giovanni Gadda
- Department
of Chemistry, ‡Department of Biology, §Center for Diagnostics and Therapeutics, and ∥Center for Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
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28
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Abstract
Whereas protein-ligand binding affinities have long-established prominence, binding rate constants and binding mechanisms have gained increasing attention in recent years. Both new computational methods and new experimental techniques have been developed to characterize the latter properties. It is now realized that binding mechanisms, like binding rate constants, can and should be quantitatively determined. In this review, we summarize studies and synthesize ideas on several topics in the hope of providing a coherent picture of and physical insight into binding kinetics. The topics include microscopic formulation of the kinetic problem and its reduction to simple rate equations; computation of binding rate constants; quantitative determination of binding mechanisms; and elucidation of physical factors that control binding rate constants and mechanisms.
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Affiliation(s)
- Xiaodong Pang
- Department of Physics, Florida State University, Tallahassee, Florida 32306; .,Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306
| | - Huan-Xiang Zhou
- Department of Physics, Florida State University, Tallahassee, Florida 32306; .,Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306
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29
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Escalante DE, Aukema KG, Wackett LP, Aksan A. Simulation of the Bottleneck Controlling Access into a Rieske Active Site: Predicting Substrates of Naphthalene 1,2-Dioxygenase. J Chem Inf Model 2017; 57:550-561. [PMID: 28170277 DOI: 10.1021/acs.jcim.6b00469] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Naphthalene 1,2-dioxygenase (NDO) has been computationally understudied despite the extensive experimental knowledge obtained for this enzyme, including numerous crystal structures and over 100 demonstrated substrates. In this study, we have developed a substrate prediction model that moves away from the traditional active-site-centric approach to include the energetics of substrate entry into the active site. By comparison with experimental data, the accuracy of the model for predicting substrate oxidation is 92%, with a positive predictive value of 93% and a negative predictive value of 98%. Also, the present analysis has revealed that the amino acid residues that provided the largest energetic barrier for compounds entering the active site are residues F224, L227, P234, and L235. In addition, F224 is proposed to play a role in controlling ligand entrance via π-π stacking stabilization as well as providing stabilization via T-shaped π-π interactions once the ligand has reached the active-site cavity. Overall, we present a method capable of being scaled to computationally discover thousands of substrates of NDO, and we present parameters to be used for expanding the prediction method to other members of the Rieske non-heme iron oxygenase family.
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Affiliation(s)
- Diego E Escalante
- Department of Mechanical Engineering, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Kelly G Aukema
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota , Minneapolis, Minnesota 55455, United States.,BioTechnology Institute, University of Minnesota , St. Paul, Minnesota 55108, United States
| | - Lawrence P Wackett
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota , Minneapolis, Minnesota 55455, United States.,BioTechnology Institute, University of Minnesota , St. Paul, Minnesota 55108, United States
| | - Alptekin Aksan
- Department of Mechanical Engineering, University of Minnesota , Minneapolis, Minnesota 55455, United States.,BioTechnology Institute, University of Minnesota , St. Paul, Minnesota 55108, United States
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30
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Monzon AM, Zea DJ, Fornasari MS, Saldaño TE, Fernandez-Alberti S, Tosatto SCE, Parisi G. Conformational diversity analysis reveals three functional mechanisms in proteins. PLoS Comput Biol 2017; 13:e1005398. [PMID: 28192432 PMCID: PMC5330503 DOI: 10.1371/journal.pcbi.1005398] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 02/28/2017] [Accepted: 02/02/2017] [Indexed: 02/02/2023] Open
Abstract
Protein motions are a key feature to understand biological function. Recently, a large-scale analysis of protein conformational diversity showed a positively skewed distribution with a peak at 0.5 Å C-alpha root-mean-square-deviation (RMSD). To understand this distribution in terms of structure-function relationships, we studied a well curated and large dataset of ~5,000 proteins with experimentally determined conformational diversity. We searched for global behaviour patterns studying how structure-based features change among the available conformer population for each protein. This procedure allowed us to describe the RMSD distribution in terms of three main protein classes sharing given properties. The largest of these protein subsets (~60%), which we call "rigid" (average RMSD = 0.83 Å), has no disordered regions, shows low conformational diversity, the largest tunnels and smaller and buried cavities. The two additional subsets contain disordered regions, but with differential sequence composition and behaviour. Partially disordered proteins have on average 67% of their conformers with disordered regions, average RMSD = 1.1 Å, the highest number of hinges and the longest disordered regions. In contrast, malleable proteins have on average only 25% of disordered conformers and average RMSD = 1.3 Å, flexible cavities affected in size by the presence of disordered regions and show the highest diversity of cognate ligands. Proteins in each set are mostly non-homologous to each other, share no given fold class, nor functional similarity but do share features derived from their conformer population. These shared features could represent conformational mechanisms related with biological functions.
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Affiliation(s)
- Alexander Miguel Monzon
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes (CONICET), Bernal, Buenos Aires, Argentina
| | - Diego Javier Zea
- Bioinformatics Unit, Fundación Instituto Leloir (CONICET), Buenos Aires, Argentina
| | - María Silvina Fornasari
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes (CONICET), Bernal, Buenos Aires, Argentina
| | - Tadeo E. Saldaño
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes (CONICET), Bernal, Buenos Aires, Argentina
| | - Sebastian Fernandez-Alberti
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes (CONICET), Bernal, Buenos Aires, Argentina
| | | | - Gustavo Parisi
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes (CONICET), Bernal, Buenos Aires, Argentina
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31
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Zheng Y, Cui Q. Microscopic mechanisms that govern the titration response and pK a values of buried residues in staphylococcal nuclease mutants. Proteins 2016; 85:268-281. [PMID: 27862310 DOI: 10.1002/prot.25213] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 10/19/2016] [Accepted: 10/28/2016] [Indexed: 01/09/2023]
Abstract
To probe the microscopic mechanisms that govern the titration behavior of buried ionizable groups, microsecond explicit solvent molecular dynamics simulations are carried out for several mutants of Staphylococcal nuclease using both fixed charge and polarizable force fields. While the ionization of Asp 66, Glu 66, and Lys 125 lead to enhanced structural fluctuations and partial unfolding of adjacent α-helical regions, the ionization of Lys 25 causes local unfolding of adjacent β sheets. Using the sampled conformational ensembles, good agreement with experimental pKa values is obtained with Poisson-Boltzmann calculations using a protein dielectric constant of 2-4 for V66D/E; slightly larger dielectric constants are needed for Lys mutants especially L25K, suggesting that structural responses beyond microseconds are involved in ionization of Lys 25. Overall, the set of unbiased simulations provides insights into the spatial and temporal scales of protein and solvent motions that dictate the diverse titration behaviors of buried protein residues. Proteins 2017; 85:268-281. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Yuqing Zheng
- Graduate Program in Biophysics, University of Wisconsin-Madison, 1525 Linden Drive, Madison, Wisconsin, 53706
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin, 53706
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32
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Marques SM, Daniel L, Buryska T, Prokop Z, Brezovsky J, Damborsky J. Enzyme Tunnels and Gates As Relevant Targets in Drug Design. Med Res Rev 2016; 37:1095-1139. [PMID: 27957758 DOI: 10.1002/med.21430] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/11/2016] [Accepted: 11/07/2016] [Indexed: 12/28/2022]
Abstract
Many enzymes contain tunnels and gates that are essential to their function. Gates reversibly switch between open and closed conformations and thereby control the traffic of small molecules-substrates, products, ions, and solvent molecules-into and out of the enzyme's structure via molecular tunnels. Many transient tunnels and gates undoubtedly remain to be identified, and their functional roles and utility as potential drug targets have received comparatively little attention. Here, we describe a set of general concepts relating to the structural properties, function, and classification of these interesting structural features. In addition, we highlight the potential of enzyme tunnels and gates as targets for the binding of small molecules. The different types of binding that are possible and the potential pharmacological benefits of such targeting are discussed. Twelve examples of ligands bound to the tunnels and/or gates of clinically relevant enzymes are used to illustrate the different binding modes and to explain some new strategies for drug design. Such strategies could potentially help to overcome some of the problems facing medicinal chemists and lead to the discovery of more effective drugs.
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Affiliation(s)
- Sergio M Marques
- Loschmidt Laboratories, Faculty of Science, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, RECETOX, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Lukas Daniel
- Loschmidt Laboratories, Faculty of Science, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, RECETOX, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic
| | - Tomas Buryska
- Loschmidt Laboratories, Faculty of Science, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, RECETOX, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Faculty of Science, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, RECETOX, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic
| | - Jan Brezovsky
- Loschmidt Laboratories, Faculty of Science, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, RECETOX, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Faculty of Science, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, RECETOX, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic
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33
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Brezovsky J, Babkova P, Degtjarik O, Fortova A, Gora A, Iermak I, Rezacova P, Dvorak P, Smatanova IK, Prokop Z, Chaloupkova R, Damborsky J. Engineering a de Novo Transport Tunnel. ACS Catal 2016. [DOI: 10.1021/acscatal.6b02081] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Jan Brezovsky
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Petra Babkova
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Oksana Degtjarik
- Faculty
of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 37005 Ceske Budejovice, Czech Republic
- Center for Nanobiology and Structural Biology ASCR, Zamek 136, 37333 Nove Hrady, Czech Republic
| | - Andrea Fortova
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Artur Gora
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Iuliia Iermak
- Faculty
of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 37005 Ceske Budejovice, Czech Republic
- Center for Nanobiology and Structural Biology ASCR, Zamek 136, 37333 Nove Hrady, Czech Republic
| | - Pavlina Rezacova
- Institute of Organic Chemistry and Biochemistry ASCR, v.v.i. Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
- Institute of Molecular Genetics of the ASCR, v.v.i. Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Pavel Dvorak
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Ivana Kuta Smatanova
- Faculty
of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 37005 Ceske Budejovice, Czech Republic
- Center for Nanobiology and Structural Biology ASCR, Zamek 136, 37333 Nove Hrady, Czech Republic
| | - Zbynek Prokop
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Radka Chaloupkova
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
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34
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Ozboyaci M, Martinez M, Wade RC. An Efficient Low Storage and Memory Treatment of Gridded Interaction Fields for Simulations of Macromolecular Association. J Chem Theory Comput 2016; 12:4563-77. [DOI: 10.1021/acs.jctc.6b00350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Musa Ozboyaci
- Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
- Heidelberg Graduate School of Mathematical and Computational Methods for the Sciences, Heidelberg University, INF 205, 69120 Heidelberg, Germany
| | - Michael Martinez
- Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
| | - Rebecca C. Wade
- Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Allianz, INF 282, 69120 Heidelberg, Germany
- Interdisciplinary Center for Scientific Computing, Heidelberg University, INF 205, 69120 Heidelberg, Germany
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35
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Xu J, Xie Y, Lu B, Zhang L. Charged Substrate and Product Together Contribute Like a Nonreactive Species to the Overall Electrostatic Steering in Diffusion-Reaction Processes. J Phys Chem B 2016; 120:8147-53. [PMID: 27070411 DOI: 10.1021/acs.jpcb.6b01393] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Debye-Hückel limiting law is used to study the binding kinetics of substrate-enzyme system as well as to estimate the reaction rate of a electrostatically steered diffusion-controlled reaction process. It is based on a linearized Poisson-Boltzmann model and known for its accurate predictions in dilute solutions. However, the substrate and product particles are in nonequilibrium states and are possibly charged, and their contributions to the total electrostatic field cannot be explicitly studied in the Poisson-Boltzmann model. Hence the influences of substrate and product on reaction rate coefficient were not known. In this work, we consider all the charged species, including the charged substrate, product, and mobile salt ions in a Poisson-Nernst-Planck model, and then compare the results with previous work. The results indicate that both the charged substrate and product can significantly influence the reaction rate coefficient with different behaviors under different setups of computational conditions. It is interesting to find that when substrate and product are both considered, under an overall neutral boundary condition for all the bulk charged species, the computed reaction rate kinetics recovers a similar Debye-Hückel limiting law again. This phenomenon implies that the charged product counteracts the influence of charged substrate on reaction rate coefficient. Our analysis discloses the fact that the total charge concentration of substrate and product, though in a nonequilibrium state individually, obeys an equilibrium Boltzmann distribution, and therefore contributes as a normal charged ion species to ionic strength. This explains why the Debye-Hückel limiting law still works in a considerable range of conditions even though the effects of charged substrate and product particles are not specifically and explicitly considered in the theory.
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Affiliation(s)
- Jingjie Xu
- School of Mathematical Sciences, University of Science and Technology of China , Hefei, China
| | - Yan Xie
- State Key Laboratory of Scientific and Engineering Computing, Academy of Mathematics and Systems Science, Chinese Academy of Sciences , Beijing, China
| | - Benzhuo Lu
- State Key Laboratory of Scientific and Engineering Computing, Academy of Mathematics and Systems Science, Chinese Academy of Sciences , Beijing, China
| | - Linbo Zhang
- State Key Laboratory of Scientific and Engineering Computing, Academy of Mathematics and Systems Science, Chinese Academy of Sciences , Beijing, China
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36
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Li Y, Li X, Dong Z. Exploration of gated ligand binding recognizes an allosteric site for blocking FABP4-protein interaction. Phys Chem Chem Phys 2016; 17:32257-67. [PMID: 26580122 DOI: 10.1039/c5cp04784f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fatty acid binding protein 4 (FABP4), reversibly binding to fatty acids and other lipids with high affinities, is a potential target for treatment of cancers. The binding site of FABP4 is buried in an interior cavity and thereby ligand binding/unbinding is coupled with opening/closing of FABP4. It is a difficult task both experimentally and computationally to illuminate the entry or exit pathway, especially with the conformational gating. In this report we combine extensive computer simulations, clustering analysis, and the Markov state model to investigate the binding mechanism of FABP4 and troglitazone. Our simulations capture spontaneous binding and unbinding events as well as the conformational transition of FABP4 between the open and closed states. An allosteric binding site on the protein surface is recognized for the development of novel FABP4 inhibitors. The binding affinity is calculated and compared with the experimental value. The kinetic analysis suggests that ligand residence on the protein surface may delay the binding process. Overall, our results provide a comprehensive picture of ligand diffusion on the protein surface, ligand migration into the buried cavity, and the conformational change of FABP4 at an atomic level.
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Affiliation(s)
- Yan Li
- The Hormel Institute, University of Minnesota, Austin Minnesota 55912, USA.
| | - Xiang Li
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, 450001 Zhengzhou, Henan, China
| | - Zigang Dong
- The Hormel Institute, University of Minnesota, Austin Minnesota 55912, USA.
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37
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Argikar UA, Potter PM, Hutzler JM, Marathe PH. Challenges and Opportunities with Non-CYP Enzymes Aldehyde Oxidase, Carboxylesterase, and UDP-Glucuronosyltransferase: Focus on Reaction Phenotyping and Prediction of Human Clearance. AAPS JOURNAL 2016; 18:1391-1405. [PMID: 27495117 DOI: 10.1208/s12248-016-9962-6] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 07/13/2016] [Indexed: 01/28/2023]
Abstract
Over the years, significant progress has been made in reducing metabolic instability due to cytochrome P450-mediated oxidation. High-throughput metabolic stability screening has enabled the advancement of compounds with little to no oxidative metabolism. Furthermore, high lipophilicity and low aqueous solubility of presently pursued chemotypes reduces the probability of renal excretion. As such, these low microsomal turnover compounds are often substrates for non-CYP-mediated metabolism. UGTs, esterases, and aldehyde oxidase are major enzymes involved in catalyzing such metabolism. Hepatocytes provide an excellent tool to identify such pathways including elucidation of major metabolites. To predict human PK parameters for P450-mediated metabolism, in vitro-in vivo extrapolation using hepatic microsomes, hepatocytes, and intestinal microsomes has been actively investigated. However, such methods have not been sufficiently evaluated for non-P450 enzymes. In addition to the involvement of the liver, extrahepatic enzymes (intestine, kidney, lung) are also likely to contribute to these pathways. While there has been considerable progress in predicting metabolic pathways and clearance primarily mediated by the liver, progress in characterizing extrahepatic metabolism and prediction of clearance has been slow. Well-characterized in vitro systems or in vivo animal models to assess drug-drug interaction potential and intersubject variability due to polymorphism are not available. Here we focus on the utility of appropriate in vitro studies to characterize non-CYP-mediated metabolism and to understand the enzymes involved followed by pharmacokinetic studies in the appropriately characterized surrogate species. The review will highlight progress made in establishing in vitro-in vivo correlation, predicting human clearance and avoiding costly clinical failures when non-CYP-mediated metabolic pathways are predominant.
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Affiliation(s)
- Upendra A Argikar
- Analytical Sciences and Imaging, Novartis Institutes for Biomedical Research, Inc., Cambridge, Massachusetts, USA
| | - Philip M Potter
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - J Matthew Hutzler
- Q2 Solutions, Bioanalytical and ADME Labs, Indianapolis, Indiana, USA
| | - Punit H Marathe
- Department of Metabolism and Pharmacokinetics, Bristol-Myers Squibb, Princeton, New Jersey, USA.
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38
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Abstract
The dynamics of protein binding pockets are crucial for their interaction specificity. Structural flexibility allows proteins to adapt to their individual molecular binding partners and facilitates the binding process. This implies the necessity to consider protein internal motion in determining and predicting binding properties and in designing new binders. Although accounting for protein dynamics presents a challenge for computational approaches, it expands the structural and physicochemical space for compound design and thus offers the prospect of improved binding specificity and selectivity. A cavity on the surface or in the interior of a protein that possesses suitable properties for binding a ligand is usually referred to as a binding pocket. The set of amino acid residues around a binding pocket determines its physicochemical characteristics and, together with its shape and location in a protein, defines its functionality. Residues outside the binding site can also have a long-range effect on the properties of the binding pocket. Cavities with similar functionalities are often conserved across protein families. For example, enzyme active sites are usually concave surfaces that present amino acid residues in a suitable configuration for binding low molecular weight compounds. Macromolecular binding pockets, on the other hand, are located on the protein surface and are often shallower. The mobility of proteins allows the opening, closing, and adaptation of binding pockets to regulate binding processes and specific protein functionalities. For example, channels and tunnels can exist permanently or transiently to transport compounds to and from a binding site. The influence of protein flexibility on binding pockets can vary from small changes to an already existent pocket to the formation of a completely new pocket. Here, we review recent developments in computational methods to detect and define binding pockets and to study pocket dynamics. We introduce five different classes of protein pocket dynamics: (1) appearance/disappearance of a subpocket in an existing pocket; (2) appearance/disappearance of an adjacent pocket on the protein surface in the direct vicinity of an already existing pocket; (3) pocket breathing, which may be caused by side-chain fluctuations or backbone or interdomain vibrational motion; (4) opening/closing of a channel or tunnel, connecting a pocket inside the protein with solvent, including lid motion; and (5) the appearance/disappearance of an allosteric pocket at a site on a protein distinct from an already existing pocket with binding of a ligand to the allosteric binding site affecting the original pocket. We suggest that the class of pocket dynamics, as well as the type and extent of protein motion affecting the binding pocket, should be factors considered in choosing the most appropriate computational approach to study a given binding pocket. Furthermore, we examine the relationship between pocket dynamics classes and induced fit, conformational selection, and gating models of ligand binding on binding kinetics and thermodynamics. We discuss the implications of protein binding pocket dynamics for drug design and conclude with potential future directions for computational analysis of protein binding pocket dynamics.
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Affiliation(s)
- Antonia Stank
- Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
| | - Daria B. Kokh
- Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
| | - Jonathan C. Fuller
- Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
| | - Rebecca C. Wade
- Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
- Center
for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
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39
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Kolb JJ, Angioletti-Uberti S, Dzubiella J. Communication: Resonance reaction in diffusion-influenced bimolecular reactions. J Chem Phys 2016; 144:081102. [DOI: 10.1063/1.4942998] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Jakob J. Kolb
- Institut für Physik, Humboldt-Universität zu Berlin, 12489 Berlin, Germany
| | - Stefano Angioletti-Uberti
- International Center for Soft Matter Research, Beijing University of Chemical Technology, Beijing 100029, China
| | - Joachim Dzubiella
- Institut für Physik, Humboldt-Universität zu Berlin, 12489 Berlin, Germany
- Institut für Weiche Materie und Funktionale Materialen, Helmholtz-Zentrum Berlin für Materialien und Energie, 14109 Berlin, Germany
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40
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Dröse S, Stepanova A, Galkin A. Ischemic A/D transition of mitochondrial complex I and its role in ROS generation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:946-57. [PMID: 26777588 PMCID: PMC4893024 DOI: 10.1016/j.bbabio.2015.12.013] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 12/11/2015] [Accepted: 12/25/2015] [Indexed: 12/12/2022]
Abstract
Mitochondrial complex I (NADH:ubiquinone oxidoreductase) is a key enzyme in cellular energy metabolism and provides approximately 40% of the proton-motive force that is utilized during mitochondrial ATP production. The dysregulation of complex I function – either genetically, pharmacologically, or metabolically induced – has severe pathophysiological consequences that often involve an imbalance in the production of reactive oxygen species (ROS). Slow transition of the active (A) enzyme to the deactive, dormant (D) form takes place during ischemia in metabolically active organs such as the heart and brain. The reactivation of complex I occurs upon reoxygenation of ischemic tissue, a process that is usually accompanied by an increase in cellular ROS production. Complex I in the D-form serves as a protective mechanism preventing the oxidative burst upon reperfusion. Conversely, however, the D-form is more vulnerable to oxidative/nitrosative damage. Understanding the so-called active/deactive (A/D) transition may contribute to the development of new therapeutic interventions for conditions like stroke, cardiac infarction, and other ischemia-associated pathologies. In this review, we summarize current knowledge on the mechanism of A/D transition of mitochondrial complex I considering recently available structural data and site-specific labeling experiments. In addition, this review discusses in detail the impact of the A/D transition on ROS production by complex I and the S-nitrosation of a critical cysteine residue of subunit ND3 as a strategy to prevent oxidative damage and tissue damage during ischemia–reperfusion injury. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt. The current knowledge on active/deactive (A/D) transition of complex I is reviewed. The mechanism and driving force of the A/D conformational change are discussed. The A/D transition can affect ROS production and ischemia/reperfusion injury.
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Affiliation(s)
- Stefan Dröse
- Clinic of Anesthesiology, Intensive-Care Medicine and Pain Therapy, University Hospital Frankfurt, Frankfurt am Main 60590, Germany.
| | - Anna Stepanova
- Medical Biology Centre, School of Biological Sciences, Queens University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Alexander Galkin
- Medical Biology Centre, School of Biological Sciences, Queens University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; Feil Family Brain and Mind Research Institute, Weill Cornell Medical College, 407 East 61st Street, New York, NY 10065, USA.
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41
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Konkle ME, Blobaum AL, Moth CW, Prusakiewicz JJ, Xu S, Ghebreselasie K, Akingbade D, Jacobs AT, Rouzer CA, Lybrand TP, Marnett LJ. Conservative Secondary Shell Substitution In Cyclooxygenase-2 Reduces Inhibition by Indomethacin Amides and Esters via Altered Enzyme Dynamics. Biochemistry 2015; 55:348-59. [PMID: 26704937 PMCID: PMC4721528 DOI: 10.1021/acs.biochem.5b01222] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The cyclooxygenase enzymes (COX-1 and COX-2) are the therapeutic targets of nonsteroidal anti-inflammatory drugs (NSAIDs). Neutralization of the carboxylic acid moiety of the NSAID indomethacin to an ester or amide functionality confers COX-2 selectivity, but the molecular basis for this selectivity has not been completely revealed through mutagenesis studies and/or X-ray crystallographic attempts. We expressed and assayed a number of divergent secondary shell COX-2 active site mutants and found that a COX-2 to COX-1 change at position 472 (Leu in COX-2, Met in COX-1) reduced the potency of enzyme inhibition by a series of COX-2-selective indomethacin amides and esters. In contrast, the potencies of indomethacin, arylacetic acid, propionic acid, and COX-2-selective diarylheterocycle inhibitors were either unaffected or only mildly affected by this mutation. Molecular dynamics simulations revealed identical equilibrium enzyme structures around residue 472; however, calculations indicated that the L472M mutation impacted local low-frequency dynamical COX constriction site motions by stabilizing the active site entrance and slowing constriction site dynamics. Kinetic analysis of inhibitor binding is consistent with the computational findings.
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Affiliation(s)
- Mary E Konkle
- Departments of Biochemistry, ‡Chemistry, and §Pharmacology, Vanderbilt Institute of Chemical Biology, Center for Structural Biology, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine , Nashville Tennessee 37232-0146, United States
| | - Anna L Blobaum
- Departments of Biochemistry, ‡Chemistry, and §Pharmacology, Vanderbilt Institute of Chemical Biology, Center for Structural Biology, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine , Nashville Tennessee 37232-0146, United States
| | - Christopher W Moth
- Departments of Biochemistry, ‡Chemistry, and §Pharmacology, Vanderbilt Institute of Chemical Biology, Center for Structural Biology, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine , Nashville Tennessee 37232-0146, United States
| | - Jeffery J Prusakiewicz
- Departments of Biochemistry, ‡Chemistry, and §Pharmacology, Vanderbilt Institute of Chemical Biology, Center for Structural Biology, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine , Nashville Tennessee 37232-0146, United States
| | - Shu Xu
- Departments of Biochemistry, ‡Chemistry, and §Pharmacology, Vanderbilt Institute of Chemical Biology, Center for Structural Biology, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine , Nashville Tennessee 37232-0146, United States
| | - Kebreab Ghebreselasie
- Departments of Biochemistry, ‡Chemistry, and §Pharmacology, Vanderbilt Institute of Chemical Biology, Center for Structural Biology, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine , Nashville Tennessee 37232-0146, United States
| | - Dapo Akingbade
- Departments of Biochemistry, ‡Chemistry, and §Pharmacology, Vanderbilt Institute of Chemical Biology, Center for Structural Biology, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine , Nashville Tennessee 37232-0146, United States
| | - Aaron T Jacobs
- Departments of Biochemistry, ‡Chemistry, and §Pharmacology, Vanderbilt Institute of Chemical Biology, Center for Structural Biology, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine , Nashville Tennessee 37232-0146, United States
| | - Carol A Rouzer
- Departments of Biochemistry, ‡Chemistry, and §Pharmacology, Vanderbilt Institute of Chemical Biology, Center for Structural Biology, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine , Nashville Tennessee 37232-0146, United States
| | - Terry P Lybrand
- Departments of Biochemistry, ‡Chemistry, and §Pharmacology, Vanderbilt Institute of Chemical Biology, Center for Structural Biology, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine , Nashville Tennessee 37232-0146, United States
| | - Lawrence J Marnett
- Departments of Biochemistry, ‡Chemistry, and §Pharmacology, Vanderbilt Institute of Chemical Biology, Center for Structural Biology, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine , Nashville Tennessee 37232-0146, United States
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42
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Abstract
Protein dynamics is essential for proteins to function. Here we predicted the existence of rare, large nonlinear excitations, termed intrinsic localized modes (ILMs), of the main chain of proteins based on all-atom molecular dynamics simulations of two fast-folder proteins and of a rigid α/β protein at 300 K and at 380 K in solution. These nonlinear excitations arise from the anharmonicity of the protein dynamics. The ILMs were detected by computing the Shannon entropy of the protein main-chain fluctuations. In the non-native state (significantly explored at 380 K), the probability of their excitation was increased by a factor between 9 and 28 for the fast-folder proteins and by a factor 2 for the rigid protein. This enhancement in the non-native state was due to glycine, as demonstrated by simulations in which glycine was mutated to alanine. These ILMs might play a functional role in the flexible regions of proteins and in proteins in a non-native state (i.e. misfolded or unfolded states).
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Guo Q, He Y, Lu HP. Interrogating the activities of conformational deformed enzyme by single-molecule fluorescence-magnetic tweezers microscopy. Proc Natl Acad Sci U S A 2015; 112:13904-9. [PMID: 26512103 PMCID: PMC4653173 DOI: 10.1073/pnas.1506405112] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Characterizing the impact of fluctuating enzyme conformation on enzymatic activity is critical in understanding the structure-function relationship and enzymatic reaction dynamics. Different from studying enzyme conformations under a denaturing condition, it is highly informative to manipulate the conformation of an enzyme under an enzymatic reaction condition while monitoring the real-time enzymatic activity changes simultaneously. By perturbing conformation of horseradish peroxidase (HRP) molecules using our home-developed single-molecule total internal reflection magnetic tweezers, we successfully manipulated the enzymatic conformation and probed the enzymatic activity changes of HRP in a catalyzed H2O2-amplex red reaction. We also observed a significant tolerance of the enzyme activity to the enzyme conformational perturbation. Our results provide a further understanding of the relation between enzyme behavior and enzymatic conformational fluctuation, enzyme-substrate interactions, enzyme-substrate active complex formation, and protein folding-binding interactions.
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Affiliation(s)
- Qing Guo
- Department of Chemistry, Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH 43403
| | - Yufan He
- Department of Chemistry, Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH 43403
| | - H Peter Lu
- Department of Chemistry, Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH 43403
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44
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Pan W, Daily M, Baker NA. Numerical calculation of protein-ligand binding rates through solution of the Smoluchowski equation using smoothed particle hydrodynamics. BMC BIOPHYSICS 2015; 8:7. [PMID: 25995835 PMCID: PMC4438506 DOI: 10.1186/s13628-015-0021-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 03/30/2015] [Indexed: 11/13/2022]
Abstract
Background The calculation of diffusion-controlled ligand binding rates is important for understanding enzyme mechanisms as well as designing enzyme inhibitors. Methods We demonstrate the accuracy and effectiveness of a Lagrangian particle-based method, smoothed particle hydrodynamics (SPH), to study diffusion in biomolecular systems by numerically solving the time-dependent Smoluchowski equation for continuum diffusion. Unlike previous studies, a reactive Robin boundary condition (BC), rather than the absolute absorbing (Dirichlet) BC, is considered on the reactive boundaries. This new BC treatment allows for the analysis of enzymes with “imperfect” reaction rates. Results The numerical method is first verified in simple systems and then applied to the calculation of ligand binding to a mouse acetylcholinesterase (mAChE) monomer. Rates for inhibitor binding to mAChE are calculated at various ionic strengths and compared with experiment and other numerical methods. We find that imposition of the Robin BC improves agreement between calculated and experimental reaction rates. Conclusions Although this initial application focuses on a single monomer system, our new method provides a framework to explore broader applications of SPH in larger-scale biomolecular complexes by taking advantage of its Lagrangian particle-based nature.
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Affiliation(s)
- Wenxiao Pan
- Advanced Computing, Mathematics and Data Division, Pacific Northwest National Laboratory, MSID K7-90, 99352, Richland, PO Box 999 WA USA
| | - Michael Daily
- Chemical Physics and Analysis Division, Mathematics and Data Division, Pacific Northwest National Laboratory, MSID K1-83, 99352, Richland, PO Box 999 WA USA
| | - Nathan A Baker
- Computational and Statistical Analytics Division, Pacific Northwest National Laboratory, MSID K7-20, 99352, Richland, PO Box 999 WA USA
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45
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Abstract
In this review, we describe the construction of gated molecular baskets, discuss their mechanism of action in regulating the exchange of guests and illustrate the potential of these concave hosts to act as catalysts for controlling chemical reactions. Importantly, a number of computational and experimental studies have suggested that gated baskets ought to unfold their gates at the rim for permitting the passage of guests to/from their inner space. These dynamic hosts are therefore offered as useful models for investigating the process of gating in artificial systems. Furthermore, gated baskets should permit examining the benefit of controlling the rate by which reactants access a gated catalyst for promoting chemical reactions occurring in its confined space.
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Affiliation(s)
- Keith Hermann
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA.
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46
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Bennion BJ, Essiz SG, Lau EY, Fattebert JL, Emigh A, Lightstone FC. A wrench in the works of human acetylcholinesterase: soman induced conformational changes revealed by molecular dynamics simulations. PLoS One 2015; 10:e0121092. [PMID: 25874456 PMCID: PMC4395452 DOI: 10.1371/journal.pone.0121092] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 01/27/2015] [Indexed: 01/06/2023] Open
Abstract
Irreversible inactivation of human acetylcholinesterase (hAChE) by organophosphorous pesticides (OPs) and chemical weapon agents (CWA) has severe morbidity and mortality consequences. We present data from quantum mechanics/molecular mechanics (QM/MM) and 80 classical molecular dynamics (MD) simulations of the apo and soman-adducted forms of hAChE to investigate the effects on the dynamics and protein structure when the catalytic Serine 203 is phosphonylated. We find that the soman phosphonylation of the active site Ser203 follows a water assisted addition-elimination mechanism with the elimination of the fluoride ion being the highest energy barrier at 6.5 kcal/mole. We observe soman-dependent changes in backbone and sidechain motions compared to the apo form of the protein. These alterations restrict the soman-adducted hAChE to a structural state that is primed for the soman adduct to be cleaved and removed from the active site. The altered motions and resulting structures provide alternative pathways into and out of the hAChE active site. In the soman-adducted protein both side and back door pathways are viable for soman adduct access. Correlation analysis of the apo and soman adducted MD trajectories shows that the correlation of gorge entrance and back door motion is disrupted when hAChE is adducted. This supports the hypothesis that substrate and product can use two different pathways as entry and exit sites in the apo form of the protein. These alternative pathways have important implications for the rational design of medical countermeasures.
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Affiliation(s)
- Brian J. Bennion
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, 7000 East Ave, Livermore CA, United States of America
| | - Sebnem G. Essiz
- Bioinformatics and Genetics Department, Faculty of Engineering and Natural Sciences, Kadir Has University, 34083 Fatih, Istanbul, Turkey
| | - Edmond Y. Lau
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, 7000 East Ave, Livermore CA, United States of America
| | - Jean-Luc Fattebert
- Center for Applied Scientific Computing, Lawrence Livermore National Laboratory, 7000 East Ave, Livermore CA, United States of America
| | - Aiyana Emigh
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, 7000 East Ave, Livermore CA, United States of America
| | - Felice C. Lightstone
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, 7000 East Ave, Livermore CA, United States of America
- * E-mail:
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47
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Trapp M, Tehei M, Trovaslet M, Nachon F, Martinez N, Koza MM, Weik M, Masson P, Peters J. Correlation of the dynamics of native human acetylcholinesterase and its inhibited huperzine A counterpart from sub-picoseconds to nanoseconds. J R Soc Interface 2015; 11:20140372. [PMID: 24872501 DOI: 10.1098/rsif.2014.0372] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
It is a long debated question whether catalytic activities of enzymes, which lie on the millisecond timescale, are possibly already reflected in variations in atomic thermal fluctuations on the pico- to nanosecond timescale. To shed light on this puzzle, the enzyme human acetylcholinesterase in its wild-type form and complexed with the inhibitor huperzine A were investigated by various neutron scattering techniques and molecular dynamics simulations. Previous results on elastic neutron scattering at various timescales and simulations suggest that dynamical processes are not affected on average by the presence of the ligand within the considered time ranges between 10 ps and 1 ns. In the work presented here, the focus was laid on quasi-elastic (QENS) and inelastic neutron scattering (INS). These techniques give access to different kinds of individual diffusive motions and to the density of states of collective motions at the sub-picoseconds timescale. Hence, they permit going beyond the first approach of looking at mean square displacements. For both samples, the autocorrelation function was well described by a stretched-exponential function indicating a linkage between the timescales of fast and slow functional relaxation dynamics. The findings of the QENS and INS investigation are discussed in relation to the results of our earlier elastic incoherent neutron scattering and molecular dynamics simulations.
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Affiliation(s)
- M Trapp
- Helmholtz-Zentrum Berlin für Materialien und Energie, Lise-Meitner Campus, Hahn-Meitner-Platz 1, 14109 Berlin, Germany
| | - M Tehei
- School of Chemistry, University of Wollongong, New South Wales 2522, Australia Centre for Medical Bioscience, Australian Institute of Nuclear Science and Engineering (AINSE), Menai, New South Wales, Australia
| | - M Trovaslet
- Institut de Biologie Structurale J.-P. Ebel, UMR 5075, CNRS-CEA-UJF, 38042 Grenoble Cédex 9, France Institut de Recherche Biomédicale des Armées, 91223 Brétigny sur Orge, France
| | - F Nachon
- Institut de Biologie Structurale J.-P. Ebel, UMR 5075, CNRS-CEA-UJF, 38042 Grenoble Cédex 9, France Institut de Recherche Biomédicale des Armées, 91223 Brétigny sur Orge, France
| | - N Martinez
- Institut de Biologie Structurale J.-P. Ebel, UMR 5075, CNRS-CEA-UJF, 38042 Grenoble Cédex 9, France Institut Laue Langevin, 38042 Grenoble Cédex 9, France Université Joseph Fourier, UFR PhITEM, 38041 Grenoble Cédex 9, France
| | - M M Koza
- Institut Laue Langevin, 38042 Grenoble Cédex 9, France
| | - M Weik
- Institut de Biologie Structurale J.-P. Ebel, UMR 5075, CNRS-CEA-UJF, 38042 Grenoble Cédex 9, France
| | - P Masson
- Institut de Biologie Structurale J.-P. Ebel, UMR 5075, CNRS-CEA-UJF, 38042 Grenoble Cédex 9, France
| | - J Peters
- Institut de Biologie Structurale J.-P. Ebel, UMR 5075, CNRS-CEA-UJF, 38042 Grenoble Cédex 9, France Institut Laue Langevin, 38042 Grenoble Cédex 9, France Université Joseph Fourier, UFR PhITEM, 38041 Grenoble Cédex 9, France
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48
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Maiti KS. Broadband two dimensional infrared spectroscopy of cyclic amide 2-Pyrrolidinone. Phys Chem Chem Phys 2015; 17:24998-5003. [DOI: 10.1039/c5cp04272k] [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
In the past one-and-a-half decade there has been a significant methodological and technological development of two dimensional infrared (2DIR) spectroscopy, which unfolds many underlying physical and chemical processes of complex molecules, especially for biological molecules.
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Affiliation(s)
- Kiran Sankar Maiti
- Lehrstuhl für Physikalische Chemie
- Technische Universität München
- D-85747 Garching
- Germany
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49
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van der Loop TH, Ruesink F, Amirjalayer S, Sanders HJ, Buma WJ, Woutersen S. Unraveling the Mechanism of a Reversible Photoactivated Molecular Proton Crane. J Phys Chem B 2014; 118:12965-71. [DOI: 10.1021/jp508911v] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Tibert H. van der Loop
- Van
’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Freek Ruesink
- Van
’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Saeed Amirjalayer
- Van
’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Hans J. Sanders
- Van
’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Wybren J. Buma
- Van
’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - S. Woutersen
- Van
’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
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50
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Pang X, Zhou HX. Distinct mechanisms of a phosphotyrosyl peptide binding to two SH2 domains. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2014; 13:1440003. [DOI: 10.1142/s0219633614400033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Protein phosphorylation is a very common post-translational modification, catalyzed by kinases, for signaling and regulation. Phosphotyrosines frequently target SH2 domains. The spleen tyrosine kinase (Syk) is critical for tyrosine phosphorylation of multiple proteins and for regulation of important pathways. Phosphorylation of both Y342 and Y346 in Syk linker B is required for optimal signaling. The SH2 domains of Vav1 and PLC-γ both bind this doubly phosphorylated motif. Here we used a recently developed method to calculate the effects of Y342 and Y346 phosphorylation on the rate constants of a peptide from Syk linker B binding to the SH2 domains of Vav1 and PLC-γ. The predicted effects agree well with experimental observations. Moreover, we found that the same doubly phosphorylated peptide binds the two SH2 domains via distinct mechanism, with apparent rigid docking for Vav1 SH2 and dock-and-coalesce for PLC-γ SH2.
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Affiliation(s)
- Xiaodong Pang
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Huan-Xiang Zhou
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
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