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Espinosa YR, Caffarena ER, Grigera JR. The role of hydrophobicity in the cold denaturation of proteins under high pressure: A study on apomyoglobin. J Chem Phys 2019; 150:075102. [PMID: 30795674 DOI: 10.1063/1.5080942] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
An exciting debate arises when microscopic mechanisms involved in the denaturation of proteins at high pressures are explained. In particular, the issue emerges when the hydrophobic effect is invoked, given that hydrophobicity cannot elucidate by itself the volume changes measured during protein unfolding. In this work, we study by the use of molecular dynamics simulations and essential dynamics analysis the relation between the solvation dynamics, volume, and water structure when apomyoglobin is subjected to a hydrostatic pressure regime. Accordingly, the mechanism of cold denaturation of proteins under high-pressure can be related to the disruption of the hydrogen-bond network of water favoring the coexistence of two states, low-density and high-density water, which directly implies in the formation of a molten globule once the threshold of 200 MPa has been overcome.
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Affiliation(s)
- Yanis R Espinosa
- Instituto de Física de Líquidos y Sistemas Biológicos (CONICET-UNLP), Calle 59 Nro 789, B1900BTE La Plata, Argentina
| | - Ernesto R Caffarena
- Programa de Computação Científica (PROCC), Fundação Oswaldo Cruz, Manguinhos, CEP 21040-360 Rio de Janeiro, Brazil
| | - J Raúl Grigera
- CEQUINOR, Universidad de La Plata and CONICET, 47 y 115, B1900 La Plata, Argentina
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52
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Diddens D, Baschnagel J, Johner A. Microscopic Structure of Compacted Polyelectrolyte Complexes: Insights from Molecular Dynamics Simulations. ACS Macro Lett 2019; 8:123-127. [PMID: 35619419 DOI: 10.1021/acsmacrolett.8b00630] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We utilize atomistic molecular dynamics (MD) simulations to study local structural changes inside a polyelectrolyte complex consisting of poly(styrenesulfonate) (PSS) and poly(diallyldimethylammonium) (PDADMA) upon densification, in analogy to ultracentrifugation in experiments. In particular, we focus on the water content and on the reinforcement of the PSS-PDADMA network for various external accelerations. We demonstrate that apart from the formation of mesoscopic pores observed experimentally also the microscopic structure and the local relaxation processes likely affect the unique rheological properties of compacted polyelectrolyte complexes, as densification increases both the number of PSS-PDADMA coordinations and the intermixing of PSS and PDADMA. These processes slow down local rearrangements, thus further stabilizing the compacted state. We find that the concept of binary PSS-PDADMA salt bonds-relevant for theoretical models-is not strictly valid in the dense limit.
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Affiliation(s)
- Diddo Diddens
- Institut Charles Sadron, Université de Strasbourg, CNRS UPR22, 23 Rue du Loess, Strasbourg 67034 Cedex 2, France
| | - Jörg Baschnagel
- Institut Charles Sadron, Université de Strasbourg, CNRS UPR22, 23 Rue du Loess, Strasbourg 67034 Cedex 2, France
| | - Albert Johner
- Institut Charles Sadron, Université de Strasbourg, CNRS UPR22, 23 Rue du Loess, Strasbourg 67034 Cedex 2, France
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53
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Elder RM, Long TR, Bain ED, Lenhart JL, Sirk TW. Mechanics and nanovoid nucleation dynamics: effects of polar functionality in glassy polymer networks. SOFT MATTER 2018; 14:8895-8911. [PMID: 30209509 DOI: 10.1039/c8sm01483c] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We use molecular simulations and experiments to rationalize the properties of a class of networks based on dicyclopentadiene (DCPD), a polymer with excellent fracture toughness and a high glass transition temperature (Tg), copolymerized with 5-norbornene-2-methanol (NBOH). DCPD is a highly non-polar hydrocarbon, while NBOH contains a hydroxy group, introducing polar functionality and hydrogen bonds (H-bonds). NBOH thus represents a possible route to improve the chemical compatibility of DCPD-based networks with less-hydrophobic materials. We systematically vary the NBOH content (polar chemistry) in DCPD networks, while keeping other network parameters nearly constant, including the molecular weight between cross-links, chain rigidity, and Tg. Using molecular dynamics (MD) simulations, we quantify the thermovolumetric and mechanical properties, including Tg, cohesive energy density, stiffness, and yield strength. We compare these results with experiments on networks of similar composition, finding good agreement. The relation between these properties and polar chemistry are studied by examining a secondary network of physical cross-links, formed by hydrogen bonds between NBOH units. Further, we examine nanovoid formation, an energy dissipation mechanism hypothesized to contribute to the toughness of pDCPD. Using metadynamics to accelerate sampling, we quantify the nanovoid nucleation rate under hydrostatic tension, similar to the stress state in the plastic zone preceding a crack tip. Small additions of NBOH have minimal effect, but the rate drops steeply with larger amounts. Several properties are mapped at nanometer scales, including stiffness and mobility, and associated with void nucleation. Estimates of the length- and time-scale of the plastic zone near a crack tip are used in discussing nanovoid formation as a plausible toughening mechanism in these materials. Overall, the results suggest that pDCPD tolerates the addition of some polar chemistry without degrading its excellent mechanical properties.
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Affiliation(s)
- Robert M Elder
- Polymers Branch, U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005, USA.
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Role of Extracellular Loops and Membrane Lipids for Ligand Recognition in the Neuronal Adenosine Receptor Type 2A: An Enhanced Sampling Simulation Study. Molecules 2018; 23:molecules23102616. [PMID: 30322034 PMCID: PMC6222423 DOI: 10.3390/molecules23102616] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 10/09/2018] [Accepted: 10/10/2018] [Indexed: 01/12/2023] Open
Abstract
Human G-protein coupled receptors (GPCRs) are important targets for pharmaceutical intervention against neurological diseases. Here, we use molecular simulation to investigate the key step in ligand recognition governed by the extracellular domains in the neuronal adenosine receptor type 2A (hA2AR), a target for neuroprotective compounds. The ligand is the high-affinity antagonist (4-(2-(7-amino-2-(furan-2-yl)-[1,2,4]triazolo[1,5-a][1,3,5]triazin-5-ylamino)ethyl)phenol), embedded in a neuronal membrane mimic environment. Free energy calculations, based on well-tempered metadynamics, reproduce the experimentally measured binding affinity. The results are consistent with the available mutagenesis studies. The calculations identify a vestibular binding site, where lipids molecules can actively participate to stabilize ligand binding. Bioinformatic analyses suggest that such vestibular binding site and, in particular, the second extracellular loop, might drive the ligand toward the orthosteric binding pocket, possibly by allosteric modulation. Taken together, these findings point to a fundamental role of the interaction between extracellular loops and membrane lipids for ligands’ molecular recognition and ligand design in hA2AR.
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55
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An Algorithm for Computing Side Chain Conformational Variations of a Protein Tunnel/Channel. Molecules 2018; 23:molecules23102459. [PMID: 30261587 PMCID: PMC6222877 DOI: 10.3390/molecules23102459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 09/21/2018] [Accepted: 09/22/2018] [Indexed: 11/16/2022] Open
Abstract
In this paper, a novel method to compute side chain conformational variations for a protein molecule tunnel (or channel) is proposed. From the conformational variations, we compute the flexibly deformed shapes of the initial tunnel, and present a way to compute the maximum size of the ligand that can pass through the deformed tunnel. By using the two types of graphs corresponding to amino acids and their side chain rotamers, the suggested algorithm classifies amino acids and rotamers which possibly have collisions. Based on the divide and conquer technique, local side chain conformations are computed first, and then a global conformation is generated by combining them. With the exception of certain cases, experimental results show that the algorithm finds up to 327,680 valid side chain conformations from 128~1233 conformation candidates within three seconds.
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56
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Liu Y, Liu Z, Zeng G, Chen M, Jiang Y, Shao B, Li Z, Liu Y. Effect of surfactants on the interaction of phenol with laccase: Molecular docking and molecular dynamics simulation studies. JOURNAL OF HAZARDOUS MATERIALS 2018; 357:10-18. [PMID: 29859460 DOI: 10.1016/j.jhazmat.2018.05.042] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 05/01/2018] [Accepted: 05/21/2018] [Indexed: 06/08/2023]
Abstract
Some surfactants can enhance the removal of phenol by laccase (Lac) in various industrial effluents. Their behavior and function in the biodegradation of phenolic wastewater have been experimentally reported by many researchers, but the underlying molecular mechanism is still unclear. Therefore, the interaction mechanisms of phenol with Lac from Trametes versicolor were investigated in the presence or absence of Triton X-100 (TX100) or rhamnolipid (RL) by molecular docking and molecular dynamics (MD) simulations. The results indicate that phenol contacts with an active site of Lac by hydrogen bonds (HBs) and van der Waals (vdW) interactions in aqueous solution for maintaining its stability. The presence of TX100 or RL results in the significant changes of enzymatic conformations. Meanwhile, the hydrophobic parts of surfactants contact with the outside surface of Lac. These changes lead to the decrease of binding energy between phenol and Lac. The migration behavior of water molecules within hydration shell is also inevitably affected. Therefore, the amphipathic TX100 or RL may influence the phenol degradation ability of Lac by modulating their interactions and water environment. This study offers molecular level of understanding on the function of surfactants in biosystem.
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Affiliation(s)
- Yujie Liu
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha, 410082, PR China
| | - Zhifeng Liu
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha, 410082, PR China.
| | - Guangming Zeng
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha, 410082, PR China.
| | - Ming Chen
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha, 410082, PR China
| | - Yilin Jiang
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha, 410082, PR China
| | - Binbin Shao
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha, 410082, PR China
| | - Zhigang Li
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha, 410082, PR China
| | - Yang Liu
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha, 410082, PR China
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57
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Zeng J, Guareschi R, Damre M, Cao R, Kless A, Neumaier B, Bauer A, Giorgetti A, Carloni P, Rossetti G. Structural Prediction of the Dimeric Form of the Mammalian Translocator Membrane Protein TSPO: A Key Target for Brain Diagnostics. Int J Mol Sci 2018; 19:E2588. [PMID: 30200318 PMCID: PMC6165245 DOI: 10.3390/ijms19092588] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 08/21/2018] [Accepted: 08/28/2018] [Indexed: 11/17/2022] Open
Abstract
Positron emission tomography (PET) radioligands targeting the human translocator membrane protein (TSPO) are broadly used for the investigations of neuroinflammatory conditions associated with neurological disorders. Structural information on the mammalian protein homodimers-the suggested functional state of the protein-is limited to a solid-state nuclear magnetic resonance (NMR) study and to a model based on the previously-deposited solution NMR structure of the monomeric mouse protein. Computational studies performed here suggest that the NMR-solved structure in the presence of detergents is not prone to dimer formation and is furthermore unstable in its native membrane environment. We, therefore, propose a new model of the functionally-relevant dimeric form of the mouse protein, based on a prokaryotic homologue. The model, fully consistent with solid-state NMR data, is very different from the previous predictions. Hence, it provides, for the first time, structural insights into this pharmaceutically-important target which are fully consistent with experimental data.
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Affiliation(s)
- Juan Zeng
- Institute for Advanced Simulations (IAS)-5/Institute for Neuroscience and Medicine (INM)-9, Forschungszentrum Jülich, 52428 Jülich, Germany.
- Laboratory of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, 518055 Shenzhen, China.
| | - Riccardo Guareschi
- Institute for Advanced Simulations (IAS)-5/Institute for Neuroscience and Medicine (INM)-9, Forschungszentrum Jülich, 52428 Jülich, Germany.
| | - Mangesh Damre
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy.
- Neurobiology, International School for Advanced Studies (SISSA), 34136 Trieste, Italy.
| | - Ruyin Cao
- Institute for Advanced Simulations (IAS)-5/Institute for Neuroscience and Medicine (INM)-9, Forschungszentrum Jülich, 52428 Jülich, Germany.
| | - Achim Kless
- Grünenthal Innovation, Translational Science & Intelligence, Grünenthal GmbH, 52078 Aachen, Germany.
| | - Bernd Neumaier
- Institute for Neuroscience and Medicine (INM)-5, Forschungszentrum Jülich, 52428 Jülich, Germany.
| | - Andreas Bauer
- Institute for Neuroscience and Medicine (INM)-2, Forschungszentrum Jülich, 52428 Jülich, Germany.
| | - Alejandro Giorgetti
- Institute for Advanced Simulations (IAS)-5/Institute for Neuroscience and Medicine (INM)-9, Forschungszentrum Jülich, 52428 Jülich, Germany.
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy.
| | - Paolo Carloni
- Institute for Advanced Simulations (IAS)-5/Institute for Neuroscience and Medicine (INM)-9, Forschungszentrum Jülich, 52428 Jülich, Germany.
- RWTH Aachen University, Department of Physics, 52078 Aachen, Germany.
| | - Giulia Rossetti
- Institute for Advanced Simulations (IAS)-5/Institute for Neuroscience and Medicine (INM)-9, Forschungszentrum Jülich, 52428 Jülich, Germany.
- Jülich Supercomputing Center (JSC), Forschungszentrum Jülich, 52428 Jülich, Germany.
- University Hospital Aachen, RWTH Aachen University, 52078 Aachen, Germany.
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58
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Chintapalli SV, Anishkin A, Adams SH. Exploring the entry route of palmitic acid and palmitoylcarnitine into myoglobin. Arch Biochem Biophys 2018; 655:56-66. [PMID: 30092229 DOI: 10.1016/j.abb.2018.07.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/23/2018] [Accepted: 07/31/2018] [Indexed: 11/26/2022]
Abstract
Myoglobin, besides its role in oxygen turnover, has gained recognition as a potential regulator of lipid metabolism. Previously, we confirmed the interaction of fatty acids and acylcarnitines with Oxy-Myoglobin, using both molecular dynamic simulations and Isothermal Titration Calorimetry studies. However, those studies were limited to testing only the binding sites derived from homology to fatty acid binding proteins and predictions using automated docking. To explore the entry mechanisms of the lipid ligands into myoglobin, we conducted molecular dynamic simulations of murine Oxy- and Deoxy-Mb structures with palmitate or palmitoylcarnitine starting at different positions near the protein surface. The simulations indicated that both ligands readily (under ∼10-20 ns) enter the Oxy-Mb structure through a dynamic area ("portal region") near heme, known to be the entry point for small molecule gaseous ligands like O2, CO and NO. The entry is not observed with Deoxy-Mb where lipid ligands move away from protein surface, due to a compaction of the entry portal and the heme-containing crevice in the Mb protein upon O2 removal. The results suggest quick spontaneous binding of lipids to Mb driven by hydrophobic interactions, strongly enhanced by oxygenation, and consistent with the emergent role of Mb in lipid metabolism.
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Affiliation(s)
- Sree V Chintapalli
- Arkansas Children's Nutrition Center -and- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, USA.
| | - Andriy Anishkin
- Department of Biology, University of Maryland, College Park, USA
| | - Sean H Adams
- Arkansas Children's Nutrition Center -and- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, USA
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59
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Kalli AC, Reithmeier RAF. Interaction of the human erythrocyte Band 3 anion exchanger 1 (AE1, SLC4A1) with lipids and glycophorin A: Molecular organization of the Wright (Wr) blood group antigen. PLoS Comput Biol 2018; 14:e1006284. [PMID: 30011272 PMCID: PMC6080803 DOI: 10.1371/journal.pcbi.1006284] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 08/07/2018] [Accepted: 06/08/2018] [Indexed: 11/29/2022] Open
Abstract
The Band 3 (AE1, SLC4A1) membrane protein is found in red blood cells and in kidney where it functions as an electro-neutral chloride/bicarbonate exchanger. In this study, we have used molecular dynamics simulations to provide the first realistic model of the dimeric membrane domain of human Band 3 in an asymmetric lipid bilayer containing a full complement of phospholipids, including phosphatidylinositol 4,5–bisphosphate (PIP2) and cholesterol, and its partner membrane protein Glycophorin A (GPA). The simulations show that the annular layer in the inner leaflet surrounding Band 3 was enriched in phosphatidylserine and PIP2 molecules. Cholesterol was also enriched around Band 3 but also at the dimer interface. The interaction of these lipids with specific sites on Band 3 may play a role in the folding and function of this anion transport membrane protein. GPA associates with Band 3 to form the Wright (Wr) blood group antigen, an interaction that involves an ionic bond between Glu658 in Band 3 and Arg61 in GPA. We were able to recreate this complex by performing simulations to allow the dimeric transmembrane portion of GPA to interact with Band 3 in a model membrane. Large-scale simulations showed that the GPA dimer can bridge Band 3 dimers resulting in the dynamic formation of long strands of alternating Band 3 and GPA dimers. Human Band 3 (AE1, SLC4A1), an abundant 911 amino acid glycoprotein, catalyzes the exchange of bicarbonate and chloride across the red blood cell membrane, a process necessary for efficient respiration. Malfunction of Band 3 leads to inherited diseases such as Southeast Asian Ovalocytosis, hereditary spherocytosis and distal renal tubular acidosis. Despite much available structural and functional data about Band 3, key questions about the conformational changes associated with transport and the molecular details of its interaction with lipids and other proteins remain unanswered. In this study, we have used computer simulations to investigate the dynamics of Band 3 in lipid bilayers that resemble the red blood cell plasma membrane. Our results suggest that negatively charged phospholipids and cholesterol interact strongly with Band 3 forming an annulus around the protein. Glycophorin A (GPA) interacts with Band 3 to form the Wright (Wr) blood group antigen. We were able to recreate this complex and show that GPA promotes the clustering of Band 3 in red blood cell membranes. Understanding the molecular details of the interaction of Band 3 with GPA has provided new insights into the nature of the Wright blood group antigen.
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Affiliation(s)
- Antreas C. Kalli
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
- * E-mail:
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60
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Boon PLS, Saw WG, Lim XX, Raghuvamsi PV, Huber RG, Marzinek JK, Holdbrook DA, Anand GS, Grüber G, Bond PJ. Partial Intrinsic Disorder Governs the Dengue Capsid Protein Conformational Ensemble. ACS Chem Biol 2018; 13:1621-1630. [PMID: 29792674 DOI: 10.1021/acschembio.8b00231] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The 11 kDa, positively charged dengue capsid protein (C protein) exists stably as a homodimer and colocalizes with the viral genome within mature viral particles. Its core is composed of four alpha helices encompassing a small hydrophobic patch that may interact with lipids, but approximately 20% of the protein at the N-terminus is intrinsically disordered, making it challenging to elucidate its conformational landscape. Here, we combine small-angle X-ray scattering (SAXS), amide hydrogen-deuterium exchange mass spectrometry (HDXMS), and atomic-resolution molecular dynamics (MD) simulations to probe the dynamics of dengue C proteins. We show that the use of MD force fields (FFs) optimized for intrinsically disordered proteins (IDPs) is necessary to capture their conformational landscape and validate the computationally generated ensembles with reference to SAXS and HDXMS data. Representative ensembles of the C protein dimer are characterized by alternating, clamp-like exposure and occlusion of the internal hydrophobic patch, as well as by residual helical structure at the disordered N-terminus previously identified as a potential source of autoinhibition. Such dynamics are likely to determine the multifunctionality of the C protein during the flavivirus life cycle and hence impact the design of novel antiviral compounds.
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Affiliation(s)
- Priscilla L. S. Boon
- Bioinformatics institute (BII), Agency for Science, Technology and Research (A*STAR), #07-01 Matrix, 30 Biopolis Street, Singapore 138671
- Department of Biological Sciences (DBS), National University of Singapore (NUS), 14 Science Drive 4, Singapore 117543
- NUS Graduate School for Integrated Sciences and Engineering, National University of Singapore, #05-01, 28 Medical Drive, Singapore 117456
| | - Wuan Geok Saw
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore 637551
| | - Xin Xiang Lim
- Department of Biological Sciences (DBS), National University of Singapore (NUS), 14 Science Drive 4, Singapore 117543
| | - Palur Venkata Raghuvamsi
- Department of Biological Sciences (DBS), National University of Singapore (NUS), 14 Science Drive 4, Singapore 117543
| | - Roland G. Huber
- Bioinformatics institute (BII), Agency for Science, Technology and Research (A*STAR), #07-01 Matrix, 30 Biopolis Street, Singapore 138671
| | - Jan K. Marzinek
- Bioinformatics institute (BII), Agency for Science, Technology and Research (A*STAR), #07-01 Matrix, 30 Biopolis Street, Singapore 138671
- Department of Biological Sciences (DBS), National University of Singapore (NUS), 14 Science Drive 4, Singapore 117543
| | - Daniel A. Holdbrook
- Bioinformatics institute (BII), Agency for Science, Technology and Research (A*STAR), #07-01 Matrix, 30 Biopolis Street, Singapore 138671
| | - Ganesh S. Anand
- Department of Biological Sciences (DBS), National University of Singapore (NUS), 14 Science Drive 4, Singapore 117543
| | - Gerhard Grüber
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore 637551
| | - Peter J. Bond
- Bioinformatics institute (BII), Agency for Science, Technology and Research (A*STAR), #07-01 Matrix, 30 Biopolis Street, Singapore 138671
- Department of Biological Sciences (DBS), National University of Singapore (NUS), 14 Science Drive 4, Singapore 117543
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61
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Yeow J, Tan KW, Holdbrook DA, Chong ZS, Marzinek JK, Bond PJ, Chng SS. The architecture of the OmpC-MlaA complex sheds light on the maintenance of outer membrane lipid asymmetry in Escherichia coli. J Biol Chem 2018; 293:11325-11340. [PMID: 29848551 DOI: 10.1074/jbc.ra118.002441] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 05/02/2018] [Indexed: 12/16/2022] Open
Abstract
A distinctive feature of the Gram-negative bacterial cell envelope is the asymmetric outer membrane (OM), where lipopolysaccharides and phospholipids (PLs) reside in the outer and inner leaflets, respectively. This unique lipid asymmetry renders the OM impermeable to external insults, including antibiotics and bile salts. In Escherichia coli, the complex comprising osmoporin OmpC and the OM lipoprotein MlaA is believed to maintain lipid asymmetry by removing mislocalized PLs from the outer leaflet of the OM. How this complex performs this function is unknown. Here, we defined the molecular architecture of the OmpC-MlaA complex to gain insights into its role in PL transport. Using in vivo photo-cross-linking and molecular dynamics simulations, we established that MlaA interacts extensively with OmpC and is located entirely within the lipid bilayer. In addition, MlaA forms a hydrophilic channel, likely enabling PL translocation across the OM. We further showed that flexibility in a hairpin loop adjacent to the channel is critical in modulating MlaA activity. Finally, we demonstrated that OmpC plays a functional role in maintaining OM lipid asymmetry together with MlaA. Our work offers glimpses into how the OmpC-MlaA complex transports PLs across the OM and has important implications for future antibacterial drug development.
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Affiliation(s)
- Jiang Yeow
- Department of Chemistry, National University of Singapore, Singapore 117543; National University of Singapore Graduate School for Integrative Sciences and Engineering, Singapore 117456
| | - Kang Wei Tan
- Department of Chemistry, National University of Singapore, Singapore 117543
| | - Daniel A Holdbrook
- Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR), Singapore 138671
| | - Zhi-Soon Chong
- Department of Chemistry, National University of Singapore, Singapore 117543
| | - Jan K Marzinek
- Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR), Singapore 138671; Department of Biological Sciences, National University of Singapore, Singapore 117543
| | - Peter J Bond
- Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR), Singapore 138671; Department of Biological Sciences, National University of Singapore, Singapore 117543.
| | - Shu-Sin Chng
- Department of Chemistry, National University of Singapore, Singapore 117543; Singapore Center for Environmental Life Sciences Engineering, National University of Singapore, Singapore 117456.
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62
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Revanasiddappa PD, Sankar R, Senapati S. Role of the Bound Phospholipids in the Structural Stability of Cholesteryl Ester Transfer Protein. J Phys Chem B 2018; 122:4239-4248. [DOI: 10.1021/acs.jpcb.7b12095] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Prasanna D. Revanasiddappa
- BJM School of Biosciences and Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036, India
| | - Revathi Sankar
- BJM School of Biosciences and Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036, India
| | - Sanjib Senapati
- BJM School of Biosciences and Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036, India
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63
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Patra MC, Kwon HK, Batool M, Choi S. Computational Insight Into the Structural Organization of Full-Length Toll-Like Receptor 4 Dimer in a Model Phospholipid Bilayer. Front Immunol 2018; 9:489. [PMID: 29593733 PMCID: PMC5857566 DOI: 10.3389/fimmu.2018.00489] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 02/26/2018] [Indexed: 01/07/2023] Open
Abstract
Toll-like receptors (TLRs) are a unique category of pattern recognition receptors that recognize distinct pathogenic components, often utilizing the same set of downstream adaptors. Specific molecular features of extracellular, transmembrane (TM), and cytoplasmic domains of TLRs are crucial for coordinating the complex, innate immune signaling pathway. Here, we constructed a full-length structural model of TLR4-a widely studied member of the interleukin-1 receptor/TLR superfamily-using homology modeling, protein-protein docking, and molecular dynamics simulations to understand the differential domain organization of TLR4 in a membrane-aqueous environment. Results showed that each functional domain of the membrane-bound TLR4 displayed several structural transitions that are biophysically essential for plasma membrane integration. Specifically, the extracellular and cytoplasmic domains were partially immersed in the upper and lower leaflets of the membrane bilayer. Meanwhile, TM domains tilted considerably to overcome the hydrophobic mismatch with the bilayer core. Our analysis indicates an alternate dimerization or a potential oligomerization interface of TLR4-TM. Moreover, the helical properties of an isolated TM dimer partly agree with that of the full-length receptor. Furthermore, membrane-absorbed or solvent-exposed surfaces of the toll/interleukin-1 receptor domain are consistent with previous X-ray crystallography and biochemical studies. Collectively, we provided a complete structural model of membrane-bound TLR4 that strengthens our current understanding of the complex mechanism of receptor activation and adaptor recruitment in the innate immune signaling pathway.
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Affiliation(s)
- Mahesh Chandra Patra
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Hyuk-Kwon Kwon
- Department of Orthopaedics and Rehabilitation, Yale School of Medicine, New Haven, CT, United States
| | - Maria Batool
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
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64
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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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65
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Akbar R, Helms V. ALLO: A tool to discriminate and prioritize allosteric pockets. Chem Biol Drug Des 2018; 91:845-853. [DOI: 10.1111/cbdd.13161] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 11/05/2017] [Accepted: 12/01/2017] [Indexed: 11/30/2022]
Affiliation(s)
- Rahmad Akbar
- Center for Bioinformatics; Saarland University; Saarbruecken Germany
| | - Volkhard Helms
- Center for Bioinformatics; Saarland University; Saarbruecken Germany
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66
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Kadirvel P, Anishetty S. Potential role of salt-bridges in the hinge-like movement of apicomplexa specific β-hairpin of Plasmodium and Toxoplasma profilins: A molecular dynamics simulation study. J Cell Biochem 2018; 119:3683-3696. [PMID: 29236299 DOI: 10.1002/jcb.26579] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 12/04/2017] [Indexed: 12/14/2022]
Abstract
Profilin is one of the actin-binding proteins that regulate dynamics of actin polymerization. It plays a key role in cell motility and invasion. It also interacts with several other proteins notably through its poly-L-proline (PLP) binding site. Profilin in apicomplexa is characterized by a unique mini-domain consisting of a large β-hairpin extension and an acidic loop which is relatively longer in Plasmodium species. Profilin is essential for the invasive blood stages of Plasmodium falciparum. In the current study, unbound profilins from Plasmodium falciparum (Pf), Toxoplasma gondii (Tg), and Homo sapiens (Hs) were subjected to molecular dynamics (MD) simulations for a timeframe of 100 ns each to understand the conformational dynamics of these proteins. It was found that the β-hairpin of profilins from Pf and Tg shows a hinge-like movement. This movement in Pf profilin may possibly be driven by the loss of a salt-bridge within profilin. The impact of this conformational change on actin binding was assessed by docking three dimensional (3D) structures of profilin from Pf and Tg with their corresponding actins using ClusPro2.0. The stability of docked Pf profilin-actin complex was assessed through a 50 ns MD simulation. As Hs profilin I does not have the apicomplexa specific mini-domain, MD simulation was performed for this protein and its dynamics was compared to that of profilins from Pf and Tg. Using an immunoinformatics approach, potential epitope regions were predicted for Pf profilin. This has a potential application in the design of vaccines as they mapped to its unique mini-domain.
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67
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Simões T, Lopes D, Dias S, Fernandes F, Pereira J, Jorge J, Bajaj C, Gomes A. Geometric Detection Algorithms for Cavities on Protein Surfaces in Molecular Graphics: A Survey. COMPUTER GRAPHICS FORUM : JOURNAL OF THE EUROPEAN ASSOCIATION FOR COMPUTER GRAPHICS 2017; 36:643-683. [PMID: 29520122 PMCID: PMC5839519 DOI: 10.1111/cgf.13158] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Detecting and analyzing protein cavities provides significant information about active sites for biological processes (e.g., protein-protein or protein-ligand binding) in molecular graphics and modeling. Using the three-dimensional structure of a given protein (i.e., atom types and their locations in 3D) as retrieved from a PDB (Protein Data Bank) file, it is now computationally viable to determine a description of these cavities. Such cavities correspond to pockets, clefts, invaginations, voids, tunnels, channels, and grooves on the surface of a given protein. In this work, we survey the literature on protein cavity computation and classify algorithmic approaches into three categories: evolution-based, energy-based, and geometry-based. Our survey focuses on geometric algorithms, whose taxonomy is extended to include not only sphere-, grid-, and tessellation-based methods, but also surface-based, hybrid geometric, consensus, and time-varying methods. Finally, we detail those techniques that have been customized for GPU (Graphics Processing Unit) computing.
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Affiliation(s)
- Tiago Simões
- Instituto de Telecomunicações, Portugal
- Universidade da Beira Interior, Portugal
| | | | - Sérgio Dias
- Instituto de Telecomunicações, Portugal
- Universidade da Beira Interior, Portugal
| | | | - João Pereira
- INESC-ID Lisboa, Portugal
- Instituto Superior Técnico, Universidade de Lisboa, Portugal
| | - Joaquim Jorge
- INESC-ID Lisboa, Portugal
- Instituto Superior Técnico, Universidade de Lisboa, Portugal
| | | | - Abel Gomes
- Instituto de Telecomunicações, Portugal
- Universidade da Beira Interior, Portugal
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68
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Dias SED, Martins AM, Nguyen QT, Gomes AJP. GPU-based detection of protein cavities using Gaussian surfaces. BMC Bioinformatics 2017; 18:493. [PMID: 29145826 PMCID: PMC5691400 DOI: 10.1186/s12859-017-1913-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 11/01/2017] [Indexed: 11/10/2022] Open
Abstract
Background Protein cavities play a key role in biomolecular recognition and function, particularly in protein-ligand interactions, as usual in drug discovery and design. Grid-based cavity detection methods aim at finding cavities as aggregates of grid nodes outside the molecule, under the condition that such cavities are bracketed by nodes on the molecule surface along a set of directions (not necessarily aligned with coordinate axes). Therefore, these methods are sensitive to scanning directions, a problem that we call cavity ground-and-walls ambiguity, i.e., they depend on the position and orientation of the protein in the discretized domain. Also, it is hard to distinguish grid nodes belonging to protein cavities amongst all those outside the protein, a problem that we call cavity ceiling ambiguity. Results We solve those two ambiguity problems using two implicit isosurfaces of the protein, the protein surface itself (called inner isosurface) that excludes all its interior nodes from any cavity, and the outer isosurface that excludes most of its exterior nodes from any cavity. Summing up, the cavities are formed from nodes located between these two isosurfaces. It is worth noting that these two surfaces do not need to be evaluated (i.e., sampled), triangulated, and rendered on the screen to find the cavities in between; their defining analytic functions are enough to determine which grid nodes are in the empty space between them. Conclusion This article introduces a novel geometric algorithm to detect cavities on the protein surface that takes advantage of the real analytic functions describing two Gaussian surfaces of a given protein.
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Affiliation(s)
- Sérgio E D Dias
- Universidade da Beira Interior, Av. Marques D'Ávila e Bolama, Covilhã, 6200-001, Portugal.,Instituto de Telecomunicações, Av. Marques D'Ávila e Bolama, Covilhã, 6200-001, Portugal
| | - Ana Mafalda Martins
- Universidade da Beira Interior, Av. Marques D'Ávila e Bolama, Covilhã, 6200-001, Portugal
| | - Quoc T Nguyen
- Universidade da Beira Interior, Av. Marques D'Ávila e Bolama, Covilhã, 6200-001, Portugal.,Instituto de Telecomunicações, Av. Marques D'Ávila e Bolama, Covilhã, 6200-001, Portugal
| | - Abel J P Gomes
- Universidade da Beira Interior, Av. Marques D'Ávila e Bolama, Covilhã, 6200-001, Portugal. .,Instituto de Telecomunicações, Av. Marques D'Ávila e Bolama, Covilhã, 6200-001, Portugal.
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69
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La Sala G, Decherchi S, De Vivo M, Rocchia W. Allosteric Communication Networks in Proteins Revealed through Pocket Crosstalk Analysis. ACS CENTRAL SCIENCE 2017; 3:949-960. [PMID: 28979936 PMCID: PMC5620967 DOI: 10.1021/acscentsci.7b00211] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Indexed: 05/17/2023]
Abstract
The detection and characterization of binding pockets and allosteric communication in proteins is crucial for studying biological regulation and performing drug design. Nowadays, ever-longer molecular dynamics (MD) simulations are routinely used to investigate the spatiotemporal evolution of proteins. Yet, there is no computational tool that can automatically detect all the pockets and potential allosteric communication networks along these extended MD simulations. Here, we use a novel and fully automated algorithm that examines pocket formation, dynamics, and allosteric communication embedded in microsecond-long MD simulations of three pharmaceutically relevant proteins, namely, PNP, A2A, and Abl kinase. This dynamic analysis uses pocket crosstalk, defined as the temporal exchange of atoms between adjacent pockets, along the MD trajectories as a fingerprint of hidden allosteric communication networks. Importantly, this study indicates that dynamic pocket crosstalk analysis provides new mechanistic understandings on allosteric communication networks, enriching the available experimental data. Thus, our results suggest the prospective use of this unprecedented dynamic analysis to characterize transient binding pockets for structure-based drug design.
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Affiliation(s)
- Giuseppina La Sala
- Laboratory
of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Sergio Decherchi
- CONCEPT
Lab, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
- BiKi
Technologies s.r.l., via XX Settembre 33, 16121 Genova, Italy
| | - Marco De Vivo
- Laboratory
of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
- IAS-S/INM-9
Computational Biomedicine Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
- Phone: +39 01071781577. E-mail:
| | - Walter Rocchia
- CONCEPT
Lab, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
- Phone: +39 01071781552. E-mail:
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70
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Wagner JR, Sørensen J, Hensley N, Wong C, Zhu C, Perison T, Amaro RE. POVME 3.0: Software for Mapping Binding Pocket Flexibility. J Chem Theory Comput 2017; 13:4584-4592. [PMID: 28800393 DOI: 10.1021/acs.jctc.7b00500] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We present a substantial update to the open-source POVME binding pocket analysis software. New capabilities of POVME 3.0 include a flexible chemical coloring scheme for feature identification, postanalysis tools for comparing large ensembles of pockets (e.g., from molecular dynamics simulations), and the introduction of scripts and methods that facilitate binding pocket comparison and analysis. We envision the use of this software for visualization of binding pocket dynamics, selection of representative structures for ensemble docking, and incorporation of molecular dynamics results into ligand design efforts.
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Affiliation(s)
- Jeffrey R Wagner
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093, United States
| | - Jesper Sørensen
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093, United States
| | - Nathan Hensley
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093, United States
| | - Celia Wong
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093, United States
| | - Clare Zhu
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093, United States
| | - Taylor Perison
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093, United States
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093, United States.,National Biomedical Computation Resource, University of California, San Diego , La Jolla, California 92093, United States
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71
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Krah A, Zachariae U. Insights into the ion-coupling mechanism in the MATE transporter NorM-VC. Phys Biol 2017; 14:045009. [DOI: 10.1088/1478-3975/aa5ee7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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72
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Boags A, Hsu PC, Samsudin F, Bond PJ, Khalid S. Progress in Molecular Dynamics Simulations of Gram-Negative Bacterial Cell Envelopes. J Phys Chem Lett 2017; 8:2513-2518. [PMID: 28467715 DOI: 10.1021/acs.jpclett.7b00473] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Bacteria are protected by complex molecular architectures known as the cell envelope. The cell envelope is composed of regions with distinct chemical compositions and physical properties, namely, membranes and a cell wall. To develop novel antibiotics to combat pathogenic bacteria, molecular level knowledge of the structure, dynamics, and interplay between the chemical components of the cell envelope that surrounds bacterial cells is imperative. In addition, conserved molecular patterns associated with the bacterial envelope are recognized by receptors as part of the mammalian defensive response to infection, and an improved understanding of bacteria-host interactions would facilitate the search for novel immunotherapeutics. This Perspective introduces an emerging area of computational biology: multiscale molecular dynamics simulations of chemically complex models of bacterial lipids and membranes. We discuss progress to date, and identify areas for future development that will enable the study of aspects of the membrane components that are as yet unexplored by computational methods.
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Affiliation(s)
- Alister Boags
- School of Chemistry, University of Southampton , Southampton, United Kingdom , SO17 1BJ
| | - Pin-Chia Hsu
- School of Chemistry, University of Southampton , Southampton, United Kingdom , SO17 1BJ
| | - Firdaus Samsudin
- School of Chemistry, University of Southampton , Southampton, United Kingdom , SO17 1BJ
| | - Peter J Bond
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR) , Matrix 07-01, 30 Biopolis Street, 138671 Singapore
- Department of Biological Sciences, National University of Singapore , 14 Science Drive 4, 117543 Singapore
| | - Syma Khalid
- School of Chemistry, University of Southampton , Southampton, United Kingdom , SO17 1BJ
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73
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Allosteric modulation model of the mu opioid receptor by herkinorin, a potent not alkaloidal agonist. J Comput Aided Mol Des 2017; 31:467-482. [PMID: 28364251 DOI: 10.1007/s10822-017-0016-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 03/10/2017] [Indexed: 10/19/2022]
Abstract
Modulation of opioid receptors is the primary choice for pain management and structural information studies have gained new horizons with the recently available X-ray crystal structures. Herkinorin is one of the most remarkable salvinorin A derivative with high affinity for the mu opioid receptor, moderate selectivity and lack of nitrogen atoms on its structure. Surprisingly, binding models for herkinorin are lacking. In this work, we explore binding models of herkinorin using automated docking, molecular dynamics simulations, free energy calculations and available experimental information. Our herkinorin D-ICM-1 binding model predicted a binding free energy of -11.52 ± 1.14 kcal mol-1 by alchemical free energy estimations, which is close to the experimental values -10.91 ± 0.2 and -10.80 ± 0.05 kcal mol-1 and is in agreement with experimental structural information. Specifically, D-ICM-1 molecular dynamics simulations showed a water-mediated interaction between D-ICM-1 and the amino acid H2976.52, this interaction coincides with the co-crystallized ligands. Another relevant interaction, with N1272.63, allowed to rationalize herkinorin's selectivity to mu over delta opioid receptors. Our suggested binding model for herkinorin is in agreement with this and additional experimental data. The most remarkable observation derived from our D-ICM-1 model is that herkinorin reaches an allosteric sodium ion binding site near N1503.35. Key interactions in that region appear relevant for the lack of β-arrestin recruitment by herkinorin. This interaction is key for downstream signaling pathways involved in the development of side effects, such as tolerance. Future SAR studies and medicinal chemistry efforts will benefit from the structural information presented in this work.
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74
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Choi H, Chang HJ, Lee M, Na S. Characterizing Structural Stability of Amyloid Motif Fibrils Mediated by Water Molecules. Chemphyschem 2017; 18:817-827. [PMID: 28160391 DOI: 10.1002/cphc.201601327] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 01/12/2017] [Indexed: 11/12/2022]
Abstract
In biological systems, structural confinements of amyloid fibrils can be mediated by the role of water molecules. However, the underlying effect of the dynamic behavior of water molecules on structural stabilities of amyloid fibrils is still unclear. By performing molecular dynamics simulations, we investigate the dynamic features and the effect of interior water molecules on conformations and mechanical characteristics of various amyloid fibrils. We find that a specific mechanism induced by the dynamic properties of interior water molecules can affect diffusion of water molecules inside amyloid fibrils, inducing their different structural stabilities. The conformation of amyloid fibrils induced by interior water molecules show the fibrils' different mechanical features. We elucidate the role of confined and movable interior water molecules in structural stabilities of various amyloid fibrils. Our results offer insights not only in further understanding of mechanical features of amyloids as mediated by water molecules, but also in the fine-tuning of the functional abilities of amyloid fibrils for applications.
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Affiliation(s)
- Hyunsung Choi
- Department of Mechanical Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Hyun Joon Chang
- Department of Mechanical Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Myeongsang Lee
- Department of Mechanical Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Sungsoo Na
- Department of Mechanical Engineering, Korea University, Seoul, 02841, Republic of Korea
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75
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Tiwari G, Verma CS. Toward Understanding the Molecular Recognition of Albumin by p53-Activating Stapled Peptide ATSP-7041. J Phys Chem B 2017; 121:657-670. [PMID: 28048940 DOI: 10.1021/acs.jpcb.6b09900] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Reactivation of tumor-suppressing activity of p53 protein by targeting its negative regulator MDM2/MDMX has been pursued as a potential anticancer strategy. A promising dual inhibitor of MDM2/MDMX that has been developed and is currently in clinical trials is the stapled peptide ATSP-7041. The activity of this molecule is reported to be modulated in the presence of serum. Albumin is the most abundant protein in serum and is known to bind reversibly to several molecules. To study this interaction, we develop a protocol combining molecular modeling, docking, and simulations. Exhaustive docking of the peptide with representative simulated structures of human serum albumin led to the identification of probable binding sites on the surface of the protein, including both known canonical and novel binding sites. Sequence differences at putative peptide-binding sites in human and mouse albumin result in differing interaction energies with the peptide and enable us to rationalize the observed differences in vivo. In general, the findings should help in guiding the design of features in such peptides that may affect their distribution and cell permeability, opening a new window in structure-guided design strategies.
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Affiliation(s)
- Garima Tiwari
- Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research) , 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Chandra S Verma
- Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research) , 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore.,Department of Biological sciences, National University of Singapore , 14 Science Drive 4, Singapore 117543, Singapore.,School of Biological sciences, Nanyang Technological University , 50 Nanyang Drive, Singapore 637551, Singapore
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76
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Fuchs JE, Schilling O, Liedl KR. Determinants of Macromolecular Specificity from Proteomics-Derived Peptide Substrate Data. Curr Protein Pept Sci 2017; 18:905-913. [PMID: 27455965 PMCID: PMC5898033 DOI: 10.2174/1389203717666160724211231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 03/30/2017] [Accepted: 04/15/2017] [Indexed: 11/22/2022]
Abstract
BACKGROUND Recent advances in proteomics methodologies allow for high throughput profiling of proteolytic cleavage events. The resulting substrate peptide distributions provide deep insights in the underlying macromolecular recognition events, as determinants of biomolecular specificity identified by proteomics approaches may be compared to structure-based analysis of corresponding protein-protein interfaces. METHOD Here, we present an overview of experimental and computational methodologies and tools applied in the area and provide an outlook beyond the protein class of proteases. RESULTS AND CONCLUSION We discuss here future potential, synergies and needs of the emerging overlap disciplines of proteomics and structure-based modelling.
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Affiliation(s)
- Julian E. Fuchs
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, CambridgeCB2 1EW, United Kingdom
| | - Oliver Schilling
- Institute of Molecular Medicine and Cell Research, University of Freiburg, Stefan-Meier-Str. 17, D-79104 Freiburg, Germany and BIOSS Centre for Biological Signaling Studies, University of Freiburg, D-79104Freiburg, Germany
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, A-6020Innsbruck, Austria
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77
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Baptista-Hon DT, Krah A, Zachariae U, Hales TG. A role for loop G in the β1 strand in GABAA receptor activation. J Physiol 2016; 594:5555-71. [PMID: 27195487 PMCID: PMC5043033 DOI: 10.1113/jp272463] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 05/09/2016] [Indexed: 01/18/2023] Open
Abstract
KEY POINTS The role of the β1 strand in GABAA receptor function is unclear. It lies anti-parallel to the β2 strand, which is known to participate in receptor activation. Molecular dynamics simulation revealed solvent accessible residues within the β1 strand of the GABAA β3 homopentamer that might be amenable to analysis using the substituted Cys accessibility method. Cys substitutions from Asp43 to Thr47 in the GABAA α1 subunit showed that D43C and T47C reduced the apparent potency of GABA. F45C caused a biphasic GABA concentration-response relationship and increased spontaneous gating. Cys43 and Cys47 were accessible to 2-aminoethyl methanethiosulphonate (MTSEA) modification, whereas Cys45 was not. Both GABA and the allosteric agonist propofol reduced MTSEA modification of Cys43 and Cys47. By contrast, modification of Cys64 in the β2 strand loop D was impeded by GABA but unaffected by propofol. These data reveal movement of β1 strand loop G residues during agonist activation of the GABAA receptor. ABSTRACT The GABAA receptor α subunit β1 strand runs anti-parallel to the β2 strand, which contains loop D, known to participate in receptor activation and agonist binding. However, a role for the β1 strand has yet to be established. We used molecular dynamics simulation to quantify the solvent accessible surface area (SASA) of β1 strand residues in the GABAA β3 homopentamer structure. Residues in the complementary interface equivalent to those between Asp43 and Thr47 in the α1 subunit have an alternating pattern of high and low SASA consistent with a β strand structure. We investigated the functional role of these β1 strand residues in the α1 subunit by individually replacing them with Cys residues. D43C and T47C substitutions reduced the apparent potency of GABA at α1β2γ2 receptors by 50-fold and eight-fold, respectively, whereas the F45C substitution caused a biphasic GABA concentration-response relationship and increased spontaneous gating. Receptors with D43C or T47C substitutions were sensitive to 2-aminoethyl methanethiosulphonate (MTSEA) modification. However, GABA-evoked currents mediated by α1(F45C)β2γ2 receptors were unaffected by MTSEA, suggesting that this residue is inaccessible. Both GABA and the allosteric agonist propofol reduced MTSEA modification of α1(D43C)β2γ2 and α1(T47C)β2γ2 receptors, indicating movement of the β1 strand even during allosteric activation. This is in contrast to α1(F64C)β2γ2 receptors, where only GABA, but not propofol, reduced MTSEA modification. These findings provide the first functional evidence for movement of the β1 strand during gating of the receptor and identify residues that are critical for maintaining GABAA receptor function.
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Affiliation(s)
- Daniel T Baptista-Hon
- The Institute of Academic Anaesthesia, Division of Neuroscience, School of Medicine, Ninewells Hospital, University of Dundee, Dundee, UK
| | - Alexander Krah
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Ulrich Zachariae
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Tim G Hales
- The Institute of Academic Anaesthesia, Division of Neuroscience, School of Medicine, Ninewells Hospital, University of Dundee, Dundee, UK.
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Briones R, Weichbrodt C, Paltrinieri L, Mey I, Villinger S, Giller K, Lange A, Zweckstetter M, Griesinger C, Becker S, Steinem C, de Groot BL. Voltage Dependence of Conformational Dynamics and Subconducting States of VDAC-1. Biophys J 2016; 111:1223-1234. [PMID: 27653481 PMCID: PMC5034351 DOI: 10.1016/j.bpj.2016.08.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 07/17/2016] [Accepted: 08/02/2016] [Indexed: 12/21/2022] Open
Abstract
The voltage-dependent anion channel 1 (VDAC-1) is an important protein of the outer mitochondrial membrane that transports energy metabolites and is involved in apoptosis. The available structures of VDAC proteins show a wide β-stranded barrel pore, with its N-terminal α-helix (N-α) bound to its interior. Electrophysiology experiments revealed that voltage, its polarity, and membrane composition modulate VDAC currents. Experiments with VDAC-1 mutants identified amino acids that regulate the gating process. However, the mechanisms for how these factors regulate VDAC-1, and which changes they trigger in the channel, are still unknown. In this study, molecular dynamics simulations and single-channel experiments of VDAC-1 show agreement for the current-voltage relationships of an "open" channel and they also show several subconducting transient states that are more cation selective in the simulations. We observed voltage-dependent asymmetric distortions of the VDAC-1 barrel and the displacement of particular charged amino acids. We constructed conformational models of the protein voltage response and the pore changes that consistently explain the protein conformations observed at opposite voltage polarities, either in phosphatidylethanolamine or phosphatidylcholine membranes. The submicrosecond VDAC-1 voltage response shows intrinsic structural changes that explain the role of key gating amino acids and support some of the current gating hypotheses. These voltage-dependent protein changes include asymmetric barrel distortion, its interaction with the membrane, and significant displacement of N-α amino acids.
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Affiliation(s)
- Rodolfo Briones
- Computational Biomolecular Dynamics Group, Max-Planck Institute for Biophysical Chemistry, Goettingen, Germany.
| | - Conrad Weichbrodt
- Institute of Organic and Biomolecular Chemistry, University of Goettingen, Goettingen, Germany
| | - Licia Paltrinieri
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Ingo Mey
- Institute of Organic and Biomolecular Chemistry, University of Goettingen, Goettingen, Germany
| | - Saskia Villinger
- NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Goettingen, Germany
| | - Karin Giller
- NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Goettingen, Germany
| | - Adam Lange
- NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Goettingen, Germany
| | - Markus Zweckstetter
- NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Goettingen, Germany; German Center for Neurodegenerative Diseases (DZNE), Goettingen, Germany; Department of Neurology, University Medical Center, University of Goettingen, Goettingen, Germany
| | - Christian Griesinger
- NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Goettingen, Germany
| | - Stefan Becker
- NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Goettingen, Germany
| | - Claudia Steinem
- Institute of Organic and Biomolecular Chemistry, University of Goettingen, Goettingen, Germany.
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Max-Planck Institute for Biophysical Chemistry, Goettingen, Germany.
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79
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Morrill GA, Kostellow AB. Molecular Properties of Globin Channels and Pores: Role of Cholesterol in Ligand Binding and Movement. Front Physiol 2016; 7:360. [PMID: 27656147 PMCID: PMC5011150 DOI: 10.3389/fphys.2016.00360] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 08/08/2016] [Indexed: 02/02/2023] Open
Abstract
Globins contain one or more cavities that control or affect such functions as ligand movement and ligand binding. Here we report that the extended globin family [cytoglobin (Cygb); neuroglobin (Ngb); myoglobin (Mb); hemoglobin (Hb) subunits Hba(α); and Hbb(β)] contain either a transmembrane (TM) helix or pore-lining region as well as internal cavities. Protein motif/domain analyses indicate that Ngb and Hbb each contain 5 cholesterol- binding (CRAC/CARC) domains and 1 caveolin binding motif, whereas the Cygb dimer has 6 cholesterol-binding domains but lacks caveolin-binding motifs. Mb and Hba each exhibit 2 cholesterol-binding domains and also lack caveolin-binding motifs. The Hb αβ-tetramer contains 14 cholesterol-binding domains. Computer algorithms indicate that Cygb and Ngb cavities display multiple partitions and C-terminal pore-lining regions, whereas Mb has three major cavities plus a C-terminal pore-lining region. The Hb tetramer exhibits a large internal cavity but the subunits differ in that they contain a C-terminal TM helix (Hba) and pore-lining region (Hbb). The cavities include 43 of 190 Cygb residues, 38 of 151 of Ngb residues, 55 of 154 Mb residues, and 137 of 688 residues in the Hb tetramer. Each cavity complex includes 6 to 8 residues of the TM helix or pore-lining region and CRAC/CARC domains exist within all cavities. Erythrocyte Hb αβ-tetramers are largely cytosolic but also bind to a membrane anion exchange protein, "band 3," which contains a large internal cavity and 12 TM helices (5 being pore-lining regions). The Hba TM helix may be the erythrocyte membrane "band 3" attachment site. "Band 3" contributes 4 caveolin binding motifs and 10 CRAC/CARC domains. Cholesterol binding may create lipid-disordered phases that alter globin cavities and facilitate ligand movement, permitting ion channel formation and conformational changes that orchestrate anion and ligand (O2, CO2, NO) movement within the large internal cavities and channels of the globins.
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Affiliation(s)
- Gene A Morrill
- Department of Physiology and Biophysics, Albert Einstein College of Medicine Bronx, NY, USA
| | - Adele B Kostellow
- Department of Physiology and Biophysics, Albert Einstein College of Medicine Bronx, NY, USA
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80
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Structure and Function of the Su(H)-Hairless Repressor Complex, the Major Antagonist of Notch Signaling in Drosophila melanogaster. PLoS Biol 2016; 14:e1002509. [PMID: 27404588 PMCID: PMC4942083 DOI: 10.1371/journal.pbio.1002509] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 06/10/2016] [Indexed: 11/25/2022] Open
Abstract
Notch is a conserved signaling pathway that specifies cell fates in metazoans. Receptor-ligand interactions induce changes in gene expression, which is regulated by the transcription factor CBF1/Su(H)/Lag-1 (CSL). CSL interacts with coregulators to repress and activate transcription from Notch target genes. While the molecular details of the activator complex are relatively well understood, the structure-function of CSL-mediated repressor complexes is poorly defined. In Drosophila, the antagonist Hairless directly binds Su(H) (the fly CSL ortholog) to repress transcription from Notch targets. Here, we determine the X-ray structure of the Su(H)-Hairless complex bound to DNA. Hairless binding produces a large conformational change in Su(H) by interacting with residues in the hydrophobic core of Su(H), illustrating the structural plasticity of CSL molecules to interact with different binding partners. Based on the structure, we designed mutants in Hairless and Su(H) that affect binding, but do not affect formation of the activator complex. These mutants were validated in vitro by isothermal titration calorimetry and yeast two- and three-hybrid assays. Moreover, these mutants allowed us to solely characterize the repressor function of Su(H) in vivo. The transcription factor CSL regulates gene expression in response to Notch pathway signaling. The X-ray structure of the complex between the fruit fly version of CSL, Su(H), and its antagonist, Hairless, reveals a novel binding mode and unanticipated structural plasticity. Notch signaling is a form of cell-to-cell communication, in which extracellular receptor-ligand interactions ultimately result in changes in gene expression. The Notch pathway is highly conserved from the model organism Drosophila melanogaster to humans. When mutations occur within Notch pathway components, this often leads to human disease, such as certain types of cancers and birth defects. Transcription of Notch target genes is regulated by the transcription factor CSL (for CBF1/RBP-J in mammals, Su(H) in Drosophila, and Lag-1 in Caenorhabditis elegans). CSL functions as both a transcriptional activator and repressor by forming complexes with coactivator and corepressor proteins, respectively. Here we determine the high-resolution X-ray structure of Su(H) (the fly CSL ortholog) in complex with the corepressor Hairless, which is the major antagonist of Notch signaling in Drosophila. The structure unexpectedly reveals that Hairless binding results in a dramatic conformational change in Su(H). In parallel, we designed mutations in Su(H) and Hairless based on our structure and showed that these mutants are defective in complex formation in vitro and display functional deficiencies in in vivo assays. Taken together, our work provides significant molecular insights into how CSL functions as a transcriptional repressor in the Notch pathway.
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81
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Iyer S, Anwari K, Alsop AE, Yuen WS, Huang DCS, Carroll J, Smith NA, Smith BJ, Dewson G, Kluck RM. Identification of an activation site in Bak and mitochondrial Bax triggered by antibodies. Nat Commun 2016; 7:11734. [PMID: 27217060 PMCID: PMC4890306 DOI: 10.1038/ncomms11734] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 04/25/2016] [Indexed: 12/31/2022] Open
Abstract
During apoptosis, Bak and Bax are activated by BH3-only proteins binding to the α2–α5 hydrophobic groove; Bax is also activated via a rear pocket. Here we report that antibodies can directly activate Bak and mitochondrial Bax by binding to the α1–α2 loop. A monoclonal antibody (clone 7D10) binds close to α1 in non-activated Bak to induce conformational change, oligomerization, and cytochrome c release. Anti-FLAG antibodies also activate Bak containing a FLAG epitope close to α1. An antibody (clone 3C10) to the Bax α1–α2 loop activates mitochondrial Bax, but blocks translocation of cytosolic Bax. Tethers within Bak show that 7D10 binding directly extricates α1; a structural model of the 7D10 Fab bound to Bak reveals the formation of a cavity under α1. Our identification of the α1–α2 loop as an activation site in Bak paves the way to develop intrabodies or small molecules that directly and selectively regulate these proteins. During apoptosis, Bak and Bax are activated by BH3-only proteins binding to a specific hydrophobic groove. Here, the authors show that antibodies can also activate Bak and mitochondrial Bax by binding to the α1-α2 loop, thus identifying a potential clinical target.
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Affiliation(s)
- Sweta Iyer
- Molecular Genetics of Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Victoria 3052, Australia
| | - Khatira Anwari
- Molecular Genetics of Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Victoria 3052, Australia
| | - Amber E Alsop
- Molecular Genetics of Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Victoria 3052, Australia
| | - Wai Shan Yuen
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria 3800, Australia
| | - David C S Huang
- Cancer and Haematology Division, The Walter and Eliza Hall Institute of Medical Research, Victoria 3052, Australia
| | - John Carroll
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria 3800, Australia
| | - Nicholas A Smith
- Department of Chemistry and Physics, La Trobe Institute for Molecular Sciences, La Trobe University, Victoria 3086, Australia
| | - Brian J Smith
- Department of Chemistry and Physics, La Trobe Institute for Molecular Sciences, La Trobe University, Victoria 3086, Australia
| | - Grant Dewson
- Cell Signalling and Cell Death Division, The Walter and Eliza Hall Institute of Medical Research, Victoria 3052, Australia
| | - Ruth M Kluck
- Molecular Genetics of Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Victoria 3052, Australia
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82
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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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83
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Elder RM, Knorr DB, Andzelm JW, Lenhart JL, Sirk TW. Nanovoid formation and mechanics: a comparison of poly(dicyclopentadiene) and epoxy networks from molecular dynamics simulations. SOFT MATTER 2016; 12:4418-4434. [PMID: 27087585 DOI: 10.1039/c6sm00691d] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Protective equipment in civilian and military applications requires the use of polymer materials that are both stiff and tough over a wide range of strain rates. However, typical structural materials, like tightly cross-linked epoxies, are very brittle. Recent experiments demonstrated that cross-linked poly(dicyclopentadiene) (pDCPD) networks can circumvent this trade-off by providing structural properties such as a high glass transition temperature and glassy modulus, while simultaneously exhibiting excellent toughness and high-rate impact resistance. The greater performance of pDCPD was attributed to more facile plastic deformation and nano-scale void formation, but the chemical and structural mechanisms underlying this response were not clear. Here, we use atomistic molecular dynamics to compare the molecular- and chain-level properties of pDCPD and epoxy networks undergoing high strain rate deformation. We quantify the tensile modulus and yield strength of the networks as well as the prevalence and characteristics of nanovoids that form during deformation. Networks of similar molecular weight between cross-links are compared. Two key molecular-level properties are identified - monomer flexibility and polar chemistry - that influence the behavior of the networks. Increasing monomer flexibility reduces the modulus and yield strength, while strong non-covalent interactions (e.g., hydrogen bonds) that accompany polar moieties provide higher modulus and yield strength. The lack of strong non-covalent interactions in pDCPD was found to account for its lower modulus and yield strength compared to the epoxies. We examine the molecular-level properties of nanovoids, such as shape, alignment, and local stress distribution, as well as the local chemical environment, finding that nanovoid formation and growth are increased by the monomer rigidity but decreased by polar chemistry. As a result, the pDCPD network, which has a stiff chain backbone with nonpolar alkane chemistry, exhibits more and larger nanovoids that grow more readily during deformation, which could account for the higher toughness and more ductile behavior observed in pDCPD.
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Affiliation(s)
- Robert M Elder
- U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005, USA.
| | - Daniel B Knorr
- U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005, USA.
| | - Jan W Andzelm
- U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005, USA.
| | - Joseph L Lenhart
- U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005, USA.
| | - Timothy W Sirk
- U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005, USA.
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84
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Cording A, Gormally M, Bond PJ, Carrington M, Balasubramanian S, Miska EA, Thomas B. Selective inhibitors of trypanosomal uridylyl transferase RET1 establish druggability of RNA post-transcriptional modifications. RNA Biol 2016; 14:611-619. [PMID: 26786754 PMCID: PMC5449093 DOI: 10.1080/15476286.2015.1137422] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Non-coding RNAs are crucial regulators for a vast array of cellular processes and have been implicated in human disease. These biological processes represent a hitherto untapped resource in our fight against disease. In this work we identify small molecule inhibitors of a non-coding RNA uridylylation pathway. The TUTase family of enzymes is important for modulating non-coding RNA pathways in both human cancer and pathogen systems. We demonstrate that this new class of drug target can be accessed with traditional drug discovery techniques. Using the Trypanosoma brucei TUTase, RET1, we identify TUTase inhibitors and lay the groundwork for the use of this new target class as a therapeutic opportunity for the under-served disease area of African Trypanosomiasis. In a broader sense this work demonstrates the therapeutic potential for targeting RNA post-transcriptional modifications with small molecules in human disease.
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Affiliation(s)
- Amy Cording
- a The Gurdon Institute, University of Cambridge , Cambridge , UK
| | - Michael Gormally
- b Department of Chemistry , University of Cambridge , Cambridge , UK.,c Cancer Research UK Cambridge Institute, Li Ka Shing Center , Cambridge , UK.,d National Center for Advancing Translational Sciences , National Institutes of Health , Bethesda , MD , USA
| | - Peter J Bond
- e Bioinformatics Institute (A*STAR) , Singapore.,f Department of Biological Sciences , National University of Singapore , Singapore
| | | | - Shankar Balasubramanian
- b Department of Chemistry , University of Cambridge , Cambridge , UK.,c Cancer Research UK Cambridge Institute, Li Ka Shing Center , Cambridge , UK
| | - Eric A Miska
- a The Gurdon Institute, University of Cambridge , Cambridge , UK
| | - Beth Thomas
- b Department of Chemistry , University of Cambridge , Cambridge , UK
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85
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Kong X, Sun H, Pan P, Tian S, Li D, Li Y, Hou T. Molecular principle of the cyclin-dependent kinase selectivity of 4-(thiazol-5-yl)-2-(phenylamino) pyrimidine-5-carbonitrile derivatives revealed by molecular modeling studies. Phys Chem Chem Phys 2016; 18:2034-46. [DOI: 10.1039/c5cp05622e] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Due to the high sequence identity of the binding pockets of cyclin-dependent kinases (CDKs), designing highly selective inhibitors towards a specific CDK member remains a big challenge.
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Affiliation(s)
- Xiaotian Kong
- Institute of Functional Nano and Soft Materials (FUNSOM)
- Soochow University
- Suzhou
- P. R. China
- College of Pharmaceutical Sciences
| | - Huiyong Sun
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- P. R. China
| | - Peichen Pan
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- P. R. China
| | - Sheng Tian
- Institute of Functional Nano and Soft Materials (FUNSOM)
- Soochow University
- Suzhou
- P. R. China
| | - Dan Li
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- P. R. China
| | - Youyong Li
- Institute of Functional Nano and Soft Materials (FUNSOM)
- Soochow University
- Suzhou
- P. R. China
| | - Tingjun Hou
- Institute of Functional Nano and Soft Materials (FUNSOM)
- Soochow University
- Suzhou
- P. R. China
- College of Pharmaceutical Sciences
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86
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Ortiz-Suarez M, Bond P. The Structural Basis for Lipid and Endotoxin Binding in RP105-MD-1, and Consequences for Regulation of Host Lipopolysaccharide Sensitivity. Structure 2016; 24:200-211. [DOI: 10.1016/j.str.2015.10.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 09/09/2015] [Accepted: 10/12/2015] [Indexed: 12/22/2022]
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87
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Watanabe G, Nakajima D, Hiroshima A, Suzuki H, Yoneda S. Analysis of water channels by molecular dynamics simulation of heterotetrameric sarcosine oxidase. Biophys Physicobiol 2015; 12:131-7. [PMID: 27493862 PMCID: PMC4736832 DOI: 10.2142/biophysico.12.0_131] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 11/16/2015] [Indexed: 12/01/2022] Open
Abstract
A precise 100-ns molecular dynamics simulation in aquo was performed for the heterotetrameric sarcosine oxidase bound with a substrate analogue, dimethylglycine. The spatial region including the protein was divided into small rectangular cells. The average number of the water molecules locating within each cell was calculated based on the simulation trajectory. The clusters of the cells filled with water molecules were used to determine the water channels. The narrowness of the channels, the average hydropathy indices of the residues of the channels, and the number of migration events of water molecules through the channels were consistent with the selective transport hypothesis whereby tunnel T3 is the pathway for the exit of the iminium intermediate of the enzyme reaction.
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Affiliation(s)
- Go Watanabe
- School of Science, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan
| | - Daisuke Nakajima
- School of Science, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan
| | - Akinori Hiroshima
- School of Science, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan
| | - Haruo Suzuki
- School of Science, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan
| | - Shigetaka Yoneda
- School of Science, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan
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88
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Pechlaner M, Oostenbrink C. Multiple Binding Poses in the Hydrophobic Cavity of Bee Odorant Binding Protein AmelOBP14. J Chem Inf Model 2015; 55:2633-43. [PMID: 26633245 PMCID: PMC4695918 DOI: 10.1021/acs.jcim.5b00673] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
In the first step of olfaction, odorants
are bound and solubilized
by small globular odorant binding proteins (OBPs) which shuttle them
to the membrane of a sensory neuron. Low ligand affinity and selectivity
at this step enable the recognition of a wide range of chemicals.
Honey bee Apis mellifera’s OBP14 (AmelOBP14)
binds different plant odorants in a largely hydrophobic cavity. In
long molecular dynamics simulations in the presence and absence of
ligand eugenol, we observe a highly dynamic C-terminal region which
forms one side of the ligand-binding cavity, and the ligand drifts
away from its crystallized orientation. Hamiltonian replica exchange
simulations, allowing exchanges of conformations sampled by the real
ligand with those sampled by a noninteracting dummy molecule and several
intermediates, suggest an alternative, quite different ligand pose
which is adopted immediately and which is stable in long simulations.
Thermodynamic integration yields binding free energies which are in
reasonable agreement with experimental data.
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Affiliation(s)
- Maria Pechlaner
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences , Muthgasse 18, 1190 Vienna, Austria
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences , Muthgasse 18, 1190 Vienna, Austria
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89
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Paramo T, Tomasio SM, Irvine KL, Bryant CE, Bond PJ. Energetics of Endotoxin Recognition in the Toll-Like Receptor 4 Innate Immune Response. Sci Rep 2015; 5:17997. [PMID: 26647780 PMCID: PMC4673606 DOI: 10.1038/srep17997] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 10/12/2015] [Indexed: 01/08/2023] Open
Abstract
Bacterial outer membrane lipopolysaccharide (LPS) potently stimulates the mammalian innate immune system, and can lead to sepsis, the primary cause of death from infections. LPS is sensed by Toll-like receptor 4 (TLR4) in complex with its lipid-binding coreceptor MD-2, but subtle structural variations in LPS can profoundly modulate the response. To better understand the mechanism of LPS-induced stimulation and bacterial evasion, we have calculated the binding affinity to MD-2 of agonistic and antagonistic LPS variants including lipid A, lipid IVa, and synthetic antagonist Eritoran, and provide evidence that the coreceptor is a molecular switch that undergoes ligand-induced conformational changes to appropriately activate or inhibit the receptor complex. The plasticity of the coreceptor binding cavity is shown to be essential for distinguishing between ligands, whilst similar calculations for a model bacterial LPS bilayer reveal the "membrane-like" nature of the protein cavity. The ability to predict the activity of LPS variants should facilitate the rational design of TLR4 therapeutics.
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Affiliation(s)
- Teresa Paramo
- Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Susana M. Tomasio
- Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
- Current Address: Cresset Biomolecular Discovery, New Cambridge House, Bassingbourn Road, Litlington SG8 0SS, UK
| | - Kate L. Irvine
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Clare E. Bryant
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Peter J. Bond
- Bioinformatics Institute (A*STAR), 30 Biopolis Str, #07-01 Matrix, Singapore 138671
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543 Singapore
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90
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The Structural Basis for Activation and Inhibition of ZAP-70 Kinase Domain. PLoS Comput Biol 2015; 11:e1004560. [PMID: 26473606 PMCID: PMC4608720 DOI: 10.1371/journal.pcbi.1004560] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 09/15/2015] [Indexed: 11/29/2022] Open
Abstract
ZAP–70 (Zeta-chain-associated protein kinase 70) is a tyrosine kinase that interacts directly with the activated T-cell receptor to transduce downstream signals, and is hence a major player in the regulation of the adaptive immune response. Dysfunction of ZAP–70 causes selective T cell deficiency that in turn results in persistent infections. ZAP–70 is activated by a variety of signals including phosphorylation of the kinase domain (KD), and binding of its regulatory tandem Src homology 2 (SH2) domains to the T cell receptor. The present study investigates molecular mechanisms of activation and inhibition of ZAP–70 via atomically detailed molecular dynamics simulation approaches. We report microsecond timescale simulations of five distinct states of the ZAP–70 KD, comprising apo, inhibited and three phosphorylated variants. Extensive analysis of local flexibility and correlated motions reveal crucial transitions between the states, thus elucidating crucial steps in the activation mechanism of the ZAP–70 KD. Furthermore, we rationalize previously observed staurosporine-bound crystal structures, suggesting that whilst the KD superficially resembles an “active-like” conformation, the inhibitor modulates the underlying protein dynamics and restricts it in a compact, rigid state inaccessible to ligands or cofactors. Finally, our analysis reveals a novel, potentially druggable pocket in close proximity to the activation loop of the kinase, and we subsequently use its structure in fragment-based virtual screening to develop a pharmacophore model. The pocket is distinct from classical type I or type II kinase pockets, and its discovery offers promise in future design of specific kinase inhibitors, whilst mutations in residues associated with this pocket are implicated in immunodeficiency in humans. ZAP–70 is a key protein kinase in the adaptive immune system. It is essential for development and function of T cells and natural killer cells, and associated mutations can lead to conditions such as severe combined immunodeficiency (SCID). Here, simulations of the ZAP–70 kinase domain are used to study its dynamics in response to different mechanistic signals. We identify crucial motions over microsecond timescales, which help to rationalize in atomic detail previous structural and experimental data regarding its biological regulation. We subsequently propose a scheme for the phosphorylation-dependent activation cascade of ZAP–70, and for its ligand-dependent inhibition. Finally, we characterize a novel cryptic pocket adjacent to the active site and activation loop, which is distinct from classical type I or type II kinase sites. The pocket is in close proximity to several residues whose mutations cause SCID in humans, and its identification offers promise in future drug design efforts.
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91
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Berglund NA, Kargas V, Ortiz-Suarez ML, Bond PJ. The role of protein–protein interactions in Toll-like receptor function. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 119:72-83. [DOI: 10.1016/j.pbiomolbio.2015.06.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 06/29/2015] [Accepted: 06/30/2015] [Indexed: 12/12/2022]
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92
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Fuchs JE, Bender A, Glen RC. Cheminformatics Research at the Unilever Centre for Molecular Science Informatics Cambridge. Mol Inform 2015; 34:626-633. [PMID: 26435758 PMCID: PMC4583778 DOI: 10.1002/minf.201400166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 12/16/2014] [Indexed: 11/12/2022]
Abstract
The Centre for Molecular Informatics, formerly Unilever Centre for Molecular Science Informatics (UCMSI), at the University of Cambridge is a world-leading driving force in the field of cheminformatics. Since its opening in 2000 more than 300 scientific articles have fundamentally changed the field of molecular informatics. The Centre has been a key player in promoting open chemical data and semantic access. Though mainly focussing on basic research, close collaborations with industrial partners ensured real world feedback and access to high quality molecular data. A variety of tools and standard protocols have been developed and are ubiquitous in the daily practice of cheminformatics. Here, we present a retrospective of cheminformatics research performed at the UCMSI, thereby highlighting historical and recent trends in the field as well as indicating future directions.
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Affiliation(s)
- Julian E Fuchs
- Centre for Molecular Informatics, Department of Chemistry, University of CambridgeLensfield Road, Cambridge CB2 1EW, UK phone/fax: +44 (0)1223 336472/+44 (0)1223 763076
| | - Andreas Bender
- Centre for Molecular Informatics, Department of Chemistry, University of CambridgeLensfield Road, Cambridge CB2 1EW, UK phone/fax: +44 (0)1223 336472/+44 (0)1223 763076
| | - Robert C Glen
- Centre for Molecular Informatics, Department of Chemistry, University of CambridgeLensfield Road, Cambridge CB2 1EW, UK phone/fax: +44 (0)1223 336472/+44 (0)1223 763076
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93
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Ain QU, Méndez-Lucio O, Ciriano IC, Malliavin T, van Westen GJP, Bender A. Modelling ligand selectivity of serine proteases using integrative proteochemometric approaches improves model performance and allows the multi-target dependent interpretation of features. Integr Biol (Camb) 2015; 6:1023-33. [PMID: 25255469 DOI: 10.1039/c4ib00175c] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Serine proteases, implicated in important physiological functions, have a high intra-family similarity, which leads to unwanted off-target effects of inhibitors with insufficient selectivity. However, the availability of sequence and structure data has now made it possible to develop approaches to design pharmacological agents that can discriminate successfully between their related binding sites. In this study, we have quantified the relationship between 12,625 distinct protease inhibitors and their bioactivity against 67 targets of the serine protease family (20,213 data points) in an integrative manner, using proteochemometric modelling (PCM). The benchmarking of 21 different target descriptors motivated the usage of specific binding pocket amino acid descriptors, which helped in the identification of active site residues and selective compound chemotypes affecting compound affinity and selectivity. PCM models performed better than alternative approaches (models trained using exclusively compound descriptors on all available data, QSAR) employed for comparison with R(2)/RMSE values of 0.64 ± 0.23/0.66 ± 0.20 vs. 0.35 ± 0.27/1.05 ± 0.27 log units, respectively. Moreover, the interpretation of the PCM model singled out various chemical substructures responsible for bioactivity and selectivity towards particular proteases (thrombin, trypsin and coagulation factor 10) in agreement with the literature. For instance, absence of a tertiary sulphonamide was identified to be responsible for decreased selective activity (by on average 0.27 ± 0.65 pChEMBL units) on FA10. Among the binding pocket residues, the amino acids (arginine, leucine and tyrosine) at positions 35, 39, 60, 93, 140 and 207 were observed as key contributing residues for selective affinity on these three targets.
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Affiliation(s)
- Qurrat U Ain
- Centre for Molecular Informatics, Department of Chemistry, Lensfield Road, CB2 1EW, University of Cambridge, UK.
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94
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Fernandes CL, Ligabue-Braun R, Verli H. Structural glycobiology of human α1-acid glycoprotein and its implications for pharmacokinetics and inflammation. Glycobiology 2015; 25:1125-33. [PMID: 26088564 DOI: 10.1093/glycob/cwv041] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 06/11/2015] [Indexed: 12/20/2022] Open
Abstract
Human α1-acid glycoprotein (AGP) is an abundant human plasma glycoprotein that may be N-glycosylated at five positions. AGP plays important roles on pharmacokinetics and can rise up to 5-fold in inflammatory events. In such events, the glycan chains attached to Asn54, Asn75 and Asn85 may become fucosylated, originating a sialyl-Lewis X epitope. This epitope, in turn, can bind selectin proteins. Such interplay is important for immunomodulation. While the X-ray structure of unglycosylated AGP has been reported, the absence of the glycan chains hampered the further insights into its structural biology and, ultimately, into its biological function. Thus, the current work intends to contribute in the characterization of the structural glycobiology and function of AGP by building a structural model of its fully glycosylated form, taking into account the different glycoforms that are found in vivo. The obtained data points to the absence of a major influence of glycosylation on AGP's secondary structure, in agreement with crystallography observations. However, the glycan chains seem able to interfere with the protein dynamics, mainly at the AGP-ligand-binding site, indicating a possible role in its complexation to drugs and other bioactive compounds. By examining the influence of fucosylation on AGP structure and binding to selectins, it is proposed that the latter may bind to glycan chains linked to Asn54 and Asn75, and that this binding may involve other glycans, such as the one attached to Asn15. These results point to an increased participation of carbohydrates on the observed AGP roles in pharmacokinetics and inflammation.
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Affiliation(s)
- Cláudia L Fernandes
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av Bento Gonçalves 9500, CP 15005, Porto Alegre, RS 91500-970, Brazil
| | - Rodrigo Ligabue-Braun
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av Bento Gonçalves 9500, CP 15005, Porto Alegre, RS 91500-970, Brazil
| | - Hugo Verli
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av Bento Gonçalves 9500, CP 15005, Porto Alegre, RS 91500-970, Brazil
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95
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Sherlin D, Anishetty S. Mechanistic insights from molecular dynamic simulation of Rv0045c esterase in Mycobacterium tuberculosis. J Mol Model 2015; 21:90. [DOI: 10.1007/s00894-015-2630-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 02/22/2015] [Indexed: 11/29/2022]
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96
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Kaucikas M, Fitzpatrick A, Bryan E, Struve A, Henning R, Kosheleva I, Srajer V, Groenhof G, Van Thor JJ. Room temperature crystal structure of the fast switching M159T mutant of the fluorescent protein dronpa. Proteins 2015; 83:397-402. [PMID: 25524427 DOI: 10.1002/prot.24742] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Revised: 11/15/2014] [Accepted: 11/26/2014] [Indexed: 01/01/2023]
Abstract
The fluorescent protein Dronpa undergoes reversible photoswitching reactions between the bright "on" and dark "off" states via photoisomerization and proton transfer reactions. We report the room temperature crystal structure of the fast switching Met159Thr mutant of Dronpa at 2.0-Å resolution in the bright on state. Structural differences with the wild type include shifted backbone positions of strand β8 containing Thr159 as well as an altered A-C dimer interface involving strands β7, β8, β10, and β11. The Met159Thr mutation increases the cavity volume for the p-hydroxybenzylidene-imidazolinone chromophore as a result of both the side chain difference and the backbone positional differences.
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Affiliation(s)
- Marius Kaucikas
- Division of Molecular Biosciences, Imperial College London, London, SW7 2AZ, United Kingdom
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97
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Singh B, Bulusu G, Mitra A. Understanding the thermostability and activity of Bacillus subtilis lipase mutants: insights from molecular dynamics simulations. J Phys Chem B 2015; 119:392-409. [PMID: 25495458 DOI: 10.1021/jp5079554] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Improving the thermostability of industrial enzymes is an important protein engineering challenge. Point mutations, induced to increase thermostability, affect the structure and dynamics of the target protein in several ways and thus can also affect its activity. There appears to be no general rules for improving the thermostabilty of enzymes without adversely affecting their enzymatic activity. We report MD simulations, of wild type Bacillus subtilis lipase (WT) and its six progressively thermostable mutants (2M, 3M, 4M, 6M, 9M, and 12M), performed at different temperatures, to address this issue. Less thermostable mutants (LTMs), 2M to 6M, show WT-like dynamics at all simulation temperatures. However, the two more thermostable mutants (MTMs) show the required flexibility at appropriate temperature ranges and maintain conformational stability at high temperature. They show a deep and rugged free-energy landscape, confining them within a near-native conformational space by conserving noncovalent interactions, and thus protecting them from possible aggregation. In contrast, the LTMs having marginally higher thermostabilities than WT show greater probabilities of accessing non-native conformations, which, due to aggregation, have reduced possibilities of reverting to their respective native states under refolding conditions. Our analysis indicates the possibility of nonadditive effects of point mutations on the conformational stability of LTMs.
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Affiliation(s)
- Bipin Singh
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology Hyderabad (IIIT-H) , Gachibowli, Hyderabad, 500032, India
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98
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Laurent B, Chavent M, Cragnolini T, Dahl ACE, Pasquali S, Derreumaux P, Sansom MSP, Baaden M. Epock: rapid analysis of protein pocket dynamics. ACTA ACUST UNITED AC 2014; 31:1478-80. [PMID: 25505095 PMCID: PMC4410650 DOI: 10.1093/bioinformatics/btu822] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 12/08/2014] [Indexed: 11/12/2022]
Abstract
Summary: The volume of an internal protein pocket is fundamental to ligand accessibility. Few programs that compute such volumes manage dynamic data from molecular dynamics (MD) simulations. Limited performance often prohibits analysis of large datasets. We present Epock, an efficient command-line tool that calculates pocket volumes from MD trajectories. A plugin for the VMD program provides a graphical user interface to facilitate input creation, run Epock and analyse the results. Availability and implementation: Epock C++ source code, Python analysis scripts, VMD Tcl plugin, documentation and installation instructions are freely available at http://epock.bitbucket.org. Contact:benoist.laurent@gmail.com or baaden@smplinux.de Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Benoist Laurent
- Laboratoire de Biochimie Théorique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cité, F-75005 Paris, France and Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Matthieu Chavent
- Laboratoire de Biochimie Théorique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cité, F-75005 Paris, France and Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Tristan Cragnolini
- Laboratoire de Biochimie Théorique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cité, F-75005 Paris, France and Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Anna Caroline E Dahl
- Laboratoire de Biochimie Théorique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cité, F-75005 Paris, France and Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Samuela Pasquali
- Laboratoire de Biochimie Théorique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cité, F-75005 Paris, France and Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cité, F-75005 Paris, France and Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Mark S P Sansom
- Laboratoire de Biochimie Théorique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cité, F-75005 Paris, France and Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Marc Baaden
- Laboratoire de Biochimie Théorique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cité, F-75005 Paris, France and Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
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99
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Jónsdóttir LB, Ellertsson BÖ, Invernizzi G, Magnúsdóttir M, Thorbjarnardóttir SH, Papaleo E, Kristjánsson MM. The role of salt bridges on the temperature adaptation of aqualysin I, a thermostable subtilisin-like proteinase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:2174-81. [DOI: 10.1016/j.bbapap.2014.08.011] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 08/05/2014] [Accepted: 08/20/2014] [Indexed: 11/30/2022]
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100
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Durrant JD, Votapka L, Sørensen J, Amaro RE. POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics. J Chem Theory Comput 2014; 10:5047-5056. [PMID: 25400521 PMCID: PMC4230373 DOI: 10.1021/ct500381c] [Citation(s) in RCA: 173] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Indexed: 02/08/2023]
Abstract
![]()
Analysis of macromolecular/small-molecule
binding pockets can provide
important insights into molecular recognition and receptor dynamics.
Since its release in 2011, the POVME (POcket Volume MEasurer) algorithm
has been widely adopted as a simple-to-use tool for measuring and
characterizing pocket volumes and shapes. We here present POVME 2.0,
which is an order of magnitude faster, has improved accuracy, includes
a graphical user interface, and can produce volumetric density maps
for improved pocket analysis. To demonstrate the utility of the algorithm,
we use it to analyze the binding pocket of RNA editing ligase 1 from
the unicellular parasite Trypanosoma brucei, the
etiological agent of African sleeping sickness. The POVME analysis
characterizes the full dynamics of a potentially druggable transient
binding pocket and so may guide future antitrypanosomal drug-discovery
efforts. We are hopeful that this new version will be a useful tool
for the computational- and medicinal-chemist community.
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Affiliation(s)
- Jacob D Durrant
- Department of Chemistry & Biochemistry, University of California San Diego , La Jolla, California 92093, United States ; National Biomedical Computation Resource, Center for Research in Biological Systems, University of California San Diego , La Jolla, California 92093, United States
| | - Lane Votapka
- Department of Chemistry & Biochemistry, University of California San Diego , La Jolla, California 92093, United States
| | - Jesper Sørensen
- Department of Chemistry & Biochemistry, University of California San Diego , La Jolla, California 92093, United States
| | - Rommie E Amaro
- Department of Chemistry & Biochemistry, University of California San Diego , La Jolla, California 92093, United States ; National Biomedical Computation Resource, Center for Research in Biological Systems, University of California San Diego , La Jolla, California 92093, United States
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