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Gahlawat A, Singh A, Sandhu H, Garg P. CRAFT: a web-integrated cavity prediction tool based on flow transfer algorithm. J Cheminform 2024; 16:12. [PMID: 38291536 PMCID: PMC10829215 DOI: 10.1186/s13321-024-00803-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 01/13/2024] [Indexed: 02/01/2024] Open
Abstract
Numerous computational methods, including evolutionary-based, energy-based, and geometrical-based methods, are utilized to identify cavities inside proteins. Cavity information aids protein function annotation, drug design, poly-pharmacology, and allosteric site investigation. This article introduces "flow transfer algorithm" for rapid and effective identification of diverse protein cavities through multidimensional cavity scan. Initially, it identifies delimiter and susceptible tetrahedra to establish boundary regions and provide seed tetrahedra. Seed tetrahedron faces are precisely scanned using the maximum circle radius to transfer seed flow to neighboring tetrahedra. Seed flow continues until terminated by boundaries or forbidden faces, where a face is forbidden if the estimated maximum circle radius is less or equal to the user-defined maximum circle radius. After a seed scanning, tetrahedra involved in the flow are clustered to locate the cavity. The CRAFT web interface integrates this algorithm for protein cavity identification with enhanced user control. It supports proteins with cofactors, hydrogens, and ligands and provides comprehensive features such as 3D visualization, cavity physicochemical properties, percentage contribution graphs, and highlighted residues for each cavity. CRAFT can be accessed through its web interface at http://pitools.niper.ac.in/CRAFT , complemented by the command version available at https://github.com/PGlab-NIPER/CRAFT/ .Scientific contribution: Flow transfer algorithm is a novel geometric approach for accurate and reliable prediction of diverse protein cavities. This algorithm employs a distinct concept involving maximum circle radius within the 3D Delaunay triangulation to address diverse van der Waals radii while existing methods overlook atom specific van der Waals radii or rely on complex weighted geometric techniques.
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Affiliation(s)
- Anuj Gahlawat
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, 160062, Punjab, India
| | - Anjali Singh
- Department of Computer Science, Kurukshetra University, Kurukshetra, Haryana, India
| | - Hardeep Sandhu
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, 160062, Punjab, India
| | - Prabha Garg
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, 160062, Punjab, India.
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Diaz-Bárcena A, Fernandez-Pacios L, Giraldo P. Structural Characterization and Molecular Dynamics Study of the REPI Fusion Protein from Papaver somniferum L. Biomolecules 2023; 14:2. [PMID: 38275743 PMCID: PMC10813097 DOI: 10.3390/biom14010002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/11/2023] [Accepted: 12/14/2023] [Indexed: 01/27/2024] Open
Abstract
REPI is a pivotal point enzyme in plant benzylisoquinoline alkaloid metabolism as it promotes the evolution of the biosynthetic branch of morphinan alkaloids. Experimental studies of its activity led to the identification of two modules (DRS and DRR) that catalyze two sequential steps of the epimerization of (S)- to (R)-reticuline. Recently, special attention has been paid to its genetic characterization and evolutionary history, but no structural analyses of the REPI protein have been conducted to date. We present here a computational structural characterization of REPI with heme and NADP cofactors in the apo state and in three complexes with substrate (S)-reticuline in DRS and intermediate 1,2-dehydroreticuline in DRS and in DRR. Since no experimental structure exists for REPI, we used its AlphaFold model as a scaffold to build up these four systems, which were submitted to all-atom molecular dynamics (MD) simulations. A comparison of MD results for the four systems revealed key dynamic changes associated with cofactor and ligand binding and provided a dynamic picture of the evolution of their structures and interactions. We also explored the possible dynamic occurrence of tunnels and electrostatic highways potentially involved in alternative mechanisms for channeling the intermediate from DRS to DRR.
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Affiliation(s)
- Alba Diaz-Bárcena
- Department of Biotechnology-Plant Biology, School of Agricultural, Food and Biosystems Engineering, Universidad Politécnica de Madrid, 28040 Madrid, Spain; (L.F.-P.); (P.G.)
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Understanding Life at High Temperatures: Relationships of Molecular Channels in Enzymes of Methanogenic Archaea and Their Growth Temperatures. Int J Mol Sci 2022; 23:ijms232315149. [PMID: 36499474 PMCID: PMC9741079 DOI: 10.3390/ijms232315149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/18/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022] Open
Abstract
Analyses of protein structures have shown the existence of molecular channels in enzymes from Prokaryotes. Those molecular channels suggest a critical role of spatial voids in proteins, above all, in those enzymes functioning under high temperature. It is expected that these spaces within the protein structure are required to access the active site and to maximize availability and thermal stability of their substrates and cofactors. Interestingly, numerous substrates and cofactors have been reported to be highly temperature-sensitive biomolecules. Methanogens represent a singular phylogenetic group of Archaea that performs anaerobic respiration producing methane during growth. Methanogens inhabit a variety of environments including the full range of temperatures for the known living forms. Herein, we carry out a dimensional analysis of molecular tunnels in key enzymes of the methanogenic pathway from methanogenic Archaea growing optimally over a broad temperature range. We aim to determine whether the dimensions of the molecular tunnels are critical for those enzymes from thermophiles. Results showed that at increasing growth temperature the dimensions of molecular tunnels in the enzymes methyl-coenzyme M reductase and heterodisulfide reductase become increasingly restrictive and present strict limits at the highest growth temperatures, i.e., for hyperthermophilic methanogens. However, growth at lower temperature allows a wide dimensional range for the molecular spaces in these enzymes. This is in agreement with previous suggestions on a potential major role of molecular tunnels to maintain biomolecule stability and activity of some enzymes in microorganisms growing at high temperatures. These results contribute to better understand archaeal growth at high temperatures. Furthermore, an optimization of the dimensions of molecular tunnels would represent an important adaptation required to maintain the activity of key enzymes of the methanogenic pathway for those methanogens growing optimally at high temperatures.
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Alvarado YJ, Olivarez Y, Lossada C, Vera-Villalobos J, Paz JL, Vera E, Loroño M, Vivas A, Torres FJ, Jeffreys LN, Hurtado-León ML, González-Paz L. Interaction of the new inhibitor paxlovid (PF-07321332) and ivermectin with the monomer of the main protease SARS-CoV-2: A volumetric study based on molecular dynamics, elastic networks, classical thermodynamics and SPT. Comput Biol Chem 2022; 99:107692. [PMID: 35640480 PMCID: PMC9107165 DOI: 10.1016/j.compbiolchem.2022.107692] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/28/2022] [Accepted: 05/02/2022] [Indexed: 02/04/2023]
Abstract
The COVID-19 pandemic has accelerated the study of drugs, most notably ivermectin and more recently Paxlovid (PF-07321332) which is in phase III clinical trials with experimental data showing covalent binding to the viral protease Mpro. Theoretical developments of catalytic site-directed docking support thermodynamically feasible non-covalent binding to Mpro. Here we show that Paxlovid binds non-covalently at regions other than the catalytic sites with energies stronger than reported and at the same binding site as the ivermectin B1a homologue, all through theoretical methodologies, including blind docking. We volumetrically characterize the non-covalent interaction of the ivermectin homologues (avermectins B1a and B1b) and Paxlovid with the mMpro monomer, through molecular dynamics and scaled particle theory (SPT). Using the fluctuation-dissipation theorem (FDT), we estimated the electric dipole moment fluctuations at the surface of each of complex involved in this study, with similar trends to that observed in the interaction volume. Using fluctuations of the intrinsic volume and the number of flexible fragments of proteins using anisotropic and Gaussian elastic networks (ANM+GNM) suggests the complexes with ivermectin are more dynamic and flexible than the unbound monomer. In contrast, the binding of Paxlovid to mMpro shows that the mMpro-PF complex is the least structurally dynamic of all the species measured in this investigation. The results support a differential molecular mechanism of the ivermectin and PF homologues in the mMpro monomer. Finally, the results showed that Paxlovid despite beingbound in different sites through covalent or non-covalent forms behaves similarly in terms of its structural flexibility and volumetric behaviour.
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Affiliation(s)
- Ysaias José Alvarado
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Investigación y Tecnología de Materiales (CITeMA), Laboratorio de Caracterización Molecular y Biomolecular, 4001 Maracaibo, Bolivarian Republic of Venezuela,Corresponding author
| | - Yosmari Olivarez
- Universidad del Zulia (LUZ). Facultad Experimental de Ciencias (FEC), Departamento de Quimica, Laboratorio de Electronica Molecular, 4001 Maracaibo, Bolivarian Republic of Venezuela
| | - Carla Lossada
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Investigación y Tecnología de Materiales (CITeMA), Laboratorio de Caracterización Molecular y Biomolecular, 4001 Maracaibo, Bolivarian Republic of Venezuela
| | - Joan Vera-Villalobos
- Facultad de Ciencias Naturales y Matemáticas, Departamento de Química y Ciencias Ambientales, Laboratorio de Análisis Químico Instrumental (LAQUINS), Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador
| | - José Luis Paz
- Departamento Académico de Química Inorgánica, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Eddy Vera
- Universidad del Zulia (LUZ). Facultad Experimental de Ciencias (FEC), Departamento de Quimica, Laboratorio de Electronica Molecular, 4001 Maracaibo, Bolivarian Republic of Venezuela
| | - Marcos Loroño
- Departamento Académico de Química Analítica e Instrumental, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Alejandro Vivas
- Universidad del Zulia (LUZ). Facultad Experimental de Ciencias (FEC), Departamento de Quimica, Laboratorio de Electronica Molecular, 4001 Maracaibo, Bolivarian Republic of Venezuela
| | - Fernando Javier Torres
- Grupo de Química Computacional y Teórica (QCT-UR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia,Grupo de Química Computacional y Teórica (QCT-USFQ), Instituto de Simulación Computacional (ISC-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - Laura N. Jeffreys
- Centre for Drugs and Diagnostics, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - María Laura Hurtado-León
- Universidad del Zulia (LUZ), Facultad Experimental de Ciencias (FEC), Departamento de Biología, Laboratorio de Genética y Biología Molecular (LGBM), Maracaibo 4001, Zulia, Bolivarian Republic of Venezuela
| | - Lenin González-Paz
- Universidad del Zulia (LUZ), Facultad Experimental de Ciencias (FEC), Departamento de Biología, Laboratorio de Genética y Biología Molecular (LGBM), Maracaibo 4001, Zulia, Bolivarian Republic of Venezuela,Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Estudios Botanicos y Agroforestales, (CEBA), Laboratorio de Proteccion Vegetal, 4001 Maracaibo, Bolivarian Republic of Venezuela,Corresponding author at: Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Estudios Botanicos y Agroforestales, (CEBA), Laboratorio de Proteccion Vegetal, 4001 Maracaibo, Bolivarian Republic of Venezuela
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Raffo A, Gagliardi L, Fugacci U, Sagresti L, Grandinetti S, Brancato G, Biasotti S, Rocchia W. Chanalyzer: A Computational Geometry Approach for the Analysis of Protein Channel Shape and Dynamics. Front Mol Biosci 2022; 9:933924. [PMID: 35959458 PMCID: PMC9358003 DOI: 10.3389/fmolb.2022.933924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 06/13/2022] [Indexed: 11/18/2022] Open
Abstract
Morphological analysis of protein channels is a key step for a thorough understanding of their biological function and mechanism. In this respect, molecular dynamics (MD) is a very powerful tool, enabling the description of relevant biological events at the atomic level, which might elude experimental observations, and pointing to the molecular determinants thereof. In this work, we present a computational geometry-based approach for the characterization of the shape and dynamics of biological ion channels or pores to be used in combination with MD trajectories. This technique relies on the earliest works of Edelsbrunner and on the NanoShaper software, which makes use of the alpha shape theory to build the solvent-excluded surface of a molecular system in an aqueous solution. In this framework, a channel can be simply defined as a cavity with two entrances on the opposite sides of a molecule. Morphological characterization, which includes identification of the main axis, the corresponding local radius, and the detailed description of the global shape of the cavity, is integrated with a physico-chemical description of the surface facing the pore lumen. Remarkably, the possible existence or temporary appearance of fenestrations from the channel interior towards the outer lipid matrix is also accounted for. As a test case, we applied the present approach to the analysis of an engineered protein channel, the mechanosensitive channel of large conductance.
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Affiliation(s)
- Andrea Raffo
- Istituto di Matematica Applicata e Tecnologie Informatiche “E. Magenes”, Consiglio Nazionale delle Ricerche, Genova, Italy
| | - Luca Gagliardi
- CONCEPT Lab, Istituto Italiano di Tecnologia, Genova, Italy
| | - Ulderico Fugacci
- Istituto di Matematica Applicata e Tecnologie Informatiche “E. Magenes”, Consiglio Nazionale delle Ricerche, Genova, Italy
- *Correspondence: Ulderico Fugacci, ; Silvia Biasotti, ; Walter Rocchia,
| | - Luca Sagresti
- Scuola Normale Superiore, Pisa, Italy
- Istituto Nazionale di Fisica Nucleare (INFN), Pisa, Italy
- Consorzio Interuniversitario per lo sviluppo dei Sistemi a Grande Interfase (CSGI), Sesto Fiorentino, Italy
| | - Simone Grandinetti
- Scuola Normale Superiore, Pisa, Italy
- Dipartimento di Ingegneria Civile ed Industriale, Università di Pisa, Pisa, Italy
| | - Giuseppe Brancato
- Scuola Normale Superiore, Pisa, Italy
- Istituto Nazionale di Fisica Nucleare (INFN), Pisa, Italy
- Consorzio Interuniversitario per lo sviluppo dei Sistemi a Grande Interfase (CSGI), Sesto Fiorentino, Italy
| | - Silvia Biasotti
- Istituto di Matematica Applicata e Tecnologie Informatiche “E. Magenes”, Consiglio Nazionale delle Ricerche, Genova, Italy
- *Correspondence: Ulderico Fugacci, ; Silvia Biasotti, ; Walter Rocchia,
| | - Walter Rocchia
- Istituto di Matematica Applicata e Tecnologie Informatiche “E. Magenes”, Consiglio Nazionale delle Ricerche, Genova, Italy
- CONCEPT Lab, Istituto Italiano di Tecnologia, Genova, Italy
- *Correspondence: Ulderico Fugacci, ; Silvia Biasotti, ; Walter Rocchia,
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6
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Tariq M, Ozbek P, Moin ST. Hydration modulates oxygen channel residues for oxygenation of cysteine dioxygenase: Perspectives from molecular dynamics simulations. J Mol Graph Model 2021; 110:108060. [PMID: 34768230 DOI: 10.1016/j.jmgm.2021.108060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/25/2021] [Accepted: 10/25/2021] [Indexed: 11/26/2022]
Abstract
Cysteine dioxygenase (CDO) regulates the concentration of l-cysteine substrate by its oxidation in the body to prevent different diseases, including neurodegenerative and autoimmune diseases. CDO catalyzes the oxidation of thiol group of l-cysteine to l-cysteine sulfinic acid using molecular oxygen. In this study, molecular dynamics simulations were applied to ligand-free CDO, cysteine-bound CDO, and oxygen-bound CDO-cysteine complex which were primarily subjected to the evaluation of their structural and dynamical properties. The simulation data provided significant information not only on the conformational changes of the enzyme after its ligation but also on the co-ligation by sequential binding of l-cysteine and molecular oxygen. It was found that the ligation and co-ligation perturbed the active site region as well as the overall protein dynamics which were analyzed in terms of root mean square deviation, root mean square fluctuation and dynamic cross correlation matrices as well as principal component analysis. Furthermore, oxygen transport pathways were successfully explored by taking various tunnel clusters into account and one of those clusters was given preference based on the throughput value. The bottleneck formed by different amino acid residues was examined to figure out their role in the oxygenation process of the enzyme. The residues forming the tunnel's bottleneck and their dynamics mediated by water molecules were further investigated using radial distribution functions which gave insights into the hydration behavior of these residues. The findings based on the hydration behavior in turn served to explore the water-mediated dynamics of these residues in the modulation of the pathway, including tunnel gating for the oxygen entry and diffusion to the active site, which is essential for the CDO's catalytic function.
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Affiliation(s)
- Muhammad Tariq
- Third World Center for Science and Technology, H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Pemra Ozbek
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, 34722, Turkey.
| | - Syed Tarique Moin
- Third World Center for Science and Technology, H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan.
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Ghorbani SM, Housaindokht MR, Bozorgmehr MR. Investigating the effect of 1-Butyl-3-methylimidazolium bromide and 1-Butyl-3-methylimidazolium methyl sulfate ionic liquids on structure and function of Chloroproxidase by molecular dynamics simulation. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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8
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Hao D, Wang H, Zang Y, Zhang L, Yang Z, Zhang S. Mechanism of Glycans Modulating Cholesteryl Ester Transfer Protein: Unveiled by Molecular Dynamics Simulation. J Chem Inf Model 2021; 62:5246-5257. [PMID: 33858135 DOI: 10.1021/acs.jcim.1c00233] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Inhibition of the cholesteryl ester transfer protein (CETP) has been considered as a promising way for the treatment of cardiovascular disease (CVD) for three decades. However, clinical trials of several CETP inhibitors with various potencies have been marginally successful at best, raising doubts on the target drugability of CETP. The in-depth understanding of the glycosylated CETP structure could be beneficial to more definitive descriptions of the CETP function and the underlying mechanism. In this work, large-scale molecular dynamics simulations were performed to thoroughly explore the mechanism of glycans modulating CETP. Here, the extensive simulation results intensely suggest that glycan88 tends to assist CETP in forming a continuous tunnel throughout interacting with the upper-right region of the N-barrel, while it also could prevent the formation of a continuous tunnel by swinging toward the right-rear of the N-barrel. Furthermore, glycan240 formed stable H-bonds with Helix-B and might further stabilize the central cavity of CETP. Furthermore, the nonspecific involvement of the hydroxyl groups from the various glycans with protein core interactions and the similar influence of different glycans trapped at similar regions on the protein structure suggest that physiological glycan may lead to a similar effect. This study would provide valuable insights into devising novel methods for CVD treatment targeting CETP and functional studies about glycosylation for other systems.
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Affiliation(s)
- Dongxiao Hao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - He Wang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Yongjian Zang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Zhiwei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China.,School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Shengli Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
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9
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Bier I, Marom N. Machine Learned Model for Solid Form Volume Estimation Based on Packing-Accessible Surface and Molecular Topological Fragments. J Phys Chem A 2020; 124:10330-10345. [DOI: 10.1021/acs.jpca.0c06791] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Imanuel Bier
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Noa Marom
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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Xu B, Hrmova M, Gilliham M. High affinity Na + transport by wheat HKT1;5 is blocked by K . PLANT DIRECT 2020; 4:e00275. [PMID: 33103046 PMCID: PMC7576878 DOI: 10.1002/pld3.275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/21/2020] [Indexed: 05/11/2023]
Abstract
The wheat sodium transporters TmHKT1;5-A and TaHKT1;5-D are encoded by genes underlying the major shoot Na+ exclusion loci Nax2 and Kna1 from Triticum monococcum (Tm) and Triticum aestivum (Ta), respectively. In contrast to HKT2 transporters that have been shown to exhibit high affinity K+-dependent Na+ transport, HKT1 proteins have, with one exception, only been shown to catalyze low affinity Na+ transport and no K+ transport. Here, using heterologous expression in Xenopus laevis oocytes we uncover a novel property of HKT1 proteins, that both TmHKT1;5-A and TaHKT1;5-D encode dual (high and low) affinity Na+-transporters with the high-affinity component being abolished when external K+ is in excess of external Na+. Three-dimensional structural modeling suggested that, compared to Na+, K+ is bound more tightly in the selectivity filter region by means of additional van der Waals forces, which is likely to explain the K+ block at the molecular level. The low-affinity component for Na+ transport of TmHKT1;5-A had a lower K m than that of TaHKT1;5-D and was less sensitive to external K+. We propose that these properties contribute towards the improvements in shoot Na+-exclusion and crop plant salt tolerance following the introgression of TmHKT1;5-A into diverse wheat backgrounds.
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Affiliation(s)
- Bo Xu
- Australian Research Council Centre of Excellence in Plant Energy BiologyUniversity of AdelaideWaite Research PrecinctGlen OsmondSAAustralia
- School of Agriculture, Food and Wine, and Waite Research InstituteUniversity of AdelaideWaite Research PrecinctGlen OsmondSAAustralia
| | - Maria Hrmova
- School of Agriculture, Food and Wine, and Waite Research InstituteUniversity of AdelaideWaite Research PrecinctGlen OsmondSAAustralia
- School of Life ScienceHuaiyin Normal UniversityHuai’anChina
| | - Matthew Gilliham
- Australian Research Council Centre of Excellence in Plant Energy BiologyUniversity of AdelaideWaite Research PrecinctGlen OsmondSAAustralia
- School of Agriculture, Food and Wine, and Waite Research InstituteUniversity of AdelaideWaite Research PrecinctGlen OsmondSAAustralia
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11
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Weighted persistent homology for osmolyte molecular aggregation and hydrogen-bonding network analysis. Sci Rep 2020; 10:9685. [PMID: 32546801 PMCID: PMC7297731 DOI: 10.1038/s41598-020-66710-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 05/20/2020] [Indexed: 12/24/2022] Open
Abstract
It has long been observed that trimethylamine N-oxide (TMAO) and urea demonstrate dramatically different properties in a protein folding process. Even with the enormous theoretical and experimental research work on these two osmolytes, various aspects of their underlying mechanisms still remain largely elusive. In this paper, we propose to use the weighted persistent homology to systematically study the osmolytes molecular aggregation and their hydrogen-bonding network from a local topological perspective. We consider two weighted models, i.e., localized persistent homology (LPH) and interactive persistent homology (IPH). Boltzmann persistent entropy (BPE) is proposed to quantitatively characterize the topological features from LPH and IPH, together with persistent Betti number (PBN). More specifically, from the localized persistent homology models, we have found that TMAO and urea have very different local topology. TMAO is found to exhibit a local network structure. With the concentration increase, the circle elements in these networks show a clear increase in their total numbers and a decrease in their relative sizes. In contrast, urea shows two types of local topological patterns, i.e., local clusters around 6 Å and a few global circle elements at around 12 Å. From the interactive persistent homology models, it has been found that our persistent radial distribution function (PRDF) from the global-scale IPH has same physical properties as the traditional radial distribution function. Moreover, PRDFs from the local-scale IPH can also be generated and used to characterize the local interaction information. Other than the clear difference of the first peak value of PRDFs at filtration size 4 Å, TMAO and urea also shows very different behaviors at the second peak region from filtration size 5 Å to 10 Å. These differences are also reflected in the PBNs and BPEs of the local-scale IPH. These localized topological information has never been revealed before. Since graphs can be transferred into simplicial complexes by the clique complex, our weighted persistent homology models can be used in the analysis of various networks and graphs from any molecular structures and aggregation systems.
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Yang Q, Guo Y, Yan B, Wang C, Liu Z, Huang Z, Wang Y, Li Y, Li H, Song L, Fan J, Zhi C. Hydrogen-Substituted Graphdiyne Ion Tunnels Directing Concentration Redistribution for Commercial-Grade Dendrite-Free Zinc Anodes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e2001755. [PMID: 32406976 DOI: 10.1002/adma.202001755] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/17/2020] [Accepted: 04/20/2020] [Indexed: 06/11/2023]
Abstract
Current aqueous Zn batteries (ZBs) seriously suffer from dendrite issues caused by rough electrode surfaces. Despite significant efforts in prolonging lifespan of these batteries, little effort has been devoted to dendrite elimination in commercial-grade cathode loading mass. Instead, demonstrations have only been done at the laboratory level (≤2 mg cm-2 ). Additionally, new dilemmas regarding change of the proton-storage behavior and interface pulverization have emerged in turn. Herein, hydrogen-substituted graphdiyne (HsGDY), with sub-ångström level ion tunnels and robust chemical stability, is designed as an artificial interface layer to address these issues. This strategy prolongs the symmetric cell lifespan to >2400 h (100 days), which is 37 times larger than without protection (63 h). The simulation of dual fields reveals that HsGDY can redistribute the Zn2+ concentration field by spatially forcing Zn2+ to deviate from the irregular electric field. During practical use, the as-assembled full batteries deliver a long lifespan 50 000 cycles and remain stable even at a commercial-grade cathode loading mass of up to 22.95 mg cm-2 . This HsGDY-protection methodology represents great progress in Zn dendrite protection and demonstrates enormous potential in metal batteries.
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Affiliation(s)
- Qi Yang
- Department of Materials Science and Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong SAR, 999077, China
| | - Ying Guo
- Department of Materials Science and Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong SAR, 999077, China
| | - Boxun Yan
- Department of Materials Science and Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong SAR, 999077, China
| | - Changda Wang
- National Synchrotron Radiation Laboratory CAS Center for Excellence in Nanoscience, University of Science and Technology of China, Hefei, 230029, China
| | - Zhuoxin Liu
- Department of Materials Science and Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong SAR, 999077, China
| | - Zhaodong Huang
- Department of Materials Science and Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong SAR, 999077, China
| | - Yukun Wang
- Department of Materials Science and Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong SAR, 999077, China
| | - Yiran Li
- Department of Materials Science and Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong SAR, 999077, China
| | - Hongfei Li
- Department of Materials Science and Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong SAR, 999077, China
| | - Li Song
- National Synchrotron Radiation Laboratory CAS Center for Excellence in Nanoscience, University of Science and Technology of China, Hefei, 230029, China
| | - Jun Fan
- Department of Materials Science and Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong SAR, 999077, China
| | - Chunyi Zhi
- Department of Materials Science and Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong SAR, 999077, China
- Center for Advanced Nuclear Safety and Sustainable Development, City University of Hong Kong, Kowloon, 999077, Hong Kong
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13
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14
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Ghorbani Sangoli M, Housaindokht MR, Bozorgmehr MR. Effects of the deglycosylation on the structure and activity of chloroperoxidase: Molecular dynamics simulation approach. J Mol Graph Model 2020; 97:107570. [PMID: 32097885 DOI: 10.1016/j.jmgm.2020.107570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 02/15/2020] [Accepted: 02/16/2020] [Indexed: 10/25/2022]
Abstract
Chloroperoxidase (CPO) is a versatile fungal heme-thiolate protein that catalyzes a variety of one electron and two-electron oxidations. Chloroperoxidase is a versatile fungal heme-thiolate protein that catalyzes a variety of oxidations. CPO enzyme contains thirteen sugars, including five N-acetyl D-glucosamines (NAG) and eight mannoses (MAN), which are attached to the protein via the glycosidic bonds. Removal of the sugars from CPO leads to increase the hydrophobicity of the enzyme, as well as the reduction of the alkylation reactions. However, due to the lack of the proper force field for the sugars, they are ignored in the theoretical studies. The present study aims to assess the effects of the sugar segments on the structure and activity of CPO through the simulation of the halo structure and the structures without the sugar segment. Despite the difficulty of the process and being time-consuming, the suitable force field is introduced successfully for the sugars. According to molecular dynamics simulation (MD), seven channels and fifteen cavities are identified in the CPO structure. Two of the channels provide the substrate access to the active site. The MD simulation results reveal that the removal of NAG decreases the number of the cavities from fifteen to eleven. Besides, the removal of NAG is associated with removing the channel providing the substrate access. The number of the cavities decreases from fifteen to fourteen through the removal of MAN; however, channel providing the substrate access to the active site is partly preserved. The MD simulation results indicate that the structures without the sugar units are more compact in comparison with the halo structures. The removal of the sugar segments induces the significant changes in the flexibility of the residues that affect the catalytic activity of the enzyme. As a result, the enzyme activities, such as the oxidation, alkylation, halogenation, and epoxidation cannot occur when the sugar segments of the enzyme are removed.
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Affiliation(s)
| | - Mohammad Reza Housaindokht
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran; Research and Technology Center of Biomolecules, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran.
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15
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Banach M, Piotr F, Katarzyna S, Leszek K, Roterman I. Identification of tunnels as in potato hydrolases. Bioinformation 2020; 16:21-25. [PMID: 32025157 PMCID: PMC6986939 DOI: 10.6026/97320630016021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 01/07/2020] [Indexed: 11/29/2022] Open
Abstract
Enzymes with an active center hidden in the middle of the molecule in a tunnel-like cavity constitute an interesting object of analysis due to the highly specialized environment for the course of the catalytic reaction. Identifying the tunnel is a challenge in itself. Moreover, the structural conditioning for the course of the reaction provides information on the diversity of the environment, which must necessarily meet the conditions of high specificity. The use of a fuzzy oil drop model to identify residues constituting the walls of the tunnel located in the center of the protein seems highly justified. The fuzzy oil drop model, which assumes the highest concentration of hydrophobicity in the center of the molecule, in these enzymes shows a significant hydrophobicity deficit resulting from the absence of any residues in the central part of the molecule. Comparison of the expected distribution in consistent with the 3D Gaussian distribution where the observed distribution resulting from the interaction of residues in the protein shows significant differences precisely in the positions of residues located near the center of the molecule. The inside characteristics of the tunnel are the background for the enzymatic reaction. This environment additionally constitutes an external force field, which creates favorable conditions for carrying out the catalytic process. The use of fuzzy oil drop model has been verified using the potato (solanum tuberosum) epoxide hydrolase I. This forms the preliminary basis for testing the fuzzy oil drop model. The data presented here provides an impetus for a large scale analysis of all proteins containing tunnels in enzyme structures available in the Protein Data Bank (PDB).
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Affiliation(s)
- Mateusz Banach
- Department of bioinformatics and Telemedicine, Jagiellonian University - Medical College, Lazarza 16, 31-530 Krakow, Poland
| | - Fabian Piotr
- Silesian Technical University, Institute of Computer Science, 44-100 Gliwice, Akademicka 16 Poland
| | - Stapor Katarzyna
- Silesian Technical University, Institute of Computer Science, 44-100 Gliwice, Akademicka 16 Poland
| | - Konieczny Leszek
- Chair of Medical Biochemistry, Jagiellonian University - Medical College 31-034 Kraków Kopernika 7, Poland
| | - Irena Roterman
- Department of bioinformatics and Telemedicine, Jagiellonian University - Medical College, Lazarza 16, 31-530 Krakow, Poland
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16
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Wang KW, Hall CK. Characterising the throat diameter of through-pores in network structures using a percolation criterion. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1654140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Kye Won Wang
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Carol K. Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
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17
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Molecular Cavity Topological Representation for Pattern Analysis: A NLP Analogy-Based Word2Vec Method. Int J Mol Sci 2019; 20:ijms20236019. [PMID: 31795343 PMCID: PMC6928730 DOI: 10.3390/ijms20236019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 11/23/2019] [Accepted: 11/26/2019] [Indexed: 12/31/2022] Open
Abstract
Cavity analysis in molecular dynamics is important for understanding molecular function. However, analyzing the dynamic pattern of molecular cavities remains a difficult task. In this paper, we propose a novel method to topologically represent molecular cavities by vectorization. First, a characterization of cavities is established through Word2Vec model, based on an analogy between the cavities and natural language processing (NLP) terms. Then, we use some techniques such as dimension reduction and clustering to conduct an exploratory analysis of the vectorized molecular cavity. On a real data set, we demonstrate that our approach is applicable to maintain the topological characteristics of the cavity and can find the change patterns from a large number of cavities.
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18
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Rajagopal N, Irudayanathan FJ, Nangia S. Computational Nanoscopy of Tight Junctions at the Blood-Brain Barrier Interface. Int J Mol Sci 2019; 20:E5583. [PMID: 31717316 PMCID: PMC6888702 DOI: 10.3390/ijms20225583] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/05/2019] [Accepted: 11/06/2019] [Indexed: 12/16/2022] Open
Abstract
The selectivity of the blood-brain barrier (BBB) is primarily maintained by tight junctions (TJs), which act as gatekeepers of the paracellular space by blocking blood-borne toxins, drugs, and pathogens from entering the brain. The BBB presents a significant challenge in designing neurotherapeutics, so a comprehensive understanding of the TJ architecture can aid in the design of novel therapeutics. Unraveling the intricacies of TJs with conventional experimental techniques alone is challenging, but recently developed computational tools can provide a valuable molecular-level understanding of TJ architecture. We employed the computational methods toolkit to investigate claudin-5, a highly expressed TJ protein at the BBB interface. Our approach started with the prediction of claudin-5 structure, evaluation of stable dimer conformations and nanoscale assemblies, followed by the impact of lipid environments, and posttranslational modifications on these claudin-5 assemblies. These led to the study of TJ pores and barriers and finally understanding of ion and small molecule transport through the TJs. Some of these in silico, molecular-level findings, will need to be corroborated by future experiments. The resulting understanding can be advantageous towards the eventual goal of drug delivery across the BBB. This review provides key insights gleaned from a series of state-of-the-art nanoscale simulations (or computational nanoscopy studies) performed on the TJ architecture.
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Affiliation(s)
| | | | - Shikha Nangia
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY 13244, USA
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19
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CavBench: A benchmark for protein cavity detection methods. PLoS One 2019; 14:e0223596. [PMID: 31609980 PMCID: PMC6791542 DOI: 10.1371/journal.pone.0223596] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/24/2019] [Indexed: 11/19/2022] Open
Abstract
Extensive research has been applied to discover new techniques and methods to model protein-ligand interactions. In particular, considerable efforts focused on identifying candidate binding sites, which quite often are active sites that correspond to protein pockets or cavities. Thus, these cavities play an important role in molecular docking. However, there is no established benchmark to assess the accuracy of new cavity detection methods. In practice, each new technique is evaluated using a small set of proteins with known binding sites as ground-truth. However, studies supported by large datasets of known cavities and/or binding sites and statistical classification (i.e., false positives, false negatives, true positives, and true negatives) would yield much stronger and reliable assessments. To this end, we propose CavBench, a generic and extensible benchmark to compare different cavity detection methods relative to diverse ground truth datasets (e.g., PDBsum) using statistical classification methods.
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20
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Pravda L, Sehnal D, Toušek D, Navrátilová V, Bazgier V, Berka K, Svobodová Vareková R, Koca J, Otyepka M. MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update). Nucleic Acids Res 2019; 46:W368-W373. [PMID: 29718451 PMCID: PMC6030847 DOI: 10.1093/nar/gky309] [Citation(s) in RCA: 185] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/12/2018] [Indexed: 12/27/2022] Open
Abstract
MOLEonline is an interactive, web-based application for the detection and characterization of channels (pores and tunnels) within biomacromolecular structures. The updated version of MOLEonline overcomes limitations of the previous version by incorporating the recently developed LiteMol Viewer visualization engine and providing a simple, fully interactive user experience. The application enables two modes of calculation: one is dedicated to the analysis of channels while the other was specifically designed for transmembrane pores. As the application can use both PDB and mmCIF formats, it can be leveraged to analyze a wide spectrum of biomacromolecular structures, e.g. stemming from NMR, X-ray and cryo-EM techniques. The tool is interconnected with other bioinformatics tools (e.g., PDBe, CSA, ChannelsDB, OPM, UniProt) to help both setup and the analysis of acquired results. MOLEonline provides unprecedented analytics for the detection and structural characterization of channels, as well as information about their numerous physicochemical features. Here we present the application of MOLEonline for structural analyses of α-hemolysin and transient receptor potential mucolipin 1 (TRMP1) pores. The MOLEonline application is freely available via the Internet at https://mole.upol.cz.
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Affiliation(s)
- Lukáš Pravda
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - David Sehnal
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Dominik Toušek
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17. Listopadu 12, 771 46 Olomouc, Czech Republic
| | - Veronika Navrátilová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tr. 17. Listopadu 12, 771 46 Olomouc, Czech Republic
| | - Václav Bazgier
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tr. 17. Listopadu 12, 771 46 Olomouc, Czech Republic
| | - Karel Berka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tr. 17. Listopadu 12, 771 46 Olomouc, Czech Republic
| | - Radka Svobodová Vareková
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Jaroslav Koca
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tr. 17. Listopadu 12, 771 46 Olomouc, Czech Republic
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21
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Leano JB, Batarni S, Eriksen J, Juge N, Pak JE, Kimura-Someya T, Robles-Colmenares Y, Moriyama Y, Stroud RM, Edwards RH. Structures suggest a mechanism for energy coupling by a family of organic anion transporters. PLoS Biol 2019; 17:e3000260. [PMID: 31083648 PMCID: PMC6532931 DOI: 10.1371/journal.pbio.3000260] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 05/23/2019] [Accepted: 04/24/2019] [Indexed: 11/30/2022] Open
Abstract
Members of the solute carrier 17 (SLC17) family use divergent mechanisms to concentrate organic anions. Membrane potential drives uptake of the principal excitatory neurotransmitter glutamate into synaptic vesicles, whereas closely related proteins use proton cotransport to drive efflux from the lysosome. To delineate the divergent features of ionic coupling by the SLC17 family, we determined the structure of Escherichia coli D-galactonate/H+ symporter D-galactonate transporter (DgoT) in 2 states: one open to the cytoplasmic side and the other open to the periplasmic side with substrate bound. The structures suggest a mechanism that couples H+ flux to substrate recognition. A transition in the role of H+ from flux coupling to allostery may confer regulation by trafficking to and from the plasma membrane. The first structures of a family of organic anion transporters reveal an interaction with protons that is conserved from bacterial transporters to the mammalian proteins that transport glutamate into synaptic vesicles.
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Affiliation(s)
- Jonathan B. Leano
- Department of Biochemistry & Biophysics, University of California San Francisco School of Medicine, San Francisco, California, United States of America
| | - Samir Batarni
- Departments of Neurology and Physiology, University of California San Francisco School of Medicine, San Francisco, California, United States of America
| | - Jacob Eriksen
- Departments of Neurology and Physiology, University of California San Francisco School of Medicine, San Francisco, California, United States of America
| | - Narinobu Juge
- Departments of Neurology and Physiology, University of California San Francisco School of Medicine, San Francisco, California, United States of America
| | - John E. Pak
- Department of Biochemistry & Biophysics, University of California San Francisco School of Medicine, San Francisco, California, United States of America
| | - Tomomi Kimura-Someya
- Departments of Neurology and Physiology, University of California San Francisco School of Medicine, San Francisco, California, United States of America
| | - Yaneth Robles-Colmenares
- Department of Biochemistry & Biophysics, University of California San Francisco School of Medicine, San Francisco, California, United States of America
| | - Yoshinori Moriyama
- Department of Membrane Biochemistry, Advanced Science Research Center, Okayama University, Okayama, Japan
| | - Robert M. Stroud
- Department of Biochemistry & Biophysics, University of California San Francisco School of Medicine, San Francisco, California, United States of America
- * E-mail: (RMS); (RHE)
| | - Robert H. Edwards
- Departments of Neurology and Physiology, University of California San Francisco School of Medicine, San Francisco, California, United States of America
- * E-mail: (RMS); (RHE)
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22
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Sampling-Based Motion Planning for Tracking Evolution of Dynamic Tunnels in Molecular Dynamics Simulations. J INTELL ROBOT SYST 2019. [DOI: 10.1007/s10846-018-0877-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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23
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Xia K, Anand DV, Shikhar S, Mu Y. Persistent homology analysis of osmolyte molecular aggregation and their hydrogen-bonding networks. Phys Chem Chem Phys 2019; 21:21038-21048. [DOI: 10.1039/c9cp03009c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Dramatically different patterns can be observed in the topological fingerprints for hydrogen-bonding networks from two types of osmolyte systems.
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Affiliation(s)
- Kelin Xia
- Division of Mathematical Sciences
- School of Physical and Mathematical Sciences
- School of Biological Sciences
- Nanyang Technological University
- Singapore
| | - D. Vijay Anand
- Division of Mathematical Sciences
- School of Physical and Mathematical Sciences
- School of Biological Sciences
- Nanyang Technological University
- Singapore
| | - Saxena Shikhar
- School of Biological Sciences
- Nanyang Technological University
- Singapore
| | - Yuguang Mu
- School of Biological Sciences
- Nanyang Technological University
- Singapore
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24
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Gonzalez JM. Molecular Tunnels in Enzymes and Thermophily: A Case Study on the Relationship to Growth Temperature. Microorganisms 2018; 6:microorganisms6040109. [PMID: 30347813 PMCID: PMC6313320 DOI: 10.3390/microorganisms6040109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 10/11/2018] [Accepted: 10/16/2018] [Indexed: 11/21/2022] Open
Abstract
Developments in protein expression, analysis and computational capabilities are decisively contributing to a better understanding of the structure of proteins and their relationship to function. Proteins are known to be adapted to the growth rate of microorganisms and some microorganisms (named (hyper)thermophiles) thrive optimally at high temperatures, even above 100 °C. Nevertheless, some biomolecules show great instability at high temperatures and some of them are universal and required substrates and cofactors in multiple enzymatic reactions for all (both mesophiles and thermophiles) living cells. Only a few possibilities have been pointed out to explain the mechanisms that thermophiles use to successfully thrive under high temperatures. As one of these alternatives, the role of molecular tunnels or channels in enzymes has been suggested but remains to be elucidated. This study presents an analysis of channels in proteins (i.e., substrate tunnels), comparing two different protein types, glutamate dehydrogenase and glutamine phosphoribosylpyrophosphate amidotransferase, which are supposed to present a different strategy on the requirement for substrate tunnels with low and high needs for tunneling, respectively. The search and comparison of molecular tunnels in these proteins from microorganisms thriving optimally from 15 °C to 100 °C suggested that those tunnels in (hyper)thermophiles are required and optimized to specific dimensions at high temperatures for the enzyme glutamine phosphoribosylpyrophosphate amidotransferase. For the enzyme glutamate dehydrogenase, a reduction of empty spaces within the protein could explain the optimization at increasing temperatures. This analysis provides further evidence on molecular channeling as a feasible mechanism in hyperthermophiles with multiple relevant consequences contributing to better understand how they live under those extreme conditions.
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Affiliation(s)
- Juan Miguel Gonzalez
- Instituto de Recursos Naturales y Agrobiología, Consejo Superior de Investigaciones Científicas, IRNAS-CSIC, Avda. Reina Mercedes 10, 41702 Sevilla, Spain.
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25
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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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26
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Esque J, Sansom MSP, Baaden M, Oguey C. Analyzing protein topology based on Laguerre tessellation of a pore-traversing water network. Sci Rep 2018; 8:13540. [PMID: 30202114 PMCID: PMC6131185 DOI: 10.1038/s41598-018-31422-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 08/17/2018] [Indexed: 11/15/2022] Open
Abstract
Given the tight relation between protein structure and function, we present a set of methods to analyze protein topology, implemented in the VLDP program, relying on Laguerre space partitions built from series of molecular dynamics snapshots. The Laguerre partition specifies inter-atomic contacts, formalized in graphs. The deduced properties are the existence and count of water aggregates, possible passage ways and constrictions, the structure, connectivity, stability and depth of the water network. As a test-case, the membrane protein FepA is investigated in its full environment, yielding a more precise description of the protein surface. Inside FepA, the solvent splits into isolated clusters and an intricate network connecting both sides of the lipid bilayer. The network is dynamic, connections set on and off, occasionally substantially relocating traversing paths. Subtle differences are detected between two forms of FepA, ligand-free and complexed with its natural iron carrier, the enterobactin. The complexed form has more constricted and more centered openings in the upper part whereas, in the lower part, constriction is released: two main channels between the plug and barrel lead directly to the periplasm. Reliability, precision and the variety of topological features are the main interest of the method.
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Affiliation(s)
- Jérémy Esque
- LPTM, CNRS UMR 8089, Université de Cergy-Pontoise, 95302, Cergy-Pontoise, France. .,LISBP, Université de Toulouse, CNRS, INSA, INRA, 135 Avenue de Rangueil, 31400, Toulouse, France.
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
| | - Marc Baaden
- Laboratoire de Biochimie Théorique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Christophe Oguey
- LPTM, CNRS UMR 8089, Université de Cergy-Pontoise, 95302, Cergy-Pontoise, France.
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27
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Molecular insights into antibiotic resistance - how a binding protein traps albicidin. Nat Commun 2018; 9:3095. [PMID: 30082794 PMCID: PMC6078987 DOI: 10.1038/s41467-018-05551-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 07/13/2018] [Indexed: 11/08/2022] Open
Abstract
The worldwide emergence of antibiotic resistance poses a serious threat to human health. A molecular understanding of resistance strategies employed by bacteria is obligatory to generate less-susceptible antibiotics. Albicidin is a highly potent antibacterial compound synthesized by the plant-pathogenic bacterium Xanthomonas albilineans. The drug-binding protein AlbA confers albicidin resistance to Klebsiella oxytoca. Here we show that AlbA binds albicidin with low nanomolar affinity resulting in full inhibition of its antibacterial activity. We report on the crystal structure of the drug-binding domain of AlbA (AlbAS) in complex with albicidin. Both α-helical repeat domains of AlbAS are required to cooperatively clamp albicidin, which is unusual for drug-binding proteins of the MerR family. Structure-guided NMR binding studies employing synthetic albicidin derivatives give valuable information about ligand promiscuity of AlbAS. Our findings thus expand the general understanding of antibiotic resistance mechanisms and support current drug-design efforts directed at more effective albicidin analogs.
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Ligand Access Channels in Cytochrome P450 Enzymes: A Review. Int J Mol Sci 2018; 19:ijms19061617. [PMID: 29848998 PMCID: PMC6032366 DOI: 10.3390/ijms19061617] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 05/27/2018] [Accepted: 05/28/2018] [Indexed: 12/22/2022] Open
Abstract
Quantitative structure-activity relationships may bring invaluable information on structural elements of both enzymes and substrates that, together, govern substrate specificity. Buried active sites in cytochrome P450 enzymes are connected to the solvent by a network of channels exiting at the distal surface of the protein. This review presents different in silico tools that were developed to uncover such channels in P450 crystal structures. It also lists some of the experimental evidence that actually suggest that these predicted channels might indeed play a critical role in modulating P450 functions. Amino acid residues at the entrance of the channels may participate to a first global ligand recognition of ligands by P450 enzymes before they reach the buried active site. Moreover, different P450 enzymes show different networks of predicted channels. The plasticity of P450 structures is also important to take into account when looking at how channels might play their role.
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29
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Jiang D, Gamal El-Din TM, Ing C, Lu P, Pomès R, Zheng N, Catterall WA. Structural basis for gating pore current in periodic paralysis. Nature 2018; 557:590-594. [PMID: 29769724 PMCID: PMC6708612 DOI: 10.1038/s41586-018-0120-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 04/09/2018] [Indexed: 12/19/2022]
Abstract
Potassium-sensitive Hypokalemic and Normokalemic Periodic Paralysis (HypoPP, NormoPP) are inherited skeletal muscle diseases characterized by episodes of flaccid muscle weakness1,2. They are caused by mutations in one gating charge in an S4 transmembrane segment in the voltage sensor (VS) of voltage-gated sodium channel Nav1.4 or calcium channel Cav1.11,2. Mutations of the outermost arginine gating charges (R1 and R2) cause HypoPP1,2 by creating a pathogenic gating pore in the VS through which cations leak in the resting state3,4. Mutations of the third arginine gating charge (R3) cause NormoPP5 owing to cationic leak in activated/inactivated states6. Here we present high-resolution structures of these pathogenic gating pores in the model bacterial sodium channel NaVAb7,8. Mutation of R2 in NaVAb gives gating pore current in resting states, whereas mutation of R3 gives gating pore current in activated/inactivated states. Mutations R2G and R3G have no effect on backbone structures of VS, but create aqueous space near the hydrophobic constriction site (HCS) that controls gating charge movement through VS. The R3G mutation extends the extracellular aqueous cleft completely through the activated VS. Although the R2G mutation does not create a continuous aqueous pathway in the activated state, molecular modeling of the resting state reveals a complete water-accessible pathway. Crystal structures of NaVAb/R2G in complex with guanidinium define a potential drug target site. Molecular dynamics simulations illustrate the mechanism of Na+ permeation through the mutant gating pore in concert with conformational fluctuations of gating charge R4. Our results reveal pathogenic mechanisms of periodic paralysis at the atomic level and suggest designs of drugs that may prevent ionic leak and provide symptomatic relief from these episodic diseases.
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Affiliation(s)
- Daohua Jiang
- Department of Pharmacology, University of Washington, Seattle, WA, USA
| | | | - Christopher Ing
- Molecular Medicine, Hospital for Sick Children Toronto, Toronto, Ontario, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Peilong Lu
- Department of Pharmacology, University of Washington, Seattle, WA, USA.,Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Régis Pomès
- Molecular Medicine, Hospital for Sick Children Toronto, Toronto, Ontario, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Ning Zheng
- Department of Pharmacology, University of Washington, Seattle, WA, USA. .,Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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30
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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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31
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Pravda L, Sehnal D, Svobodová Vařeková R, Navrátilová V, Toušek D, Berka K, Otyepka M, Koča J. ChannelsDB: database of biomacromolecular tunnels and pores. Nucleic Acids Res 2018; 46:D399-D405. [PMID: 29036719 PMCID: PMC5753359 DOI: 10.1093/nar/gkx868] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 09/08/2017] [Accepted: 09/28/2017] [Indexed: 01/21/2023] Open
Abstract
ChannelsDB (http://ncbr.muni.cz/ChannelsDB) is a database providing information about the positions, geometry and physicochemical properties of channels (pores and tunnels) found within biomacromolecular structures deposited in the Protein Data Bank. Channels were deposited from two sources; from literature using manual deposition and from a software tool automatically detecting tunnels leading to the enzymatic active sites and selected cofactors, and transmembrane pores. The database stores information about geometrical features (e.g. length and radius profile along a channel) and physicochemical properties involving polarity, hydrophobicity, hydropathy, charge and mutability. The stored data are interlinked with available UniProt annotation data mapping known mutation effects to channel-lining residues. All structures with channels are displayed in a clear interactive manner, further facilitating data manipulation and interpretation. As such, ChannelsDB provides an invaluable resource for research related to deciphering the biological function of biomacromolecular channels.
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Affiliation(s)
- Lukáš Pravda
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Kamenice 5, 625 00 Brno-Bohunice, Czech Republic
| | - David Sehnal
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Kamenice 5, 625 00 Brno-Bohunice, Czech Republic
| | - Radka Svobodová Vařeková
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Kamenice 5, 625 00 Brno-Bohunice, Czech Republic
| | - Veronika Navrátilová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Dominik Toušek
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Karel Berka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Jaroslav Koča
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Kamenice 5, 625 00 Brno-Bohunice, Czech Republic
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32
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Howard RJ, Carnevale V, Delemotte L, Hellmich UA, Rothberg BS. Permeating disciplines: Overcoming barriers between molecular simulations and classical structure-function approaches in biological ion transport. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1860:927-942. [PMID: 29258839 DOI: 10.1016/j.bbamem.2017.12.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 12/08/2017] [Accepted: 12/14/2017] [Indexed: 11/20/2022]
Abstract
Ion translocation across biological barriers is a fundamental requirement for life. In many cases, controlling this process-for example with neuroactive drugs-demands an understanding of rapid and reversible structural changes in membrane-embedded proteins, including ion channels and transporters. Classical approaches to electrophysiology and structural biology have provided valuable insights into several such proteins over macroscopic, often discontinuous scales of space and time. Integrating these observations into meaningful mechanistic models now relies increasingly on computational methods, particularly molecular dynamics simulations, while surfacing important challenges in data management and conceptual alignment. Here, we seek to provide contemporary context, concrete examples, and a look to the future for bridging disciplinary gaps in biological ion transport. This article is part of a Special Issue entitled: Beyond the Structure-Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain.
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Affiliation(s)
- Rebecca J Howard
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, 17121 Solna, Sweden.
| | - Vincenzo Carnevale
- Institute for Computational Molecular Science, Department of Chemistry, Temple University, Philadelphia, PA 19122, USA.
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Theoretical Physics, KTH Royal Institute of Technology, Box 1031, 17121 Solna, Sweden.
| | - Ute A Hellmich
- Johannes Gutenberg University Mainz, Institute for Pharmacy and Biochemistry, Johann-Joachim-Becherweg 30, 55128 Mainz, Germany; Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue Str. 9, 60438 Frankfurt, Germany.
| | - Brad S Rothberg
- Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA.
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33
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Rossokhin AV. Homology modeling of the transmembrane domain of the GABAA receptor. Biophysics (Nagoya-shi) 2017. [DOI: 10.1134/s0006350917050190] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Jiménez-Arroyo N, Gil-Rodríguez PC, Díaz-Vilchis A, Rojas-Trejo SP, Rudiño-Piñera E. Zo-peroxidase: Crystal structure and sequence of a highly-glycosylated peroxidase resistant to high concentrations of H 2O 2 from Japanese radish. Biochem Biophys Rep 2017; 13:32-38. [PMID: 29556562 PMCID: PMC5857146 DOI: 10.1016/j.bbrep.2017.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/24/2017] [Accepted: 09/24/2017] [Indexed: 01/07/2023] Open
Abstract
Understanding Peroxidase (PRXs) enzymatic diversity and functional significance from a three-dimensional point of view is a key point for structural and mechanistic studies. In this context, Zo-peroxidase (ZoPrx) a member of the class III peroxidases and secreted by plants, differs from all previously described PRXs because of its remarkable catalytic stability in the presence of hydrogen peroxide. In this work, we present the crystallographic structure of ZoPrx isolated from Japanese radish, at 2.05 Å resolution. The mature enzyme consists of a single monomer of 308 residues exhibiting the same fold as all previously described members of the plant PRXs superfamily. Furthermore, the enzyme contains a heme b group as the prosthetic group and two Ca2+ binding sites. Moreover, seven N-glycosylation sites were found in the structure, and 49 glycans bound to the two ZoPrx molecules found in the asymmetric unit are clearly visible in the electron density map. The comparison of ZoPrx coordinates with homologous enzymes revealed minor structural changes, in which the residue 177 appears to be responsible for enlarging the access to the heme cavity, the only structural finding which may be related to the H2O2 tolerance of ZoPrx and detected by X-ray crystallography. Because of its characteristics, ZoPrx has a broad range of potential applications from chemical synthesis to environmental biocatalysis, thus its aminoacidic sequence, partially completed using the electron density, and the three-dimensional structure itself, become a possible starting point to engineering heme-peroxidases to enhance oxidative stability.
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35
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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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36
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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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37
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Ebert MCCJC, Guzman Espinola J, Lamoureux G, Pelletier JN. Substrate-Specific Screening for Mutational Hotspots Using Biased Molecular Dynamics Simulations. ACS Catal 2017. [DOI: 10.1021/acscatal.7b02634] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maximilian C. C. J. C. Ebert
- Département
de Biochimie and Center for Green Chemistry and Catalysis (CGCC), Université de Montréal, Montréal, QC H3T 1J4, Canada
- PROTEO, The Québec
Network for Research on Protein Function, Engineering and Applications, Québec, QC G1V 0A6, Canada
| | - Joaquin Guzman Espinola
- Département
de Biochimie and Center for Green Chemistry and Catalysis (CGCC), Université de Montréal, Montréal, QC H3T 1J4, Canada
- PROTEO, The Québec
Network for Research on Protein Function, Engineering and Applications, Québec, QC G1V 0A6, Canada
| | - Guillaume Lamoureux
- PROTEO, The Québec
Network for Research on Protein Function, Engineering and Applications, Québec, QC G1V 0A6, Canada
- Department
of Chemistry and Biochemistry and Centre for Research in Molecular
Modeling (CERMM), Concordia University, Montréal, QC H4B 1R6, Canada
| | - Joelle N. Pelletier
- Département
de Biochimie and Center for Green Chemistry and Catalysis (CGCC), Université de Montréal, Montréal, QC H3T 1J4, Canada
- PROTEO, The Québec
Network for Research on Protein Function, Engineering and Applications, Québec, QC G1V 0A6, Canada
- Département
de Chimie, Université de Montréal, Montréal, QC H3T 1J4, Canada
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Membrane-bound human orphan cytochrome P450 2U1: Sequence singularities, construction of a full 3D model, and substrate docking. Biochimie 2017; 140:166-175. [DOI: 10.1016/j.biochi.2017.07.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 07/20/2017] [Indexed: 12/14/2022]
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39
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Lauterbach A, Usbeck JC, Behr J, Vogel RF. MALDI-TOF MS typing enables the classification of brewing yeasts of the genus Saccharomyces to major beer styles. PLoS One 2017; 12:e0181694. [PMID: 28792944 PMCID: PMC5549903 DOI: 10.1371/journal.pone.0181694] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 07/04/2017] [Indexed: 11/19/2022] Open
Abstract
Brewing yeasts of the genus Saccharomyces are either available from yeast distributor centers or from breweries employing their own “in-house strains”. During the last years, the classification and characterization of yeasts of the genus Saccharomyces was achieved by using biochemical and DNA-based methods. The current lack of fast, cost-effective and simple methods to classify brewing yeasts to a beer type, may be closed by Matrix Assisted Laser Desorption/Ionization–Time-Of-Flight Mass Spectrometry (MALDI-TOF MS) upon establishment of a database based on sub-proteome spectra from reference strains of brewing yeasts. In this study an extendable “brewing yeast” spectra database was established including 52 brewing yeast strains of the most important types of bottom- and top-fermenting strains as well as beer-spoiling S. cerevisiae var. diastaticus strains. 1560 single spectra, prepared with a standardized sample preparation method, were finally compared against the established database and investigated by bioinformatic analyses for similarities and distinctions. A 100% separation between bottom-, top-fermenting and S. cerevisiae var. diastaticus strains was achieved. Differentiation between Alt and Kölsch strains was not achieved because of the high similarity of their protein patterns. Whereas the Ale strains show a high degree of dissimilarity with regard to their sub-proteome. These results were supported by MDS and DAPC analysis of all recorded spectra. Within five clusters of beer types that were distinguished, and the wheat beer (WB) cluster has a clear separation from other groups. With the establishment of this MALDI-TOF MS spectra database proof of concept is provided of the discriminatory power of this technique to classify brewing yeasts into different major beer types in a rapid, easy way, and focus brewing trails accordingly. It can be extended to yeasts for specialty beer types and other applications including wine making or baking.
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Affiliation(s)
- Alexander Lauterbach
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Freising, Germany
| | - Julia C. Usbeck
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Freising, Germany
| | - Jürgen Behr
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Freising, Germany
- Bavarian Center for Biomolecular Mass Spectrometry, Freising, Germany
| | - Rudi F. Vogel
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Freising, Germany
- * E-mail:
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40
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Ahrazem O, Diretto G, Argandoña J, Rubio-Moraga Á, Julve JM, Orzáez D, Granell A, Gómez-Gómez L. Evolutionarily distinct carotenoid cleavage dioxygenases are responsible for crocetin production in Buddleja davidii. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4663-4677. [PMID: 28981773 DOI: 10.1093/jxb/erx277] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Crocetin, one of the few colored apocarotenoids known in nature, is present in flowers and fruits and has long been used medicinally and as a colorant. Saffron is the main source of crocetin, although a few other plants produce lower amounts of this apocarotenoid. Notably, Buddleja davidii accumulates crocetin in its flowers. Recently, a carotenoid dioxygenase cleavage enzyme, CCD2, has been characterized as responsible for crocetin production in Crocus species. We searched for CCD2 homologues in B. davidii and identified several CCD enzymes from the CCD1 and CCD4 subfamilies. Unexpectedly, two out of the three CCD4 enzymes, namely BdCCD4.1 and BdCCD4.3, showed 7,8;7',8' activity in vitro and in vivo over zeaxanthin. In silico analyses of these enzymes and CCD2 allowed the determination of key residues for this activity. Both BdCCD4 genes are highly expressed during flower development and transcripts levels parallel the accumulation of crocins in the petals. Phylogenetic analysis showed that BdCCD4.2 grouped with almost all the characterized CCD4 enzymes, while BdCCD4.1 and BdCCD4.3 form a new sub-cluster together with CCD4 enzymes from certain Lamiales species. The present study indicates that convergent evolution led to the acquisition of 7,8;7',8' apocarotenoid cleavage activity in two separate CCD enzyme families.
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Affiliation(s)
- Oussama Ahrazem
- Instituto Botánico, Departamento de Ciencia y Tecnología Agroforestal y Genética, Facultad de Farmacia, Universidad de Castilla-La Mancha, Campus Universitario s/n, 02071 Albacete, Spain
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Campus Tecnológico de la Fábrica de Armas, Avda, Carlos III s/n, E-45071 Toledo, Spain
| | - Gianfranco Diretto
- Italian National Agency for New Technologies, Energy, and Sustainable Development, Casaccia Research Centre, 00123 Rome, Italy
| | - Javier Argandoña
- Instituto Botánico, Departamento de Ciencia y Tecnología Agroforestal y Genética, Facultad de Farmacia, Universidad de Castilla-La Mancha, Campus Universitario s/n, 02071 Albacete, Spain
| | - Ángela Rubio-Moraga
- Instituto Botánico, Departamento de Ciencia y Tecnología Agroforestal y Genética, Facultad de Farmacia, Universidad de Castilla-La Mancha, Campus Universitario s/n, 02071 Albacete, Spain
| | - José Manuel Julve
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain
| | - Diego Orzáez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain
| | - Lourdes Gómez-Gómez
- Instituto Botánico, Departamento de Ciencia y Tecnología Agroforestal y Genética, Facultad de Farmacia, Universidad de Castilla-La Mancha, Campus Universitario s/n, 02071 Albacete, Spain
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Basak S, Schmandt N, Gicheru Y, Chakrapani S. Crystal structure and dynamics of a lipid-induced potential desensitized-state of a pentameric ligand-gated channel. eLife 2017; 6:23886. [PMID: 28262093 PMCID: PMC5378477 DOI: 10.7554/elife.23886] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 03/04/2017] [Indexed: 12/14/2022] Open
Abstract
Desensitization in pentameric ligand-gated ion channels plays an important role in regulating neuronal excitability. Here, we show that docosahexaenoic acid (DHA), a key ω−3 polyunsaturated fatty acid in synaptic membranes, enhances the agonist-induced transition to the desensitized state in the prokaryotic channel GLIC. We determined a 3.25 Å crystal structure of the GLIC-DHA complex in a potentially desensitized conformation. The DHA molecule is bound at the channel-periphery near the M4 helix and exerts a long-range allosteric effect on the pore across domain-interfaces. In this previously unobserved conformation, the extracellular-half of the pore-lining M2 is splayed open, reminiscent of the open conformation, while the intracellular-half is constricted, leading to a loss of both water and permeant ions. These findings, in combination with spin-labeling/EPR spectroscopic measurements in reconstituted-membranes, provide novel mechanistic details of desensitization in pentameric channels. DOI:http://dx.doi.org/10.7554/eLife.23886.001 The nerve cells (or neurons) in the brain communicate with each other by releasing chemicals called neurotransmitters that bind to ion channels on neighboring neurons. This ultimately causes ions to flow in or out of the receiving neuron through these ion channels; this ion flow determines how the neuron responds. One family of ion channels that is found at the junction between neurons, and between neurons and muscle fibers, is known as the pentameric ligand-gated ion channels (or pLGICs). These channels act as ‘gates’ that open to allow ions through them when a neurotransmitter binds to the channel. In addition to the open ‘active’ state, the channels can take on two different ‘inactive’ states that do not allow ions to pass through the channel: a closed (resting) state and a desensitized state (that is still bound to the neurotransmitter). Understanding how channels switch between these states is important for designing drugs that correct problems that cause the channels to work incorrectly. Problems that affect the desensitized state have been linked to neurological disorders such as epilepsy. Medically important molecules such as anesthetics and alcohols are thought to affect desensitization, and drugs that target desensitized ion channels may present ways of treating neurological disorders with fewer side effects. Docosahexaenoic acid (DHA) is an abundant lipid molecule that is present in the membranes of neurons. It is one of the key ingredients in fish oil supplements and is thought to enhance learning and memory. DHA affects the desensitization of pLGICs but it is not clear exactly how it does so. Basak et al. now show that DHA affects a bacterial pLGIC in the same way as it affects human channels – by enhancing desensitization. Using a technique called X-ray crystallography to analyze the channel while bound to DHA revealed a previously unobserved channel structure. The DHA molecule binds to a site at the edge of the channel and causes a change in its structure that leaves the upper part of the channel open while the lower part is constricted. Basak et al. predict that molecules such as anesthetics target this desensitized state. The next step will be to obtain the structures of bacterial and human pLGIC channels in a natural membrane environment. This will allow us to better understand the changes in structure that the channels go through as they transmit signals between neurons, and so help in the development of new treatments for neurological disorders. DOI:http://dx.doi.org/10.7554/eLife.23886.002
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Affiliation(s)
- Sandip Basak
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, United States
| | - Nicolaus Schmandt
- Department of Neuroscience, School of Medicine, Case Western Reserve University, Cleveland, United States
| | - Yvonne Gicheru
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, United States
| | - Sudha Chakrapani
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, United States
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42
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Reed JR, Backes WL. Physical Studies of P450-P450 Interactions: Predicting Quaternary Structures of P450 Complexes in Membranes from Their X-ray Crystal Structures. Front Pharmacol 2017; 8:28. [PMID: 28194112 PMCID: PMC5276844 DOI: 10.3389/fphar.2017.00028] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 01/16/2017] [Indexed: 01/15/2023] Open
Abstract
Cytochrome P450 enzymes, which catalyze oxygenation reactions of both exogenous and endogenous chemicals, are membrane bound proteins that require interaction with their redox partners in order to function. Those responsible for drug and foreign compound metabolism are localized primarily in the endoplasmic reticulum of liver, lung, intestine, and other tissues. More recently, the potential for P450 enzymes to exist as supramolecular complexes has been shown by the demonstration of both homomeric and heteromeric complexes. The P450 units in these complexes are heterogeneous with respect to their distribution and function, and the interaction of different P450s can influence P450-specific metabolism. The goal of this review is to examine the evidence supporting the existence of physical complexes among P450 enzymes. Additionally, the review examines the crystal lattices of different P450 enzymes derived from X-ray diffraction data to make assumptions regarding possible quaternary structures in membranes and in turn, to predict how the quaternary structures could influence metabolism and explain the functional effects of specific P450-P450 interactions.
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Affiliation(s)
- James R Reed
- Department of Pharmacology and Experimental Therapeutics, Louisiana State University Health Sciences Center New Orleans LA, USA
| | - Wayne L Backes
- Department of Pharmacology and Experimental Therapeutics, Louisiana State University Health Sciences Center New Orleans LA, USA
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43
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Abstract
Today, the development of new drugs is a challenging task of science. Researchers already applied molecular docking in the drug design field to simulate ligand- receptor interactions. Docking is a term used for computational schemes that attempt to find the “best” matching between two molecules in a complex formed from constituent molecules. It has a wide range of uses and applications in drug discovery. However, some defects still exist; the accuracy and speed of docking calculation is a challenge to explore and these methods can be enhanced as a solution to docking problem. The molecular docking problem can be defined as follows: Given the atomic coordinates of two molecules, predict their “correct” bound association. The chapter discusses common challenges critical aspects of docking method such as ligand- and receptor- conformation, flexibility and cavity detection, etc. It emphasis to the challenges and inadequacies with the theories behind as well as the examples.
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44
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Voltage-gated sodium channels viewed through a structural biology lens. Curr Opin Struct Biol 2016; 45:74-84. [PMID: 27988421 DOI: 10.1016/j.sbi.2016.11.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 11/28/2016] [Indexed: 02/07/2023]
Abstract
Voltage-gated sodium (Nav) channels initiate and propagate action potentials in excitable cells, and are frequently dysregulated or mutated in human disease. Despite decades of intense physiological and biophysical research, eukaryotic Nav channels have so far eluded high-resolution structure determination because of their biochemical complexity. Recently, simpler bacterial voltage-gated sodium (BacNav) channels have provided templates to understand the structural basis of voltage-dependent activation, inactivation, ion selectivity, and drug block in eukaryotic Nav and related voltage-gated calcium (Cav) channels. Further breakthroughs employing BacNav channels have also enabled visualization of bound small molecule modulators that can guide the rational design of next generation therapeutics. This review will highlight the emerging structural biology of BacNav channels and its contribution to our understanding of the gating, ion selectivity, and pharmacological regulation of eukaryotic Nav (and Cav) channels.
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45
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Trick JL, Chelvaniththilan S, Klesse G, Aryal P, Wallace EJ, Tucker SJ, Sansom MSP. Functional Annotation of Ion Channel Structures by Molecular Simulation. Structure 2016; 24:2207-2216. [PMID: 27866853 PMCID: PMC5145807 DOI: 10.1016/j.str.2016.10.005] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Revised: 08/12/2016] [Accepted: 10/12/2016] [Indexed: 01/30/2023]
Abstract
Ion channels play key roles in cell membranes, and recent advances are yielding an increasing number of structures. However, their functional relevance is often unclear and better tools are required for their functional annotation. In sub-nanometer pores such as ion channels, hydrophobic gating has been shown to promote dewetting to produce a functionally closed (i.e., non-conductive) state. Using the serotonin receptor (5-HT3R) structure as an example, we demonstrate the use of molecular dynamics to aid the functional annotation of channel structures via simulation of the behavior of water within the pore. Three increasingly complex simulation analyses are described: water equilibrium densities; single-ion free-energy profiles; and computational electrophysiology. All three approaches correctly predict the 5-HT3R crystal structure to represent a functionally closed (i.e., non-conductive) state. We also illustrate the application of water equilibrium density simulations to annotate different conformational states of a glycine receptor.
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Affiliation(s)
- Jemma L Trick
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Sivapalan Chelvaniththilan
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Gianni Klesse
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Prafulla Aryal
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK; OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford, UK
| | | | - Stephen J Tucker
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK; OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford, UK.
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46
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Schmandt N, Velisetty P, Chalamalasetti SV, Stein RA, Bonner R, Talley L, Parker MD, Mchaourab HS, Yee VC, Lodowski DT, Chakrapani S. A chimeric prokaryotic pentameric ligand-gated channel reveals distinct pathways of activation. ACTA ACUST UNITED AC 2016; 146:323-40. [PMID: 26415570 PMCID: PMC4586589 DOI: 10.1085/jgp.201511478] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Recent high resolution structures of several pentameric ligand-gated ion channels have provided unprecedented details of their molecular architecture. However, the conformational dynamics and structural rearrangements that underlie gating and allosteric modulation remain poorly understood. We used a combination of electrophysiology, double electron-electron resonance (DEER) spectroscopy, and x-ray crystallography to investigate activation mechanisms in a novel functional chimera with the extracellular domain (ECD) of amine-gated Erwinia chrysanthemi ligand-gated ion channel, which is activated by primary amines, and the transmembrane domain of Gloeobacter violaceus ligand-gated ion channel, which is activated by protons. We found that the chimera was independently gated by primary amines and by protons. The crystal structure of the chimera in its resting state, at pH 7.0 and in the absence of primary amines, revealed a closed-pore conformation and an ECD that is twisted with respect to the transmembrane region. Amine- and pH-induced conformational changes measured by DEER spectroscopy showed that the chimera exhibits a dual mode of gating that preserves the distinct conformational changes of the parent channels. Collectively, our findings shed light on both conserved and divergent features of gating mechanisms in this class of channels, and will facilitate the design of better allosteric modulators.
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Affiliation(s)
- Nicolaus Schmandt
- Department of Neuroscience, Department of Physiology and Biophysics, Department of Biochemistry, and Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106
| | - Phanindra Velisetty
- Department of Neuroscience, Department of Physiology and Biophysics, Department of Biochemistry, and Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106
| | - Sreevatsa V Chalamalasetti
- Department of Neuroscience, Department of Physiology and Biophysics, Department of Biochemistry, and Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106
| | - Richard A Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232
| | - Ross Bonner
- Department of Neuroscience, Department of Physiology and Biophysics, Department of Biochemistry, and Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106
| | - Lauren Talley
- Department of Neuroscience, Department of Physiology and Biophysics, Department of Biochemistry, and Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106
| | - Mark D Parker
- Department of Neuroscience, Department of Physiology and Biophysics, Department of Biochemistry, and Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232
| | - Vivien C Yee
- Department of Neuroscience, Department of Physiology and Biophysics, Department of Biochemistry, and Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106
| | - David T Lodowski
- Department of Neuroscience, Department of Physiology and Biophysics, Department of Biochemistry, and Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106
| | - Sudha Chakrapani
- Department of Neuroscience, Department of Physiology and Biophysics, Department of Biochemistry, and Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106 Department of Neuroscience, Department of Physiology and Biophysics, Department of Biochemistry, and Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106
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47
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Rossokhin AV, Zhorov BS. Side chain flexibility and the pore dimensions in the GABAA receptor. J Comput Aided Mol Des 2016; 30:559-67. [PMID: 27460059 DOI: 10.1007/s10822-016-9929-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 07/22/2016] [Indexed: 10/21/2022]
Abstract
Permeation of ions through open channels and their accessibility to pore-targeting drugs depend on the pore cross-sectional dimensions, which are known only for static X-ray and cryo-EM structures. Here, we have built homology models of the closed, open and desensitized α1β2γ2 GABAA receptor (GABAAR). The models are based, respectively, on the X-ray structure of α3 glycine receptor (α3 GlyR), cryo-EM structure of α1 GlyR and X-ray structure of β3 GABAAR. We employed Monte Carlo energy minimizations to explore how the pore lumen may increase due to repulsions of flexible side chains from a variable-diameter electroneutral atom (an expanding sphere) pulled through the pore. The expanding sphere computations predicted that the pore diameter averaged along the permeation pathway is larger by approximately 3 Å than that computed for the models with fixed sidechains. Our models predict three major pore constrictions located at the levels of -2', 9' and 20' residues. Residues around the -2' and 9' rings are known to form the desensitization and activation gates of GABAAR. Our computations predict that the 20' ring may also serve as GABAAR gate whose physiological role is unclear. The side chain flexibility of residues -2', 9' and 20' and hence the dimensions of the constrictions depend on the GABAAR functional state.
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Affiliation(s)
- Alexey V Rossokhin
- Research Center of Neurology, RAS, by-str. Obukha 5, Moscow, Russia, 105064.
| | - Boris S Zhorov
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.,Sechenov Institute of Evolutionary Physiology and Biochemistry, RAS, St. Petersburg, Russia
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48
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Marracino P, Castellani F, Vernier PT, Liberti M, Apollonio F. Geometrical Characterization of an Electropore from Water Positional Fluctuations. J Membr Biol 2016; 250:11-19. [PMID: 27435217 DOI: 10.1007/s00232-016-9917-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 07/06/2016] [Indexed: 11/30/2022]
Abstract
We present here a new method for calculating the radius of a transmembrane pore in a phospholipid bilayer. To compare size-related properties of pores in bilayers of various compositions, generated and maintained under different physical and chemical conditions, reference metrics are needed. Operational metrics can be associated with some observed behavior. For example, pore size can be defined by the largest object that will pass through the length of the pore. The novelty of the present approach resides in the characterization of electropore geometry via a statistical approach, based on essential dynamics rules. We define the pore size geometrically with an algorithm for determining the pore radius. In particular, we extract the radius from the tri-dimensional surface of a defined pore region. The method is applied to a pore formed in a phospholipid bilayer by application of an external electric field. Although the details described here are specific for lipid pores in molecular dynamics simulations, the method can be generalized for any kind of pores for which appropriate structural information is available.
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Affiliation(s)
- P Marracino
- Department of Information Engineering, Electronics, and Telecommunications, Sapienza University of Rome, Rome, Italy.
| | - F Castellani
- Frank Reidy Research Center for Bioelectrics, Old Dominion University, Norfolk, VA, 23508, USA.,Biomedical Engineering Institute, Frank Batten College of Engineering and Technology, Old Dominion University, Norfolk, VA, 23529, USA
| | - P T Vernier
- Frank Reidy Research Center for Bioelectrics, Old Dominion University, Norfolk, VA, 23508, USA
| | - M Liberti
- Department of Information Engineering, Electronics, and Telecommunications, Sapienza University of Rome, Rome, Italy
| | - F Apollonio
- Department of Information Engineering, Electronics, and Telecommunications, Sapienza University of Rome, Rome, Italy
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49
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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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50
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Pavelka A, Sebestova E, Kozlikova B, Brezovsky J, Sochor J, Damborsky J. CAVER: Algorithms for Analyzing Dynamics of Tunnels in Macromolecules. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2016; 13:505-517. [PMID: 27295634 DOI: 10.1109/tcbb.2015.2459680] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The biological function of a macromolecule often requires that a small molecule or ion is transported through its structure. The transport pathway often leads through void spaces in the structure. The properties of transport pathways change significantly in time; therefore, the analysis of a trajectory from molecular dynamics rather than of a single static structure is needed for understanding the function of pathways. The identification and analysis of transport pathways are challenging because of the high complexity and diversity of macromolecular shapes, the thermal motion of their atoms, and the large amount of conformations needed to properly describe conformational space of protein structure. In this paper, we describe the principles of the CAVER 3.0 algorithms for the identification and analysis of properties of transport pathways both in static and dynamic structures. Moreover, we introduce the improved clustering solution for finding tunnels in macromolecules, which is included in the latest CAVER 3.02 version. Voronoi diagrams are used to identify potential pathways in each snapshot of a molecular dynamics trajectory and clustering is then used to find the correspondence between tunnels from different snapshots. Furthermore, the geometrical properties of pathways and their evolution in time are computed and visualized.
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