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Gogovi GK, Silayi S, Shehu A. Computing the Structural Dynamics of RVFV L Protein Domain in Aqueous Glycerol Solutions. Biomolecules 2021; 11:biom11101427. [PMID: 34680060 PMCID: PMC8533350 DOI: 10.3390/biom11101427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/24/2021] [Accepted: 09/25/2021] [Indexed: 11/23/2022] Open
Abstract
Many biological and biotechnological processes are controlled by protein–protein and protein–solvent interactions. In order to understand, predict, and optimize such processes, it is important to understand how solvents affect protein structure during protein–solvent interactions. In this study, all-atom molecular dynamics are used to investigate the structural dynamics and energetic properties of a C-terminal domain of the Rift Valley Fever Virus L protein solvated in glycerol and aqueous glycerol solutions in different concentrations by molecular weight. The Generalized Amber Force Field is modified by including restrained electrostatic potential atomic charges for the glycerol molecules. The peptide is considered in detail by monitoring properties like the root-mean-squared deviation, root-mean-squared fluctuation, radius of gyration, hydrodynamic radius, end-to-end distance, solvent-accessible surface area, intra-potential energy, and solvent–peptide interaction energies for hundreds of nanoseconds. Secondary structure analysis is also performed to examine the extent of conformational drift for the individual helices and sheets. We predict that the peptide helices and sheets are maintained only when the modeling strategy considers the solvent with lower glycerol concentration. We also find that the solvent-peptide becomes more cohesive with decreasing glycerol concentrations. The density and radial distribution function of glycerol solvent calculated when modeled with the modified atomic charges show a very good agreement with experimental results and other simulations at 298.15K.
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Affiliation(s)
- Gideon K. Gogovi
- Department of Mathematics and Statistics, University of Houston—Downtown, Houston, TX 77054, USA
- Correspondence:
| | - Swabir Silayi
- Office of Research Computing, George Mason University, Fairfax, VA 22030, USA;
| | - Amarda Shehu
- Department of Computer Science, George Mason University, Fairfax, VA 22030, USA;
- Department of Bioengineering, George Mason University, Fairfax, VA 22030, USA
- School of Systems Biology, George Mason University, Fairfax, VA 22030, USA
- Center for Advancing Human-Machine Partnerships, George Mason University, Fairfax, VA 22030, USA
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2
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Choong YS, Lim YY, Soong JX, Savoo N, Guida C, Rhyman L, Ramracheya R, Ramasami P. Theoretical study of the interactions between peptide tyrosine tyrosine [PYY (1-36)], a newly identified modulator in type 2 diabetes pathophysiology, with receptors NPY1R and NPY4R. Hormones (Athens) 2021; 20:557-569. [PMID: 33782920 DOI: 10.1007/s42000-021-00278-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 02/10/2021] [Indexed: 11/30/2022]
Abstract
PURPOSE Diabetes mellitus is a common condition in the clinically obese. Bariatric surgery is one of the ways to put type 2 diabetes in remission. Recent findings propose the appetite-regulator peptide tyrosine tyrosine (PYY) as a therapeutic option for patients with type 2 diabetes. This novel gut hormone restores impaired insulin and glucagon secretion in pancreatic islets and is implicated in type 2 diabetes reversal after bariatric surgery. The current study elucidates the interactions between PYY and the NPY1R and NPY4R receptors using computational methods. METHODS Protein structure prediction, molecular docking simulation, and molecular dynamics (MD) simulation were performed to elucidate the interactions of PYY with NPY1R and NPY4R. RESULTS The predicted binding models of PYY-NPY receptors are in agreement with those described in the literature, although different interaction partners are presented for the C-terminal tail of PYY. Non-polar interactions are predicted to drive the formation of the protein complex. The calculated binding energies show that PYY has higher affinity for NPY4R (ΔGGBSA = -65.08 and ΔGPBSA = -87.62 kcal/mol) than for NPY1R (ΔGGBSA = -23.11 and ΔGPBSA = -50.56 kcal/mol). CONCLUSIONS Based on the constructed models, the binding conformations obtained from docking and MD simulation for both the PYY-NPY1R and PYY-NPY4R complexes provide a detailed map of possible interactions. The calculated binding energies show a higher affinity of PYY for NPY4R. These findings may help to understand the mechanisms behind the improvement of diabetes following bariatric surgery.
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Affiliation(s)
- Yee Siew Choong
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800, Penang, Malaysia.
| | - Yee Ying Lim
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Jia Xin Soong
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Nandini Savoo
- Computational Chemistry Group, Department of Chemistry, Faculty of Science, University of Mauritius, Réduit 80837, Mauritius
| | - Claudia Guida
- Oxford Centre for Diabetes, Endocrinology & Metabolism, University of Oxford, Oxford, OX3 7LJ, United Kingdom
| | - Lydia Rhyman
- Computational Chemistry Group, Department of Chemistry, Faculty of Science, University of Mauritius, Réduit 80837, Mauritius
- Department of Chemical Sciences, University of Johannesburg, Doornfontein, Johannesburg 2028, South Africa
| | - Reshma Ramracheya
- Oxford Centre for Diabetes, Endocrinology & Metabolism, University of Oxford, Oxford, OX3 7LJ, United Kingdom.
- Pharmaceutical Operations, Centre International de Dévelopment Pharmaceutique, BioPark Mauritius, Socota Phoenicia, Phoenix 73408, Mauritius.
| | - Ponnadurai Ramasami
- Computational Chemistry Group, Department of Chemistry, Faculty of Science, University of Mauritius, Réduit 80837, Mauritius.
- Department of Chemical Sciences, University of Johannesburg, Doornfontein, Johannesburg 2028, South Africa.
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Frigini EN, López Cascales JJ, Porasso RD. Influence of Lipid Composition on the Insertion Process of Glyphosate into Membranes: A Thermodynamic Study. J Phys Chem B 2021; 125:184-192. [PMID: 33375787 DOI: 10.1021/acs.jpcb.0c09561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this work, molecular dynamics simulations were applied to investigate the influence of lipid composition of the model membrane on the insertion of glyphosate (in its charged state, GLYP2-). The profiles of free energy, entropy and enthalpy were obtained through umbrella sampling calculations, for lipid bilayers composed by only 1,2-dipalmitoyl-sn-glycerol-3-phosphocholine (DPPC), only 1,2-dipalmitoyl-sn-glycerol-3-phosphoserine (DPPS) or a symmetric binary mixture of DPPC and DPPS. In general, the location, the values of minima and maxima of the free energy, and the trend of free energy profiles are influenced by the lipid composition of the lipid bilayer. The driving force in the glyphosate insertion process depends on the lipid composition of the membrane model. If the lipid bilayer is composed solely of DPPS or DPPC, GLYP2- insertion is driven by a favorable enthalpic change. However, if the membrane is composed of a mixture of both lipids, this process is driven by a favorable entropic change. In the lipid bilayer containing DPPS, the glyphosate was found to penetrate hydrated and coordinated with Na+ ions, in contrast to the pure zwitterionic lipid bilayer which penetrated only hydrated. This effect is independent of the concentration of sodium ions present in the bulk solution.
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Affiliation(s)
- Ezequiel N Frigini
- Instituto de Matemáticas Aplicada San Luis (IMASL), CONICET, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Avenue Ejército de los Andes 950, 5700 San Luis, Argentina
| | - J J López Cascales
- Universidad Politécnica de Cartagena, Grupo de Bioinformática y Macromoléculas (BioMac), Área de Química Física, Aulario II, Campus de Alfonso XIII, 30203 Cartagena, Murcia, Spain
| | - Rodolfo D Porasso
- Instituto de Matemáticas Aplicada San Luis (IMASL), CONICET, Facultad de Ciencias Física Matemáticas y Naturales, Universidad Nacional de San Luis, Avenue Ejército de los Andes 950, 5700 San Luis, Argentina
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4
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Abstract
Molecular dynamics (MD) simulations have become increasingly useful in the modern drug development process. In this review, we give a broad overview of the current application possibilities of MD in drug discovery and pharmaceutical development. Starting from the target validation step of the drug development process, we give several examples of how MD studies can give important insights into the dynamics and function of identified drug targets such as sirtuins, RAS proteins, or intrinsically disordered proteins. The role of MD in antibody design is also reviewed. In the lead discovery and lead optimization phases, MD facilitates the evaluation of the binding energetics and kinetics of the ligand-receptor interactions, therefore guiding the choice of the best candidate molecules for further development. The importance of considering the biological lipid bilayer environment in the MD simulations of membrane proteins is also discussed, using G-protein coupled receptors and ion channels as well as the drug-metabolizing cytochrome P450 enzymes as relevant examples. Lastly, we discuss the emerging role of MD simulations in facilitating the pharmaceutical formulation development of drugs and candidate drugs. Specifically, we look at how MD can be used in studying the crystalline and amorphous solids, the stability of amorphous drug or drug-polymer formulations, and drug solubility. Moreover, since nanoparticle drug formulations are of great interest in the field of drug delivery research, different applications of nano-particle simulations are also briefly summarized using multiple recent studies as examples. In the future, the role of MD simulations in facilitating the drug development process is likely to grow substantially with the increasing computer power and advancements in the development of force fields and enhanced MD methodologies.
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Abstract
Comprehensive data about the composition and structure of cellular components have enabled the construction of quantitative whole-cell models. While kinetic network-type models have been established, it is also becoming possible to build physical, molecular-level models of cellular environments. This review outlines challenges in constructing and simulating such models and discusses near- and long-term opportunities for developing physical whole-cell models that can connect molecular structure with biological function.
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Affiliation(s)
- Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA;
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
| | - Yuji Sugita
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
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Muller MP, Jiang T, Sun C, Lihan M, Pant S, Mahinthichaichan P, Trifan A, Tajkhorshid E. Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation. Chem Rev 2019; 119:6086-6161. [PMID: 30978005 PMCID: PMC6506392 DOI: 10.1021/acs.chemrev.8b00608] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The cellular membrane constitutes one of the most fundamental compartments of a living cell, where key processes such as selective transport of material and exchange of information between the cell and its environment are mediated by proteins that are closely associated with the membrane. The heterogeneity of lipid composition of biological membranes and the effect of lipid molecules on the structure, dynamics, and function of membrane proteins are now widely recognized. Characterization of these functionally important lipid-protein interactions with experimental techniques is however still prohibitively challenging. Molecular dynamics (MD) simulations offer a powerful complementary approach with sufficient temporal and spatial resolutions to gain atomic-level structural information and energetics on lipid-protein interactions. In this review, we aim to provide a broad survey of MD simulations focusing on exploring lipid-protein interactions and characterizing lipid-modulated protein structure and dynamics that have been successful in providing novel insight into the mechanism of membrane protein function.
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Affiliation(s)
- Melanie P. Muller
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tao Jiang
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chang Sun
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Muyun Lihan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shashank Pant
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Paween Mahinthichaichan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Anda Trifan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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7
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Suh Y, Pham Q, Shao B, Won Y. The Control of Colloidal Grain Boundaries through Evaporative Vertical Self-Assembly. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1804523. [PMID: 30730084 DOI: 10.1002/smll.201804523] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 12/29/2018] [Indexed: 06/09/2023]
Abstract
Self-assembly continuously gains attention as an excellent method to create novel nanoscale structures with a wide range of applications in photonics, optoelectronics, biomedical engineering, and heat transfer applications. However, self-assembly is governed by a diversity of complex interparticle forces that cause fabricating defectless large scale (>1 cm) colloidal crystals, or opals, to be a daunting challenge. Despite numerous efforts to find an optimal method that offers the perfect colloidal crystal by minimizing defects, it has been difficult to provide physical interpretations that govern the development of defects such as grain boundaries. This study reports the control over grain domains and intentional defect characteristics that develop during evaporative vertical deposition. The degree of particle crystallinity and evaporation conditions is shown to govern the grain domain characteristics, such as shapes and sizes. In particular, the grains fabricated with 300 and 600 nm sphere diameters can be tuned into single-column structures exceeding ≈1 mm by elevating heating temperature up to 93 °C. The understanding of self-assembly physics presented in this work will enable the fabrication of novel self-assembled structures with high periodicity and offer fundamental groundworks for developing large-scale crack-free structures.
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Affiliation(s)
- Youngjoon Suh
- Department of Mechanical and Aerospace Engineering, University of California, 5200 Engineering Hall Irvine, Irvine, CA, 92697-2700, USA
| | - Quang Pham
- Department of Mechanical and Aerospace Engineering, University of California, 5200 Engineering Hall Irvine, Irvine, CA, 92697-2700, USA
| | - Bowen Shao
- Department of Mechanical and Aerospace Engineering, University of California, 5200 Engineering Hall Irvine, Irvine, CA, 92697-2700, USA
| | - Yoonjin Won
- Department of Mechanical and Aerospace Engineering, University of California, 5200 Engineering Hall Irvine, Irvine, CA, 92697-2700, USA
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8
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Huber RG, Carpenter TS, Dube N, Holdbrook DA, Ingólfsson HI, Irvine WA, Marzinek JK, Samsudin F, Allison JR, Khalid S, Bond PJ. Multiscale Modeling and Simulation Approaches to Lipid-Protein Interactions. Methods Mol Biol 2019; 2003:1-30. [PMID: 31218611 DOI: 10.1007/978-1-4939-9512-7_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Lipid membranes play a crucial role in living systems by compartmentalizing biological processes and forming a barrier between these processes and the environment. Naturally, a large apparatus of biomolecules is responsible for construction, maintenance, transport, and degradation of these lipid barriers. Additional classes of biomolecules are tasked with transport of specific substances or transduction of signals from the environment across lipid membranes. In this article, we intend to describe a set of techniques that enable one to build accurate models of lipid systems and their associated proteins, and to simulate their dynamics over a variety of time and length scales. We discuss the methods and challenges that allow us to derive structural, mechanistic, and thermodynamic information from these models. We also show how these models have recently been applied in research to study some of the most complex lipid-protein systems to date, including bacterial and viral envelopes, neuronal membranes, and mammalian signaling systems.
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Affiliation(s)
- Roland G Huber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Timothy S Carpenter
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Namita Dube
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Daniel A Holdbrook
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Helgi I Ingólfsson
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - William A Irvine
- Centre for Theoretical Chemistry and Physics, Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - Jan K Marzinek
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | | | - Jane R Allison
- School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
| | - Syma Khalid
- School of Chemistry, University of Southampton, Southampton, UK
| | - Peter J Bond
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
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9
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Arnott PM, Joshi H, Aksimentiev A, Howorka S. Dynamic Interactions between Lipid-Tethered DNA and Phospholipid Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:15084-15092. [PMID: 30350681 PMCID: PMC6458106 DOI: 10.1021/acs.langmuir.8b02271] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Lipid-anchored DNA can attach functional cargo to bilayer membranes in DNA nanotechnology, synthetic biology, and cell biology research. To optimize DNA anchoring, an understanding of DNA-membrane interactions in terms of binding strength, extent, and structural dynamics is required. Here we use experiments and molecular dynamics (MD) simulations to determine how the membrane binding of cholesterol-modified DNA depends on electrostatic and steric factors involving the lipid headgroup charge, duplexed or single-stranded DNA, and the buffer composition. The experiments distinguish between free and membrane vesicle-bound DNA and thereby reveal the surface density of anchored DNA and its binding affinity, something which had previously not been known. The Kd values range from 8.5 ± 4.9 to 466 ± 134 μM whereby negatively charged headgroups led to weak binding due to the electrostatic repulsion with respect to the negatively charged DNA. Atomistic MD simulations explain the findings and elucidate the dynamic nature of anchored DNA such as the mushroom-like conformation of single-stranded DNA hovering over the bilayer surface in contrast to a straight-up conformation of double-stranded DNA. The biophysical insight into the binding strength to membranes as well as the molecular accessibility of DNA for hybridization to molecular cargo is expected to facilitate the creation of biomimetic DNA versions of natural membrane nanopores and cytoskeletons for research and nanobiotechnology.
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Affiliation(s)
- Patrick M Arnott
- Department of Chemistry, Institute of Structural and Molecular Biology , University College London , London WC1H 0AJ , United Kingdom
| | - Himanshu Joshi
- Department of Physics, and Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Aleksei Aksimentiev
- Department of Physics, and Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Stefan Howorka
- Department of Chemistry, Institute of Structural and Molecular Biology , University College London , London WC1H 0AJ , United Kingdom
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10
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Frigini EN, López Cascales JJ, Porasso RD. Molecular dynamics simulations of glyphosate in a DPPC lipid bilayer. Chem Phys Lipids 2018; 213:111-117. [PMID: 29684323 DOI: 10.1016/j.chemphyslip.2018.04.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 04/13/2018] [Accepted: 04/13/2018] [Indexed: 11/26/2022]
Abstract
Extensive molecular dynamics simulations have been performed to study the effect of glyphosate (in their neutral and charged forms, GLYP and GLYP2-, respectively) on fully hydrated DiPalmitoylPhosphatidylCholine (DPPC) lipid bilayer. First, we calculated the free energy profile (using the Umbrella Sampling technique) for both states of charge of glyphosate. The minimum value for the free energy for GLYP is ∼-60 kJ mol-1 located at z = ±1.7 nm (from the lipid bilayer center), and there is almost no maximum at the center of the lipid bilayer. By contrast, the minimum for GLYP2- is ∼-35 kJ mol-1 located at z = ± 1.4 nm (from the lipid bilayer center), and the maximum reaches ∼35 kJ mol-1 at the center of the lipid bilayer. Then, different lipid bilayer properties were analyzed for different glyphosate:lipid (G:L) ratios. The mean area per lipid was slightly affected, increasing only 5% (in the presence of glyphosate at high concentrations), which is in agreement with the slight decrease in deuterium order parameters. As for the thickness of the bilayer, it is observed that the state of charge produces opposite effects. On one hand, the neutral state produces an increase in the thickness of the lipid bilayer; on the other, the charged form produces a decrease in the thickness, which not depend linearly on the G:L ratios, either. The orientation of the DPPC head groups is practically unaffected throughout the range of the G:L ratios studied. Finally, the mobility of the lipids of the bilayer is strongly affected by the presence of glyphosate, considerably increasing its lateral diffusion coefficient noteworthy (one order of magnitude), with increasing G:L ratio.
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Affiliation(s)
- Ezequiel N Frigini
- Instituto de Matemática Aplicada San Luis, IMASL, Universidad Nacional de San Luis and CONICET, Ejército de los Andes 950, D5700HHW San Luis, Argentina
| | - J J López Cascales
- Universidad Politécnica de Cartagena, Grupo de Bioinformática y Macromoléculas (BioMac), Área de Química Física, Aulario II, Campus de Alfonso XIII, 30203 Cartagena, Murcia, Spain
| | - Rodolfo D Porasso
- Instituto de Matemática Aplicada San Luis, IMASL, Universidad Nacional de San Luis and CONICET, Ejército de los Andes 950, D5700HHW San Luis, Argentina.
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11
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Folding a viral peptide in different membrane environments: pathway and sampling analyses. J Biol Phys 2018; 44:195-209. [PMID: 29644513 DOI: 10.1007/s10867-018-9490-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 03/16/2018] [Indexed: 10/17/2022] Open
Abstract
Flock House virus (FHV) is a well-characterized model system to study infection mechanisms in non-enveloped viruses. A key stage of the infection cycle is the disruption of the endosomal membrane by a component of the FHV capsid, the membrane active γ peptide. In this study, we perform all-atom molecular dynamics simulations of the 21 N-terminal residues of the γ peptide interacting with membranes of differing compositions. We carry out umbrella sampling calculations to study the folding of the peptide to a helical state in homogenous and heterogeneous membranes consisting of neutral and anionic lipids. From the trajectory data, we evaluate folding energetics and dissect the mechanism of folding in the different membrane environments. We conclude the study by analyzing the extent of configurational sampling by performing time-lagged independent component analysis.
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12
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Mamatkulov S, Schwierz N. Force fields for monovalent and divalent metal cations in TIP3P water based on thermodynamic and kinetic properties. J Chem Phys 2018; 148:074504. [DOI: 10.1063/1.5017694] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Shavkat Mamatkulov
- Department of Physics, The Centre of Higher Technologies, Tashkent, Uzbekistan
| | - Nadine Schwierz
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
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13
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Kashefolgheta S, Vila Verde A. Developing force fields when experimental data is sparse: AMBER/GAFF-compatible parameters for inorganic and alkyl oxoanions. Phys Chem Chem Phys 2018; 19:20593-20607. [PMID: 28731091 DOI: 10.1039/c7cp02557b] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We present a set of Lennard-Jones parameters for classical, all-atom models of acetate and various alkylated and non-alkylated forms of sulfate, sulfonate and phosphate ions, optimized to reproduce their interactions with water and with the physiologically relevant sodium, ammonium and methylammonium cations. The parameters are internally consistent and are fully compatible with the Generalized Amber Force Field (GAFF), the AMBER force field for proteins, the accompanying TIP3P water model and the sodium model of Joung and Cheatham. The parameters were developed primarily relying on experimental information - hydration free energies and solution activity derivatives at 0.5 m concentration - with ab initio, gas phase calculations being used for the cases where experimental information is missing. The ab initio parameterization scheme presented here is distinct from other approaches because it explicitly connects gas phase binding energies to intermolecular interactions in solution. We demonstrate that the original GAFF/AMBER parameters often overestimate anion-cation interactions, leading to an excessive number of contact ion pairs in solutions of carboxylate ions, and to aggregation in solutions of divalent ions. GAFF/AMBER parameters lead to excessive numbers of salt bridges in proteins and of contact ion pairs between sodium and acidic protein groups, issues that are resolved by using the optimized parameters presented here.
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Affiliation(s)
- Sadra Kashefolgheta
- Department of Theory & Bio-systems, Max Planck Institute for Colloids and Interfaces, Science Park, Potsdam 14476, Germany.
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14
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De S, C. H. R, Thamleena A. H, Joseph A, Ben A, V. U. K. Roles of different amino-acid residues towards binding and selective transport of K+ through KcsA K+-ion channel. Phys Chem Chem Phys 2018; 20:17517-17529. [DOI: 10.1039/c8cp01282b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Each amino acid in the selectivity filter plays a distinct role towards binding and transport of K+ ion through KcsA.
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Affiliation(s)
- Susmita De
- Department of Applied Chemistry
- Cochin University of Science and Technology
- Trikakkara
- Kochi
- India – 682 022
| | - Rinsha C. H.
- Theoretical and Computational Chemistry Laboratory
- Department of Chemistry
- National Institute of Technology Calicut
- Kozhikode
- India – 673 601
| | - Hanna Thamleena A.
- Theoretical and Computational Chemistry Laboratory
- Department of Chemistry
- National Institute of Technology Calicut
- Kozhikode
- India – 673 601
| | - Annu Joseph
- Theoretical and Computational Chemistry Laboratory
- Department of Chemistry
- National Institute of Technology Calicut
- Kozhikode
- India – 673 601
| | - Anju Ben
- Theoretical and Computational Chemistry Laboratory
- Department of Chemistry
- National Institute of Technology Calicut
- Kozhikode
- India – 673 601
| | - Krishnapriya V. U.
- Theoretical and Computational Chemistry Laboratory
- Department of Chemistry
- National Institute of Technology Calicut
- Kozhikode
- India – 673 601
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15
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Singh A, Vanga SK, Orsat V, Raghavan V. Application of molecular dynamic simulation to study food proteins: A review. Crit Rev Food Sci Nutr 2017; 58:2779-2789. [DOI: 10.1080/10408398.2017.1341864] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Ashutosh Singh
- School of Engineering, University of Guelph, Guelph, Ontario, Canada
| | - Sai Kranthi Vanga
- Faculty of Agriculture and Environmental Studies, Department of Bioresource Engineering, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Valerie Orsat
- Faculty of Agriculture and Environmental Studies, Department of Bioresource Engineering, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Vijaya Raghavan
- Faculty of Agriculture and Environmental Studies, Department of Bioresource Engineering, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
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16
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Huber RG, Marzinek JK, Holdbrook DA, Bond PJ. Multiscale molecular dynamics simulation approaches to the structure and dynamics of viruses. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 128:121-132. [DOI: 10.1016/j.pbiomolbio.2016.09.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 09/06/2016] [Accepted: 09/27/2016] [Indexed: 12/15/2022]
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17
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Iacovelli F, Tucci FG, Macari G, Falconi M. Multiple molecular dynamics simulations of human LOX-1 and Trp150Ala mutant reveal the structural determinants causing the full deactivation of the receptor. Proteins 2017; 85:1902-1912. [DOI: 10.1002/prot.25344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 06/21/2017] [Accepted: 06/23/2017] [Indexed: 11/06/2022]
Affiliation(s)
| | | | - Gabriele Macari
- Department of Biology; University of Rome “Tor Vergata”; Rome Italy
| | - Mattia Falconi
- Department of Biology; University of Rome “Tor Vergata”; Rome Italy
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18
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Yellapu NK, Gopal J, Kasinathan G, Purushothaman J. Molecular modelling studies of kdr mutations in voltage gated sodium channel revealed significant conformational variations contributing to insecticide resistance. J Biomol Struct Dyn 2017; 36:2058-2069. [PMID: 28608751 DOI: 10.1080/07391102.2017.1341338] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Voltage gated sodium channels (VGSC) of mosquito vectors are the primary targets of dichlorodiphenyltrichloroethane (DDT) and other synthetic pyrethroids used in public health programmes. The knockdown resistant (kdr) mutations in VGSC are associated with the insecticide resistance especially in Anophelines. The present study is aimed to emphasize and demarcate the impact of three kdr-mutations such as L1014S, L1014F and L1014H on insecticide resistance. The membrane model of sodium transport domain of VGSC (STD-VGSC) was constructed using de novo approach based on domain and trans-membrane predictions. The comparative molecular modelling studies of wild type and mutant models of STD-VGSC revealed that L1014F mutant was observed to be near native to the wild type model in all the respects, but, L1014S and L1014H mutations showed drastic variations in the energy levels, root mean square fluctuations (RMSF) that resulted in conformational variations. The predicted binding sites also showed variable cavity volumes and RMSF in L1014S and L1014H mutants. Further, DDT also found be bound in near native manner to wild type in L1014F mutant and with variable orientation and affinities in L1014S and L1014H mutants. The variations and fluctuations observed in mutant structures explained that each mutation has its specific impact on the conformation of VGSC and its binding with DDT. The study provides new insights into the structure-function-correlations of mutant STD-VGSC structures and demonstrates the role and effects of kdr mutations on insecticide resistance in mosquito vectors.
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Affiliation(s)
- Nanda Kumar Yellapu
- a Biomedical Informatics Centre, Vector Control Research Centre, Indian Council of Medical Research , Puducherry 605006 , India
| | - Jeyakodi Gopal
- a Biomedical Informatics Centre, Vector Control Research Centre, Indian Council of Medical Research , Puducherry 605006 , India
| | - Gunasekaran Kasinathan
- a Biomedical Informatics Centre, Vector Control Research Centre, Indian Council of Medical Research , Puducherry 605006 , India
| | - Jambulingam Purushothaman
- a Biomedical Informatics Centre, Vector Control Research Centre, Indian Council of Medical Research , Puducherry 605006 , India
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19
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Jafari M, Mehrnejad F, Aghdami R, Chaparzadeh N, Razaghi Moghadam Kashani Z, Doustdar F. Identification of the Crucial Residues in the Early Insertion of Pardaxin into Different Phospholipid Bilayers. J Chem Inf Model 2017; 57:929-941. [DOI: 10.1021/acs.jcim.6b00693] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Majid Jafari
- Department of Life Sciences Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran 14395-1561, Iran
| | - Faramarz Mehrnejad
- Department of Life Sciences Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran 14395-1561, Iran
- School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran 19395-5746, Iran
| | - Raheleh Aghdami
- Department of Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz 53714-161, Iran
| | - Nader Chaparzadeh
- Department of Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz 53714-161, Iran
| | - Zahra Razaghi Moghadam Kashani
- Department of Life Sciences Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran 14395-1561, Iran
| | - Farahnoosh Doustdar
- Department of Microbiology, Faculty of
Medicine, Shahid Beheshti University of Medical Sciences, Tehran 19839-63113, Iran
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20
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Yellapu NK. Molecular Modelling, Dynamics, and Docking of Membrane Proteins. PHARMACEUTICAL SCIENCES 2017. [DOI: 10.4018/978-1-5225-1762-7.ch029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Computational tools and techniques are now most popular and promising to progress the research at rapid rate. Molecular modelling studies contribute their maximum role in wide variety of disciplines especially in proteomics and drug discovery strategies. Molecular dynamics and molecular docking algorithms are now became an essential part in daily research activities of every laboratory throughout the world. These strategies are now well established and standardised to study any specific protein of interest and drug molecule. But still there exist considerable drawbacks in a special concern with membrane proteins as the presently available tools and methods cannot be applied directly to them. Modelling, dynamics and docking studies of membrane proteins need a special care and attention as several challenges are to be crossed with an intensive care to produce a reliable result. This chapter is aimed to discuss such challenges and solutions to handle membrane proteins.
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21
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Zhu Z, Sheng N, Fang H, Wan R. Colored spectrum characteristics of thermal noise on the molecular scale. Phys Chem Chem Phys 2016; 18:30189-30195. [PMID: 27779258 DOI: 10.1039/c6cp04433f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Thermal noise is of fundamental importance to many processes. Traditionally, thermal noise has been treated as white noise on the macroscopic scale. Using molecular dynamics simulations and power spectrum analysis, we show that the thermal noise of solute molecules in water is non-white on the molecular scale, which is in contrast to the conventional theory. In the frequency domain from 2 × 1011 Hz to 1013 Hz, the power spectrum of thermal noise for polar solute molecules resembles the spectrum of 1/f noise. The power spectrum of thermal noise for non-polar solute molecules deviates only slightly from the spectrum of white noise. The key to this phenomenon is the existence of hydrogen bonds between polar solute molecules and solvent water molecules. Furthermore, for polar solute molecules, the degree of power spectrum deviation from that of white noise is associated with the average lifetime of the hydrogen bonds between the solute and the solvent molecules.
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Affiliation(s)
- Zhi Zhu
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China. and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nan Sheng
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China.
| | - Haiping Fang
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China.
| | - Rongzheng Wan
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China.
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22
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Huang Y, Chen W, Wallace JA, Shen J. All-Atom Continuous Constant pH Molecular Dynamics With Particle Mesh Ewald and Titratable Water. J Chem Theory Comput 2016; 12:5411-5421. [PMID: 27709966 DOI: 10.1021/acs.jctc.6b00552] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Development of a pH stat to properly control solution pH in biomolecular simulations has been a long-standing goal in the community. Toward this goal recent years have witnessed the emergence of the so-called constant pH molecular dynamics methods. However, the accuracy and generality of these methods have been hampered by the use of implicit-solvent models or truncation-based electrostatic schemes. Here we report the implementation of the particle mesh Ewald (PME) scheme into the all-atom continuous constant pH molecular dynamics (CpHMD) method, enabling CpHMD to be performed with a standard MD engine at a fractional added computational cost. We demonstrate the performance using pH replica-exchange CpHMD simulations with titratable water for a stringent test set of proteins, HP36, BBL, HEWL, and SNase. With the sampling time of 10 ns per replica, most pKa's are converged, yielding the average absolute and root-mean-square deviations of 0.61 and 0.77, respectively, from experiment. Linear regression of the calculated vs experimental pKa shifts gives a correlation coefficient of 0.79, a slope of 1, and an intercept near 0. Analysis reveals inadequate sampling of structure relaxation accompanying a protonation-state switch as a major source of the remaining errors, which are reduced as simulation prolongs. These data suggest PME-based CpHMD can be used as a general tool for pH-controlled simulations of macromolecular systems in various environments, enabling atomic insights into pH-dependent phenomena involving not only soluble proteins but also transmembrane proteins, nucleic acids, surfactants, and polysaccharides.
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Affiliation(s)
- Yandong Huang
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy , Baltimore, Maryland 21201, United States
| | - Wei Chen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy , Baltimore, Maryland 21201, United States
| | - Jason A Wallace
- University of Oklahoma College of Dentistry , Oklahoma City, Oklahoma 73117, United States
| | - Jana Shen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy , Baltimore, Maryland 21201, United States
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23
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Structure and dynamics of a free aquaporin (AQP1) by a coarse-grained Monte Carlo simulation. Struct Chem 2016. [DOI: 10.1007/s11224-016-0836-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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24
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Evaluation of diacylphospholipids as boundary lipids for bacteriorhodopsin from structural and functional aspects. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2106-2115. [DOI: 10.1016/j.bbamem.2016.06.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 06/08/2016] [Accepted: 06/10/2016] [Indexed: 11/18/2022]
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25
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Conserved methionine dictates substrate preference in Nramp-family divalent metal transporters. Proc Natl Acad Sci U S A 2016; 113:10310-5. [PMID: 27573840 DOI: 10.1073/pnas.1607734113] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Natural resistance-associated macrophage protein (Nramp) family transporters catalyze uptake of essential divalent transition metals like iron and manganese. To discriminate against abundant competitors, the Nramp metal-binding site should favor softer transition metals, which interact either covalently or ionically with coordinating molecules, over hard calcium and magnesium, which interact mainly ionically. The metal-binding site contains an unusual, but conserved, methionine, and its sulfur coordinates transition metal substrates, suggesting a vital role in their transport. Using a bacterial Nramp model system, we show that, surprisingly, this conserved methionine is dispensable for transport of the physiological manganese substrate and similar divalents iron and cobalt, with several small amino acid replacements still enabling robust uptake. Moreover, the methionine sulfur's presence makes the toxic metal cadmium a preferred substrate. However, a methionine-to-alanine substitution enables transport of calcium and magnesium. Thus, the putative evolutionary pressure to maintain the Nramp metal-binding methionine likely exists because it-more effectively than any other amino acid-increases selectivity for low-abundance transition metal transport in the presence of high-abundance divalents like calcium and magnesium.
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26
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Parkin J, Chavent M, Khalid S. Molecular Simulations of Gram-Negative Bacterial Membranes: A Vignette of Some Recent Successes. Biophys J 2016; 109:461-8. [PMID: 26244728 DOI: 10.1016/j.bpj.2015.06.050] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 06/09/2015] [Accepted: 06/24/2015] [Indexed: 01/05/2023] Open
Abstract
In the following review we use recent examples from the literature to discuss progress in the area of atomistic and coarse-grained molecular dynamics simulations of selected bacterial membranes and proteins, with a particular focus on Gram-negative bacteria. As structural biology continues to provide increasingly high-resolution data on the proteins that reside within these membranes, simulations have an important role to play in linking these data with the dynamical behavior and function of these proteins. In particular, in the last few years there has been significant progress in addressing the issue of biochemical complexity of bacterial membranes such that the heterogeneity of the lipid and protein components of these membranes are now being incorporated into molecular-level models. Thus, in future we can look forward to complementary data from structural biology and molecular simulations combining to provide key details of structure-dynamics-function relationships in bacterial membranes.
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Affiliation(s)
- Jamie Parkin
- School of Chemistry, University of Southampton, Southampton, UK
| | | | - Syma Khalid
- School of Chemistry, University of Southampton, Southampton, UK.
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27
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Sampath B, Sankaranarayanan K. Glu106 targeted inhibitors of ORAI1 as potential Ca 2+ release-activated Ca 2+ (CRAC) channel blockers - molecular modeling and docking studies. J Recept Signal Transduct Res 2016; 36:572-585. [PMID: 26895524 DOI: 10.3109/10799893.2016.1141956] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Calcium release-activated calcium modulator 1(ORAI1) is an integral component of the calcium release-activated calcium channel (CRAC) channel complex and plays a central role in regulating Ca2 + concentrations in T-lymphocytes. It is critical for many physiological processes, including cell-proliferation, cytokine production and activation of the immune system. Loss of ORAI1 function is linked with rheumatoid arthritis (RA) and hence pharmacological blockers of ORAI1 could be potential therapeutic agents for the treatment of RA. In this study, we have used a high-throughput screening approach to inhibit the binding of Ca2+ toward ORAI1 and the interactions are verified through induced fit docking. The results hint that these compounds act by possibly binding with, and thereby blocking Ca2+-binding with ORAI1 (E106). The molecular dynamics (MD) simulations shows strong support toward the hit compounds by showing the ligand potency throughout the simulation timescale of 30 ns. We have thus identified a novel class of highly stable, potential lead compounds that directly bind with the selectivity filter region E106 and block Ca2+ binding on ORAI1. This resulting alteration in the pore geometry of ORAI1 due to the strong blocking mechanism of lead compounds will greatly diminish its function and the downstream activities that result from the same including decreased production of cytokines in autoimmune disorders. This study may lay the foundation for finding novel lead compounds for clinical trials that could positively modulate the course of autoimmune disorders with ORAI1 as its specific target.
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Affiliation(s)
- Bhuvaneshwari Sampath
- a Ion Channel Biology Laboratory, AU-KBC Research Centre, Madras Institute of Technology, Anna University , Chennai , Tamil Nadu , India
| | - Kavitha Sankaranarayanan
- a Ion Channel Biology Laboratory, AU-KBC Research Centre, Madras Institute of Technology, Anna University , Chennai , Tamil Nadu , India
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28
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Pavlova A, Hwang H, Lundquist K, Balusek C, Gumbart JC. Living on the edge: Simulations of bacterial outer-membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1753-9. [PMID: 26826270 DOI: 10.1016/j.bbamem.2016.01.020] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 01/19/2016] [Accepted: 01/20/2016] [Indexed: 01/06/2023]
Abstract
Gram-negative bacteria are distinguished in part by a second, outer membrane surrounding them. This membrane is distinct from others, possessing an outer leaflet composed not of typical phospholipids but rather large, highly charged molecules known as lipopolysaccharides. Therefore, modeling the structure and dynamics of proteins embedded in the outer membrane requires careful consideration of their native environment. In this review, we examine how simulations of such outer-membrane proteins have evolved over the last two decades, culminating most recently in detailed, highly accurate atomistic models of the outer membrane. We also draw attention to how the simulations have coupled with experiments to produce novel insights unattainable through a single approach. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
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Affiliation(s)
- Anna Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Hyea Hwang
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Karl Lundquist
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Curtis Balusek
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, United States.
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29
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Mustafa G, Nandekar PP, Yu X, Wade RC. On the application of the MARTINI coarse-grained model to immersion of a protein in a phospholipid bilayer. J Chem Phys 2015; 143:243139. [DOI: 10.1063/1.4936909] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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30
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Rajapaksha SP, Pal N, Zheng D, Lu HP. Protein-fluctuation-induced water-pore formation in ion channel voltage-sensor translocation across a lipid bilayer membrane. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:052719. [PMID: 26651735 DOI: 10.1103/physreve.92.052719] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Indexed: 06/05/2023]
Abstract
We have applied a combined fluorescence microscopy and single-ion-channel electric current recording approach, correlating with molecular dynamics (MD) simulations, to study the mechanism of voltage-sensor domain translocation across a lipid bilayer. We use the colicin Ia ion channel as a model system, and our experimental and simulation results show the following: (1) The open-close activity of an activated colicin Ia is not necessarily sensitive to the amplitude of the applied cross-membrane voltage when the cross-membrane voltage is around the resting potential of excitable membranes; and (2) there is a significant probability that the activation of colicin Ia occurs by forming a transient and fluctuating water pore of ∼15 Å diameter in the lipid bilayer membrane. The location of the water-pore formation is nonrandom and highly specific, right at the insertion site of colicin Ia charged residues in the lipid bilayer membrane, and the formation is intrinsically associated with the polypeptide conformational fluctuations and solvation dynamics. Our results suggest an interesting mechanistic pathway for voltage-sensitive ion channel activation, and specifically for translocation of charged polypeptide chains across the lipid membrane under a transmembrane electric field: the charged polypeptide domain facilitates the formation of hydrophilic water pore in the membrane and diffuses through the hydrophilic pathway across the membrane; i.e., the charged polypeptide chain can cross a lipid membrane without entering into the hydrophobic core of the lipid membrane but entirely through the aqueous and hydrophilic environment to achieve a cross-membrane translocation. This mechanism sheds light on the intensive and fundamental debate on how a hydrophilic and charged peptide domain diffuses across the biologically inaccessible high-energy barrier of the hydrophobic core of a lipid bilayer: The peptide domain does not need to cross the hydrophobic core to move across a lipid bilayer.
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Affiliation(s)
- Suneth P Rajapaksha
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, USA
| | - Nibedita Pal
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, USA
| | - Desheng Zheng
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, USA
| | - H Peter Lu
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, USA
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31
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Camley BA, Brown FLH. Fluctuating hydrodynamics of multicomponent membranes with embedded proteins. J Chem Phys 2015; 141:075103. [PMID: 25149817 DOI: 10.1063/1.4892802] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A simulation method for the dynamics of inhomogeneous lipid bilayer membranes is presented. The membrane is treated using stochastic Saffman-Delbrück hydrodynamics, coupled to a phase-field description of lipid composition and discrete membrane proteins. Multiple applications are considered to validate and parameterize the model. The dynamics of membrane composition fluctuations above the critical point and phase separation dynamics below the critical point are studied in some detail, including the effects of adding proteins to the mixture.
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Affiliation(s)
- Brian A Camley
- Department of Physics and Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, California 92093, USA
| | - Frank L H Brown
- Department of Physics, University of California, Santa Barbara, Santa Barbara, California 93106, USA
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32
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Pluhackova K, Böckmann RA. Biomembranes in atomistic and coarse-grained simulations. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015. [PMID: 26194872 DOI: 10.1088/0953-8984/27/32/323103] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The architecture of biological membranes is tightly coupled to the localization, organization, and function of membrane proteins. The organelle-specific distribution of lipids allows for the formation of functional microdomains (also called rafts) that facilitate the segregation and aggregation of membrane proteins and thus shape their function. Molecular dynamics simulations enable to directly access the formation, structure, and dynamics of membrane microdomains at the molecular scale and the specific interactions among lipids and proteins on timescales from picoseconds to microseconds. This review focuses on the latest developments of biomembrane force fields for both atomistic and coarse-grained molecular dynamics (MD) simulations, and the different levels of coarsening of biomolecular structures. It also briefly introduces scale-bridging methods applicable to biomembrane studies, and highlights selected recent applications.
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Affiliation(s)
- Kristyna Pluhackova
- Computational Biology, Department of Biology, Friedrich-Alexander Universität Erlangen-Nürnberg, Staudtstr. 5, 91058 Erlangen, Germany
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33
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Noruzifar E, Camley BA, Brown FLH. Calculating hydrodynamic interactions for membrane-embedded objects. J Chem Phys 2015; 141:124711. [PMID: 25273465 DOI: 10.1063/1.4896180] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A recently introduced numerical scheme for calculating self-diffusion coefficients of solid objects embedded in lipid bilayer membranes is extended to enable calculation of hydrodynamic interactions between multiple objects. The method is used to validate recent analytical predictions by Oppenheimer and Diamant [Biophys. J. 96, 3041 2009] related to the coupled diffusion of membrane embedded proteins and is shown to converge to known near-field lubrication results as objects closely approach one another; however, the present methodology also applies outside of the limiting regimes where analytical results are available. Multiple different examples involving pairs of disk-like objects with various constraints imposed on their relative motions demonstrate the importance of hydrodynamic interactions in the dynamics of proteins and lipid domains on membrane surfaces. It is demonstrated that the relative change in self-diffusion of a membrane embedded object upon perturbation by a similar proximal solid object displays a maximum for object sizes comparable to the Saffman-Delbrück length of the membrane.
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Affiliation(s)
- Ehsan Noruzifar
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106-9510, USA
| | - Brian A Camley
- Center for Theoretical Biological Physics and Department of Physics, University of California, San Diego, La Jolla, California 92093, USA
| | - Frank L H Brown
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106-9510, USA
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34
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Supunyabut C, Fuklang S, Sompornpisut P. Continuum electrostatic approach for evaluating positions and interactions of proteins in a bilayer membrane. J Mol Graph Model 2015; 59:81-91. [DOI: 10.1016/j.jmgm.2015.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 04/02/2015] [Accepted: 04/03/2015] [Indexed: 01/08/2023]
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35
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Han E, Lee H. Structural effects of tachyplesin I and its linear derivative on their aggregation and mobility in lipid bilayers. J Mol Graph Model 2015; 59:123-8. [DOI: 10.1016/j.jmgm.2015.04.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 04/09/2015] [Accepted: 04/17/2015] [Indexed: 10/23/2022]
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36
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Abstract
Membrane protein structures are underrepresented in the Protein Data Bank (PDB) due to difficulties associated with expression and crystallization. As such, it is one area where computational studies, particularly Molecular Dynamics (MD) simulations, can provide useful additional information. Recently, there has been substantial progress in the simulation of lipid bilayers and membrane proteins embedded within them. Initial efforts at simulating membrane proteins embedded within a lipid bilayer were relatively slow and interactive processes, but recent advances now mean that the setup and running of membrane protein simulations is somewhat more straightforward, though not without its problems. In this chapter, we outline practical methods for setting up and running MD simulations of a membrane protein embedded within a lipid bilayer and discuss methodologies that are likely to contribute future improvements.
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Baowan D, Cox BJ, Hill JM. Instability of carbon nanoparticles interacting with lipid bilayers. RSC Adv 2015. [DOI: 10.1039/c4ra13496f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
For nanoparticles penetrating biological tissue, modelling indicates that without external forces, carbon nanoparticles will remain trapped in lipid bilayers.
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Affiliation(s)
- Duangkamon Baowan
- Department of Mathematics
- Faculty of Science
- Mahidol University
- Bangkok 10400
- Thailand
| | - Barry J. Cox
- Nanomechanics Group
- School of Mathematical Sciences
- The University of Adelaide
- Australia
| | - James M. Hill
- Nanomechanics Group
- School of Mathematical Sciences
- The University of Adelaide
- Australia
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38
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Jo S, Wu EL, Stuhlsatz D, Klauda JB, Widmalm G, Im W. Lipopolysaccharide membrane building and simulation. Methods Mol Biol 2015; 1273:391-406. [PMID: 25753722 PMCID: PMC4484582 DOI: 10.1007/978-1-4939-2343-4_24] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
While membrane simulations are widely employed to study the structure and dynamics of various lipid bilayers and membrane proteins in the bilayers, simulations of lipopolysaccharides (LPS) in membrane environments have been limited due to their structural complexity, difficulties in building LPS-membrane systems, and lack of the appropriate molecular force fields. In this work, as a first step to extend CHARMM-GUI Membrane Builder to incorporate LPS molecules and to explore their structures and dynamics in membrane environments using molecular dynamics simulations, we describe step-by-step procedures to build LPS bilayer systems using CHARMM and the recently developed CHARMM carbohydrate and lipid force fields. Such procedures are illustrated by building various bilayers of Escherichia coli R1.O6 LPS and the presentation of preliminary simulation results in terms of per-LPS area and density distributions of various components along the membrane normal.
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Affiliation(s)
- Sunhwan Jo
- Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, 2030 Becker Drive Lawrence, KS 66045, USA
| | - Emilia L. Wu
- Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, 2030 Becker Drive Lawrence, KS 66045, USA
| | - Danielle Stuhlsatz
- Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, 2030 Becker Drive Lawrence, KS 66045, USA
| | - Jeffery B. Klauda
- Department of Chemical and Biomolecular Engineering, The University of Maryland, 2113 Chemical and Nuclear Engineering, College Park, MD 20742, USA
| | - Göran Widmalm
- Department of Organic Chemistry and Stockholm Center for Biomembrane Research, Arrhenius Laboratory, Stockholm University, S106-91 Stockholm, Sweden
| | - Wonpil Im
- Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, 2030 Becker Drive Lawrence, KS 66045, USA
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39
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Sychev SV, Balandin SV, Panteleev PV, Barsukov LI, Ovchinnikova TV. Lipid-dependent pore formation by antimicrobial peptides arenicin-2 and melittin demonstrated by their proton transfer activity. J Pept Sci 2014; 21:71-6. [DOI: 10.1002/psc.2724] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 11/11/2014] [Accepted: 11/13/2014] [Indexed: 12/23/2022]
Affiliation(s)
- Sergei V. Sychev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry; Russian Academy of Sciences; Miklukho-Maklaya St, 16/10 117997 Moscow Russia
| | - Sergey V. Balandin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry; Russian Academy of Sciences; Miklukho-Maklaya St, 16/10 117997 Moscow Russia
| | - Pavel V. Panteleev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry; Russian Academy of Sciences; Miklukho-Maklaya St, 16/10 117997 Moscow Russia
| | - Leonid I. Barsukov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry; Russian Academy of Sciences; Miklukho-Maklaya St, 16/10 117997 Moscow Russia
| | - Tatiana V. Ovchinnikova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry; Russian Academy of Sciences; Miklukho-Maklaya St, 16/10 117997 Moscow Russia
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40
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Exploring the sequence space for (tri-)peptide self-assembly to design and discover new hydrogels. Nat Chem 2014; 7:30-7. [PMID: 25515887 DOI: 10.1038/nchem.2122] [Citation(s) in RCA: 523] [Impact Index Per Article: 52.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 10/28/2014] [Indexed: 02/07/2023]
Abstract
Peptides that self-assemble into nanostructures are of tremendous interest for biological, medical, photonic and nanotechnological applications. The enormous sequence space that is available from 20 amino acids probably harbours many interesting candidates, but it is currently not possible to predict supramolecular behaviour from sequence alone. Here, we demonstrate computational tools to screen for the aqueous self-assembly propensity in all of the 8,000 possible tripeptides and evaluate these by comparison with known examples. We applied filters to select for candidates that simultaneously optimize the apparently contradicting requirements of aggregation propensity and hydrophilicity, which resulted in a set of design rules for self-assembling sequences. A number of peptides were subsequently synthesized and characterized, including the first reported tripeptides that are able to form a hydrogel at neutral pH. These tools, which enable the peptide sequence space to be searched for supramolecular properties, enable minimalistic peptide nanotechnology to deliver on its promise.
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41
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Assembly and stability of Salmonella enterica ser. Typhi TolC protein in POPE and DMPE. J Biol Phys 2014; 40:387-400. [PMID: 25011632 DOI: 10.1007/s10867-014-9357-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 05/23/2014] [Indexed: 10/25/2022] Open
Abstract
In this work we assessed the suitability of two different lipid membranes for the simulation of a TolC protein from Salmonella enterica serovar Typhi. The TolC protein family is found in many pathogenic Gram-negative bacteria including Vibrio cholera and Pseudomonas aeruginosa and acts as an outer membrane channel for expulsion of drug and toxin from the cell. In S. typhi, the causative agent for typhoid fever, the TolC outer membrane protein is an antigen for the pathogen. The lipid environment is an important modulator of membrane protein structure and function. We evaluated the conformation of the TolC protein in the presence of DMPE and POPE bilayers using molecular dynamics simulation. The S. typhi TolC protein exhibited similar conformational dynamics to TolC and its homologues. Conformational flexibility of the protein is seen in the C-terminal, extracellular loops, and α-helical region. Despite differences in the two lipids, significant similarities in the motion of the protein in POPE and DMPE were observed, including the rotational motion of the C-terminal residues and the partially open extracellular loops. However, analysis of the trajectories demonstrated effects of hydrophobic matching of the TolC protein in the membrane, particularly in the lengthening of the lipids and subtle movements of the protein's β-barrel towards the lower leaflet in DMPE. The study exhibited the use of molecular dynamics simulation in revealing the differential effect of membrane proteins and lipids on each other. In this study, POPE is potentially a more suitable model for future simulation of the S. typhi TolC protein.
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42
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Wickles S, Singharoy A, Andreani J, Seemayer S, Bischoff L, Berninghausen O, Soeding J, Schulten K, van der Sluis EO, Beckmann R. A structural model of the active ribosome-bound membrane protein insertase YidC. eLife 2014; 3:e03035. [PMID: 25012291 PMCID: PMC4124156 DOI: 10.7554/elife.03035] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The integration of most membrane proteins into the cytoplasmic membrane of bacteria occurs co-translationally. The universally conserved YidC protein mediates this process either individually as a membrane protein insertase, or in concert with the SecY complex. Here, we present a structural model of YidC based on evolutionary co-variation analysis, lipid-versus-protein-exposure and molecular dynamics simulations. The model suggests a distinctive arrangement of the conserved five transmembrane domains and a helical hairpin between transmembrane segment 2 (TM2) and TM3 on the cytoplasmic membrane surface. The model was used for docking into a cryo-electron microscopy reconstruction of a translating YidC-ribosome complex carrying the YidC substrate FOc. This structure reveals how a single copy of YidC interacts with the ribosome at the ribosomal tunnel exit and identifies a site for membrane protein insertion at the YidC protein-lipid interface. Together, these data suggest a mechanism for the co-translational mode of YidC-mediated membrane protein insertion.
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Affiliation(s)
- Stephan Wickles
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany Center for Integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Abhishek Singharoy
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Jessica Andreani
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany Center for Integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Stefan Seemayer
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany Center for Integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Lukas Bischoff
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany Center for Integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Otto Berninghausen
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany Center for Integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Johannes Soeding
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany Center for Integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Klaus Schulten
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Eli O van der Sluis
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany Center for Integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Roland Beckmann
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany Center for Integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
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43
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Javanainen M. Universal Method for Embedding Proteins into Complex Lipid Bilayers for Molecular Dynamics Simulations. J Chem Theory Comput 2014; 10:2577-82. [DOI: 10.1021/ct500046e] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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44
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García-Beltrán O, Yañez O, Caballero J, Galdámez A, Mena N, Nuñez MT, Cassels BK. Synthesis of coumarin derivatives as fluorescent probes for membrane and cell dynamics studies. Eur J Med Chem 2014; 76:79-86. [PMID: 24576613 DOI: 10.1016/j.ejmech.2014.02.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 11/13/2013] [Accepted: 02/08/2014] [Indexed: 01/07/2023]
Abstract
Three coumarin-derived fluorescent probes, 3-acetyl-7-[(6-bromohexyl)oxy]-2H-chromen-2-one (FM1), 7-[(6-bromohexyl)oxy]-4-methyl-2H-chromen-2-one (FM2) and ethyl 2-{7-[(6-bromohexyl)oxy]-2-oxo-2H-chromen-4-yl}acetate (FM3), are described, with their photophysical constants. The compounds were tested in preliminary studies employing epifluorescence microscopy demonstrating that they allow the imaging of human neuroblastoma SH-SY5Y cell membranes. The structure of FM3 was confirmed by X-ray crystallographic analysis. Molecular dynamics (MD) simulations were used to characterize the localization and interactions of the studied compounds with a lipid bilayer model of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC).
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Affiliation(s)
- Olimpo García-Beltrán
- Department of Chemistry, Faculty of Sciences, University of Chile, Santiago, Chile; Facultad de Ciencias Naturales y Matemáticas, Universidad de Ibagué, Carrera 22 Calle 67, Ibagué, Colombia.
| | - Osvaldo Yañez
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Casilla 721, Talca, Chile
| | - Julio Caballero
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Casilla 721, Talca, Chile
| | - Antonio Galdámez
- Department of Chemistry, Faculty of Sciences, University of Chile, Santiago, Chile
| | - Natalia Mena
- Department of Biology, Faculty of Sciences, University of Chile, Santiago, Chile
| | - Marco T Nuñez
- Department of Biology, Faculty of Sciences, University of Chile, Santiago, Chile
| | - Bruce K Cassels
- Department of Chemistry, Faculty of Sciences, University of Chile, Santiago, Chile
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45
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Balupuri A, Sobhia ME. Exploring a model of human chemokine receptor CCR2 in presence of TAK779: A membrane based molecular dynamics study. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.01.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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46
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Song J, Ji C, Zhang JZH. Unveiling the gating mechanism of ECF transporter RibU. Sci Rep 2013; 3:3566. [PMID: 24356467 PMCID: PMC3868957 DOI: 10.1038/srep03566] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 12/04/2013] [Indexed: 11/11/2022] Open
Abstract
Energy-coupling factor (ECF) transporters are responsible for uptake of micronutrients in prokaryotes. The recently reported crystal structure of an ECF transporter RibU provided a foundation for understanding the structure and transport mechanism of ECF transporters. In the present study, molecular dynamics (MD) was carried out to study the conformational changes of the S component RibU upon binding by riboflavin. Our result and analysis revealed a critically important gating mechanism, in which part of loop5 (L5′) (eleven residues, missing in the crystal structure) between TM5 and TM6 is dynamically flexible and serves as a gate. Specifically, the L5′ opens a large cavity accessible to riboflavin from the extracellular space in Apo-RibU and closes the cavity upon riboflavin binding through hydrophobic packing with riboflavin. Thus, L5′is proposed to be the gate for riboflavin binding. In addition, steered molecular dynamics (SMD) simulation is employed to investigate the translocation dynamics of RibU during riboflavin transport. The simulation result does not show evidence that the S component alone can carry out the transport function. Since loop regions are very flexible and therefore could not be resolved by crystallography, their dynamics are hard to predict based on crystal structure alone.
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Affiliation(s)
- Jianing Song
- State Key Laboratory of Precision Spectroscopy, Department of Physics, Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China
| | - Changge Ji
- 1] State Key Laboratory of Precision Spectroscopy, Department of Physics, Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China [2] Institutes for Advanced Interdisciplinary Research, East China Normal University, Shanghai 200062, China [3] NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, China 200062
| | - John Z H Zhang
- 1] State Key Laboratory of Precision Spectroscopy, Department of Physics, Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China [2] Institutes for Advanced Interdisciplinary Research, East China Normal University, Shanghai 200062, China [3] NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, China 200062
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47
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Han E, Lee H. Effects of PEGylation on the binding interaction of magainin 2 and tachyplesin I with lipid bilayer surface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:14214-14221. [PMID: 24160865 DOI: 10.1021/la4036985] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Poly(ethylene glycol) (PEG)-grafted magainin 2 and tachyplesin I were simulated with lipid bilayers. In the simulations of PEGylated magainin 2 and tachyplesin I in water, both peptides are wrapped by PEG chains. The α-helical structure of PEGylated magainin 2 is broken in water, while the β-sheet of PEGylated tachyplesin I keeps stable, similar to the structural behavior of unPEGylated peptides, in agreement with experiments. Simulations of PEGylated peptides with lipid bilayers show that PEG chains block the electrostatic interaction between cationic residues of peptides and anionic phosphates of lipids, leading to the less binding of the peptide to the bilayer surface, which is observed more significantly for magainin 2 than for tachyplesin I. Since the random-coiled magainin 2 can be more completely covered by PEGs than does the β-sheet tachyplesin I, the PEGylation effect on the decreased binding is larger for magainin 2, showing the dependence of PEGylation on the peptide structure. These simulation findings qualitatively support the experimental observation of the different extents of the reduced membrane-permeabilizing activity for PEGylated magainin 2 and tachyplesin I.
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Affiliation(s)
- Eol Han
- Department of Chemical Engineering, Dankook University , Yongin 448-701, South Korea
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48
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Simulative and experimental investigation on the cleavage site that generates the soluble human LOX-1. Arch Biochem Biophys 2013; 540:9-18. [PMID: 24113299 DOI: 10.1016/j.abb.2013.10.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 09/11/2013] [Accepted: 10/01/2013] [Indexed: 12/30/2022]
Abstract
Lectin-like oxidized low-density lipoprotein receptor-1 (LOX-1) is a scavenger receptor that mediates the recognition, the binding and internalization of ox-LDL. A truncated soluble form of LOX-1 (sLOX-1) has been identified that, at elevated levels, has been associated to acute coronary syndrome. Human sLOX-1 is the extracellular part of membrane LOX-1 which is cleaved in the NECK domain with a mechanism that has not yet been identified. Purification of human sLOX-1 has been carried out to experimentally identify the cleavage site region within the NECK domain. Molecular modelling and classical molecular dynamics simulation techniques have been used to characterize the structural and dynamical properties of the LOX-1 NECK domain in the presence and absence of the CTLD recognition region, taking into account the obtained proteolysis results. The simulative data indicate that the NECK domain is stabilized by the coiled-coil heptad repeat motif along the simulations, shows a definite flexibility pattern and is characterized by specific electrostatic potentials. The detection of a mobile inter-helix space suggests an explanation for the in vivo susceptibility of the NECK domain to the proteolytic cleavage, validating the assumption that the NECK domain sequence is composed of a coiled-coil motif destabilized in specific regions of functional significance.
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49
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Wang K, Dang W, Yan J, Chen R, Liu X, Yan W, Zhang B, Xie J, Zhang J, Wang R. Membrane perturbation action mode and structure-activity relationships of Protonectin, a novel antimicrobial peptide from the venom of the neotropical social wasp Agelaia pallipes pallipes. Antimicrob Agents Chemother 2013; 57:4632-9. [PMID: 23836163 PMCID: PMC3811433 DOI: 10.1128/aac.02311-12] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2012] [Accepted: 06/20/2013] [Indexed: 01/12/2023] Open
Abstract
With the extensive use of antibiotics, multidrug-resistant bacteria emerge frequently. New antimicrobial agents with novel modes of action are urgently needed. It is now widely accepted that antimicrobial peptides (AMPs) could be promising alternatives to conventional antibiotics. In this study, we aimed to study the antimicrobial activity and mechanism of action of protonectin, a cationic peptide from the venom of the neotropical social wasp Agelaia pallipes pallipes. We demonstrated that protonectin exhibits potent antimicrobial activity against a spectrum of bacteria, including multidrug-resistant strains. To further understand this mechanism, the structural features of protonectin and its analogs were studied by circular dichroism (CD). The CD spectra demonstrated that protonectin and its natural analog polybia-CP formed a typical α-helical conformation in the membrane-mimicking environment, while its proline-substituted analog had much lower or even no α-helix conformation. Molecular dynamics simulations indicated that the α-helical conformation in the membrane is required for the exhibition of antibacterial activity. In conclusion, protonectin exhibits potent antimicrobial activity by disruption of the integrity of the bacterial membrane, and its α-helical confirmation in the membrane is essential for this action.
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Affiliation(s)
- Kairong Wang
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou, People's Republic of China
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50
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Lin MH, Hsu HJ, Bartenschlager R, Fischer WB. Membrane undulation induced by NS4A of Dengue virus: a molecular dynamics simulation study. J Biomol Struct Dyn 2013; 32:1552-62. [PMID: 23964591 DOI: 10.1080/07391102.2013.826599] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Nonstructural protein 4A (NS4A) of Dengue virus (DENV) is a membrane protein involved in rearrangements of the endoplasmic reticulum membrane that are required for formation of replication vesicles. NS4A is composed most likely of three membrane domains. The N- and C-terminal domains are supposed to traverse the lipid membrane whereas the central one is thought to reside on the membrane surface, thus forming a u-shaped protein. All three membrane domains are proposed to be helical by secondary structure prediction programs. After performing multi nanosecond molecular dynamics (MD) simulations at various temperatures (300, 310, and 315.15 K) with each of the individual domains, they are used in a docking approach to define putative association motifs of the transmembrane domains (TMDs). Two structures of the u-shaped protein are generated by separating two assembled TMDs linking them with the membrane-attached domain. Lipid undulation is monitored with the structures embedded in a fully hydrated lipid bilayer applying multiple 200 ns MD simulations at 310 K. An intact structure of the protein supports membrane undulation. The strong unwinding of the helices in the domain-linking section of one of the structures lowers its capability to induce membrane curvature. Unwinding of the link region is due to interactions of two tryptophan residues, Trp-96 and 104. These results provide first insights into the membrane-altering properties of DENV NS4A.
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Affiliation(s)
- Meng-Han Lin
- a Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University and Biophotonics & Molecular Imaging Research Center (BMIRC), National Yang-Ming University , 155, Li-Non St., Sec. 2, Taipei , 112 , Taiwan
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