51
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Lin D, Grossfield A. Thermodynamics of Micelle Formation and Membrane Fusion Modulate Antimicrobial Lipopeptide Activity. Biophys J 2016; 109:750-9. [PMID: 26287627 DOI: 10.1016/j.bpj.2015.07.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 06/04/2015] [Accepted: 07/01/2015] [Indexed: 11/18/2022] Open
Abstract
Antimicrobial lipopeptides (AMLPs) are antimicrobial drug candidates that preferentially target microbial membranes. One class of AMLPs, composed of cationic tetrapeptides attached to an acyl chain, have minimal inhibitory concentrations in the micromolar range against a range of bacteria and fungi. Previously, we used coarse-grained molecular dynamics simulations and free energy methods to study the thermodynamics of their interaction with membranes in their monomeric state. Here, we extended the study to the biologically relevant micellar state, using, to our knowledge, a novel reaction coordinate based on hydrophobic contacts. Using umbrella sampling along this reaction coordinate, we identified the critical transition states when micelles insert into membranes. The results indicate that the binding of these AMLP micelles to membranes is thermodynamically favorable, but in contrast to the monomeric case, there are significant free energy barriers. The height of these free energy barriers depends on the membrane composition, suggesting that the AMLPs' ability to selectively target bacterial membranes may be as much kinetic as thermodynamic. This mechanism highlights the importance of considering oligomeric state in solution as criterion when optimizing peptides or lipopeptides as antibiotic leads.
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Affiliation(s)
- Dejun Lin
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York
| | - Alan Grossfield
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York.
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52
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Retinal Conformation Changes Rhodopsin's Dynamic Ensemble. Biophys J 2016; 109:608-17. [PMID: 26244742 DOI: 10.1016/j.bpj.2015.06.046] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 06/17/2015] [Accepted: 06/19/2015] [Indexed: 11/23/2022] Open
Abstract
G protein-coupled receptors are vital membrane proteins that allosterically transduce biomolecular signals across the cell membrane. However, the process by which ligand binding induces protein conformation changes is not well understood biophysically. Rhodopsin, the mammalian dim-light receptor, is a unique test case for understanding these processes because of its switch-like activity; the ligand, retinal, is bound throughout the activation cycle, switching from inverse agonist to agonist after absorbing a photon. By contrast, the ligand-free opsin is outside the activation cycle and may behave differently. We find that retinal influences rhodopsin dynamics using an ensemble of all-atom molecular dynamics simulations that in aggregate contain 100 μs of sampling. Active retinal destabilizes the inactive state of the receptor, whereas the active ensemble was more structurally homogenous. By contrast, simulations of an active-like receptor without retinal present were much more heterogeneous than those containing retinal. These results suggest allosteric processes are more complicated than a ligand inducing protein conformational changes or simply capturing a shifted ensemble as outlined in classic models of allostery.
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53
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Lee CT, Comer J, Herndon C, Leung N, Pavlova A, Swift RV, Tung C, Rowley CN, Amaro RE, Chipot C, Wang Y, Gumbart JC. Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds. J Chem Inf Model 2016; 56:721-33. [PMID: 27043429 DOI: 10.1021/acs.jcim.6b00022] [Citation(s) in RCA: 150] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Predicting the rate of nonfacilitated permeation of solutes across lipid bilayers is important to drug design, toxicology, and signaling. These rates can be estimated using molecular dynamics simulations combined with the inhomogeneous solubility-diffusion model, which requires calculation of the potential of mean force and position-dependent diffusivity of the solute along the transmembrane axis. In this paper, we assess the efficiency and accuracy of several methods for the calculation of the permeability of a model DMPC bilayer to urea, benzoic acid, and codeine. We compare umbrella sampling, replica exchange umbrella sampling, adaptive biasing force, and multiple-walker adaptive biasing force for the calculation of the transmembrane PMF. No definitive advantage for any of these methods in their ability to predict the membrane permeability coefficient Pm was found, provided that a sufficiently long equilibration is performed. For diffusivities, a Bayesian inference method was compared to a generalized Langevin method, both being sensitive to chosen parameters and the slow relaxation of membrane defects. Agreement within 1.5 log units of the computed Pm with experiment is found for all permeants and methods. Remaining discrepancies can likely be attributed to limitations of the force field as well as slowly relaxing collective movements within the lipid environment. Numerical calculations based on model profiles show that Pm can be reliably estimated from only a few data points, leading to recommendations for calculating Pm from simulations.
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Affiliation(s)
- Christopher T Lee
- Department of Chemistry and Biochemistry, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Jeffrey Comer
- Nanotechnology Innovation Center of Kansas State, Institute of Computational Comparative Medicine, Department of Anatomy and Physiology, Kansas State University , P-213 Mosier Hall, Manhattan, Kansas 66506, United States
| | - Conner Herndon
- School of Physics, Georgia Institute of Technology , 837 State Street, Atlanta, Georgia 30332, United States
| | - Nelson Leung
- Department of Physics, The Chinese University of Hong Kong , Shatin, Hong Kong SAR, China
| | - Anna Pavlova
- School of Physics, Georgia Institute of Technology , 837 State Street, Atlanta, Georgia 30332, United States
| | - Robert V Swift
- Department of Chemistry and Biochemistry, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Chris Tung
- Department of Physics, The Chinese University of Hong Kong , Shatin, Hong Kong SAR, China
| | - Christopher N Rowley
- Department of Chemistry, Memorial University of Newfoundland , St. John's, NL A1B 3X7 Canada
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Christophe Chipot
- Laboratoire International Associé Centre National de la Recherche Scientifique and University of Illinois at Urbana-Champaign, UMR n° 7565, Université de Lorraine , B.P. 70239, 54506 Vandœuvre-lès-Nancy, France.,Beckman Institute for Advanced Science and Technology and Department of Physics, University of Illinois at Urbana-Champaign , 405 North Mathews, Urbana, Illinois 61801, United States
| | - Yi Wang
- Department of Physics, The Chinese University of Hong Kong , Shatin, Hong Kong SAR, China.,Shenzhen Research Institute, The Chinese University of Hong Kong , Shatin, Hong Kong SAR, China
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology , 837 State Street, Atlanta, Georgia 30332, United States.,School of Chemistry and Biochemistry, Georgia Institute of Technology , 901 Atlantic Drive NW, Atlanta, Georgia 30332, United States
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54
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Neale C, Pomès R. Sampling errors in free energy simulations of small molecules in lipid bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2539-2548. [PMID: 26952019 DOI: 10.1016/j.bbamem.2016.03.006] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 03/01/2016] [Accepted: 03/02/2016] [Indexed: 12/14/2022]
Abstract
Free energy simulations are a powerful tool for evaluating the interactions of molecular solutes with lipid bilayers as mimetics of cellular membranes. However, these simulations are frequently hindered by systematic sampling errors. This review highlights recent progress in computing free energy profiles for inserting molecular solutes into lipid bilayers. Particular emphasis is placed on a systematic analysis of the free energy profiles, identifying the sources of sampling errors that reduce computational efficiency, and highlighting methodological advances that may alleviate sampling deficiencies. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Chris Neale
- Department of Physics, Applied Physics and Astronomy, Rensselaer Polytechnic Institute, 110 8th St, Troy, New York 12180-3590, USA
| | - Régis Pomès
- Molecular Structure and Function, The Hospital for Sick Children, 686 Bay Street, Toronto, Ontario M5G 0A4, Canada; Department of Biochemistry, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada.
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55
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Sawle L, Ghosh K. Convergence of Molecular Dynamics Simulation of Protein Native States: Feasibility vs Self-Consistency Dilemma. J Chem Theory Comput 2016; 12:861-9. [DOI: 10.1021/acs.jctc.5b00999] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Lucas Sawle
- Department of Physics and
Astronomy, University of Denver, Denver, Colorado 80209, United States
| | - Kingshuk Ghosh
- Department of Physics and
Astronomy, University of Denver, Denver, Colorado 80209, United States
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56
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Shagaghi N, Palombo EA, Clayton AHA, Bhave M. Archetypal tryptophan-rich antimicrobial peptides: properties and applications. World J Microbiol Biotechnol 2016; 32:31. [PMID: 26748808 DOI: 10.1007/s11274-015-1986-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 11/25/2015] [Indexed: 12/17/2022]
Abstract
Drug-resistant microorganisms ('superbugs') present a serious challenge to the success of antimicrobial treatments. Subsequently, there is a crucial need for novel bio-control agents. Many antimicrobial peptides (AMPs) show a broad-spectrum activity against bacteria, fungi or viruses and are strong candidates to complement or substitute current antimicrobial agents. Some AMPs are also effective against protozoa or cancer cells. The tryptophan (Trp)-rich peptides (TRPs) are a subset of AMPs that display potent antimicrobial activity, credited to the unique biochemical properties of tryptophan that allow it to insert into biological membranes. Further, many Trp-rich AMPs cross bacterial membranes without compromising their integrity and act intracellularly, suggesting interactions with nucleic acids and enzymes. In this work, we overview some archetypal TRPs derived from natural sources, i.e., indolicidin, tritrpticin and lactoferricin, summarising their biochemical properties, structures, antimicrobial activities, mechanistic studies and potential applications.
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Affiliation(s)
- Nadin Shagaghi
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, PO Box 218, Hawthorn, VIC, 3122, Australia
| | - Enzo A Palombo
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, PO Box 218, Hawthorn, VIC, 3122, Australia
| | - Andrew H A Clayton
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, PO Box 218, Hawthorn, VIC, 3122, Australia
| | - Mrinal Bhave
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, PO Box 218, Hawthorn, VIC, 3122, Australia.
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57
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Ing C, Pomès R. Simulation Studies of Ion Permeation and Selectivity in Voltage-Gated Sodium Channels. CURRENT TOPICS IN MEMBRANES 2016; 78:215-60. [DOI: 10.1016/bs.ctm.2016.07.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
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58
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Zhang L, Yethiraj A, Cui Q. Free Energy Calculations for the Peripheral Binding of Proteins/Peptides to an Anionic Membrane. 1. Implicit Membrane Models. J Chem Theory Comput 2015; 10:2845-59. [PMID: 26586509 DOI: 10.1021/ct500218p] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The binding of peptides and proteins to the surface of complex lipid membranes is important in many biological processes such as cell signaling and membrane remodeling. Computational studies can aid experiments by identifying physical interactions and structural motifs that determine the binding affinity and specificity. However, previous studies focused on either qualitative behaviors of protein/membrane interactions or the binding affinity of small peptides. Motivated by this observation, we set out to develop computational protocols for bimolecular binding to charged membranes that are applicable to both peptides and large proteins. In this work, we explore a method based on an implicit membrane/solvent model (generalized Born with a simple switching in combination with the Gouy-Chapman-Stern model for a charged interface), which we expect to lead to useful results when the binding does not implicate significant membrane deformation and local demixing of lipids. We show that the binding free energy can be efficiently computed following a thermodynamic cycle similar to protein-ligand binding calculations, especially when a Bennett acceptance ratio based protocol is used to consider both the membrane bound and solution conformational ensembles. Test calculations on a series of peptides show that our computational approach leads to binding affinities in encouraging agreement with experimental data, including for the challenging example of the bringing of flexible MARCKS-ED peptides to membranes. The calculations highlight that for a membrane with a significant fraction of anionic lipids, it is essential to include the effect of ion adsorption using the Stern model, which significantly modifies the effective surface charge. This implicit membrane model based computational protocol helps lay the groundwork for more systematic analysis of protein/peptide binding to membranes of complex shape and composition.
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Affiliation(s)
- Leili Zhang
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Arun Yethiraj
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
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59
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Nishizawa M, Nishizawa K. Free energy of helical transmembrane peptide dimerization in OPLS-AA/Berger force field simulations: inaccuracy and implications for partner-specific Lennard-Jones parameters between peptides and lipids. MOLECULAR SIMULATION 2015. [DOI: 10.1080/08927022.2015.1112006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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60
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Neale C, Huang K, García AE, Tristram-Nagle S. Penetration of HIV-1 Tat47-57 into PC/PE Bilayers Assessed by MD Simulation and X-ray Scattering. MEMBRANES 2015; 5:473-94. [PMID: 26402709 PMCID: PMC4584291 DOI: 10.3390/membranes5030473] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 09/09/2015] [Indexed: 01/07/2023]
Abstract
The interactions of the basic, cell-penetrating region (Y47GRKKRRQRRR57) of the HIV-1 Tat protein with dioleoylphosphatidylcholine (DOPC) bilayers were previously assessed by comparing experimental X-ray diffuse scattering with atomistic molecular dynamics simulations. Here, we extend this investigation by evaluating the influence of phosphatidylethanolamine (PE) lipids. Using experimental bilayer form factors derivedfrom X-ray diffuse scattering data as a guide, our simulations indicate that Tat peptides localize close to the carbonyl-glycerol group in the headgroup region of bilayers composed of either DOPC or DOPC:DOPE (1:1) lipid. Our results also suggest that Tat peptides may more frequently insert into the hydrophobic core of bilayers composed of PC:PE (1:1) lipids than into bilayers composed entirely of PC lipids. PE lipids may facilitate peptide translocation across a lipid bilayer by stabilizing intermediate states in which hydrated peptides span the bilayer.
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Affiliation(s)
- Chris Neale
- Department of Physics, Applied Physics and Astronomy, Rensselaer Polytechnic Institute, 110 8th St, Troy, NY 12180-3590, USA.
| | - Kun Huang
- Department of Physics, Applied Physics and Astronomy, Rensselaer Polytechnic Institute, 110 8th St, Troy, NY 12180-3590, USA.
| | - Angel E García
- Department of Physics, Applied Physics and Astronomy, Rensselaer Polytechnic Institute, 110 8th St, Troy, NY 12180-3590, USA.
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th St, Troy, NY 12180-3590, USA.
| | - Stephanie Tristram-Nagle
- Biological Physics Group, Department of Physics, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA.
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61
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Bereau T. Better Together: Lipopeptide Micelle Formation Enhances Antimicrobial Selectivity. Biophys J 2015; 109:668-9. [PMID: 26287619 DOI: 10.1016/j.bpj.2015.07.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 07/10/2015] [Accepted: 07/10/2015] [Indexed: 10/23/2022] Open
Affiliation(s)
- Tristan Bereau
- Max Planck Institute for Polymer Research, Mainz, Germany.
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62
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Lin D, Grossfield A. Thermodynamics of antimicrobial lipopeptide binding to membranes: origins of affinity and selectivity. Biophys J 2015; 107:1862-1872. [PMID: 25418167 DOI: 10.1016/j.bpj.2014.08.026] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 08/25/2014] [Accepted: 08/29/2014] [Indexed: 10/24/2022] Open
Abstract
The development of novel antibiotic drugs is one of the most pressing biomedical problems due to the increasing number of antibiotic-resistant pathogens. Antimicrobial peptides and lipopeptides are a promising category of candidates, but the molecular origins of their antimembrane activity is unclear. Here we explore a series of recently developed antimicrobial lipopeptides, using coarse-grained molecular-dynamics simulations and free energy methods to uncover the thermodynamics governing their binding to membranes. Specifically, we quantify C16-KGGK's binding affinity to the two types of membrane by umbrella sampling. We also examined the origin of C16-KGGK's selectivity for bacterial versus mammalian membranes by systematically varying the peptide sequence and salt concentration. Our data showed that the C16 hydrophobic tail is the main contributor to its affinity to lipid membrane, whereas the peptide portion is mainly responsible for its selectivity. Furthermore, the electrostatic interaction between the cationic peptide and anionic bacterial membrane plays a significant role in the selectivity.
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Affiliation(s)
- Dejun Lin
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York
| | - Alan Grossfield
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York.
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63
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Walczewska-Szewc K, Deplazes E, Corry B. Comparing the Ability of Enhanced Sampling Molecular Dynamics Methods To Reproduce the Behavior of Fluorescent Labels on Proteins. J Chem Theory Comput 2015; 11:3455-65. [DOI: 10.1021/acs.jctc.5b00205] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Katarzyna Walczewska-Szewc
- In
Silico Numerical Laboratory and Institute
of Experimental Physics, University of Gdansk, 80-952 Gdańsk, Poland
- Research
School of Biology, Australian National University, Acton ACT 2601, Australia
| | - Evelyne Deplazes
- Institute for Molecular Bioscience and School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane QLD 4072, Australia
| | - Ben Corry
- Research
School of Biology, Australian National University, Acton ACT 2601, Australia
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64
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Misiewicz J, Afonin S, Grage SL, van den Berg J, Strandberg E, Wadhwani P, Ulrich AS. Action of the multifunctional peptide BP100 on native biomembranes examined by solid-state NMR. JOURNAL OF BIOMOLECULAR NMR 2015; 61:287-98. [PMID: 25616492 DOI: 10.1007/s10858-015-9897-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 01/10/2015] [Indexed: 05/22/2023]
Abstract
Membrane composition is a key factor that regulates the destructive activity of antimicrobial peptides and the non-leaky permeation of cell penetrating peptides in vivo. Hence, the choice of model membrane is a crucial aspect in NMR studies and should reflect the biological situation as closely as possible. Here, we explore the structure and dynamics of the short multifunctional peptide BP100 using a multinuclear solid-state NMR approach. The membrane alignment and mobility of this 11 amino acid peptide was studied in various synthetic lipid bilayers with different net charge, fluidity, and thickness, as well as in native biomembranes harvested from prokaryotic and eukaryotic cells. (19)F-NMR provided the high sensitivity and lack of natural abundance background that are necessary to observe a labelled peptide even in protoplast membranes from Micrococcus luteus and in erythrocyte ghosts. Six selectively (19)F-labeled BP100 analogues gave remarkably similar spectra in all of the macroscopically oriented membrane systems, which were studied under quasi-native conditions of ambient temperature and full hydration. This similarity suggests that BP100 has the same surface-bound helical structure and high mobility in the different biomembranes and model membranes alike, independent of charge, thickness or cholesterol content of the system. (31)P-NMR spectra of the phospholipid components did not indicate any bilayer perturbation, so the formation of toroidal wormholes or micellarization can be excluded as a mechanism of its antimicrobial or cell penetrating action. However, (2)H-NMR analysis of the acyl chain order parameter profiles showed that BP100 leads to considerable membrane thinning and thereby local destabilization.
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Affiliation(s)
- Julia Misiewicz
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
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65
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Karilainen T, Timr Š, Vattulainen I, Jungwirth P. Oxidation of Cholesterol Does Not Alter Significantly Its Uptake into High-Density Lipoprotein Particles. J Phys Chem B 2015; 119:4594-600. [DOI: 10.1021/acs.jpcb.5b00240] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Topi Karilainen
- Department
of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
| | - Štěpán Timr
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstı́ 2, 16610 Prague 6, Czech Republic
| | - Ilpo Vattulainen
- Department
of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
- MEMPHYS -
Center
for Biomembrane Physics, University of Southern Denmark, DK-5230, Odense, Denmark
| | - Pavel Jungwirth
- Department
of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstı́ 2, 16610 Prague 6, Czech Republic
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66
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Abstract
![]()
In
this work, we apply the recently developed constant pH molecular
dynamics technique to study protonation equilibria of titratable side
chains in the context of simple transmembrane (TM) helices and explore
the effect of pH on their configurations in membrane bilayers. We
observe that, despite a significant shift toward neutral states, considerable
population of different side chains stay in the charged state that
give rise to pKa values around 9.6 for
Asp and Glu and 4.5 to 6 for His and Lys side chains, respectively.
These charged states are highly stabilized by favorable interactions
between head groups, water molecules, and the charged side chains
that are facilitated by substantial changes in the configuration of
the peptides. The pH dependent configurations and the measured pKa values are in good agreement with relatively
recent solid state NMR measurements. Our results presented here demonstrate
that all-atom constant pH molecular dynamics can be applied to membrane
proteins and peptides to obtain reliable pKa values and pH dependent behavior for these systems.
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Affiliation(s)
- Afra Panahi
- †Department of Chemistry and ‡Biophysics Program, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan, 48109, United States
| | - Charles L Brooks
- †Department of Chemistry and ‡Biophysics Program, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan, 48109, United States
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67
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Romo TD, Grossfield A. How fast is your camera? Timescales for molecular motion and their role in restraining molecular dynamics. Biophys J 2015; 106:2549-51. [PMID: 24940771 DOI: 10.1016/j.bpj.2014.05.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 05/02/2014] [Accepted: 05/15/2014] [Indexed: 10/25/2022] Open
Affiliation(s)
- Tod D Romo
- Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York
| | - Alan Grossfield
- Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York.
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68
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Molecular dynamics methods to predict peptide locations in membranes: LAH4 as a stringent test case. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:581-92. [DOI: 10.1016/j.bbamem.2014.11.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 10/22/2014] [Accepted: 11/05/2014] [Indexed: 01/07/2023]
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69
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Romo TD, Grossfield A. Unknown unknowns: the challenge of systematic and statistical error in molecular dynamics simulations. Biophys J 2014; 106:1553-4. [PMID: 24739152 DOI: 10.1016/j.bpj.2014.03.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 03/07/2014] [Indexed: 01/05/2023] Open
Affiliation(s)
- Tod D Romo
- Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York
| | - Alan Grossfield
- Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York.
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70
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Baker MK, Abrams CF. Dynamics of lipids, cholesterol, and transmembrane α-helices from microsecond molecular dynamics simulations. J Phys Chem B 2014; 118:13590-600. [PMID: 25380392 PMCID: PMC4254001 DOI: 10.1021/jp507027t] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Extensive all-atom molecular dynamics (∼24 μs total) allowed exploration of configurational space and calculation of lateral diffusion coefficients of the components of a protein-embedded, cholesterol-containing model bilayer. The three model membranes are composed of an ∼50/50 (by mole) dipalmitoylphosphatidylcholine (DPPC)/cholesterol bilayer and contained an α-helical transmembrane protein (HIV-1 gp41 TM). Despite the high concentration of cholesterol, normal Brownian motion was observed and the calculated diffusion coefficients (on the order of 10(-9) cm(2)/s) are consistent with experiments. Diffusion is sensitive to a variety of parameters, and a temperature difference of ∼4 K from thermostat artifacts resulted in 2-10-fold differences in diffusion coefficients and significant differences in lipid order, membrane thickness, and unit cell area. Also, the specific peptide sequence likely underlies the consistently observed faster diffusion in one leaflet. Although the simulations here present molecular dynamics (MD) an order of magnitude longer than those from previous studies, the three systems did not approach ergodicity. The distributions of cholesterol and DPPC around the peptides changed on the microsecond time scale, but not significantly enough to thoroughly explore configurational space. These simulations support conclusions of other recent microsecond MD in that even longer time scales are needed for equilibration of model membranes and simulations of more realistic cellular or viral bilayers.
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Affiliation(s)
- Michelle K Baker
- Department of Chemical and Biological Engineering, Drexel University , 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
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Koldsø H, Shorthouse D, Hélie J, Sansom MSP. Lipid clustering correlates with membrane curvature as revealed by molecular simulations of complex lipid bilayers. PLoS Comput Biol 2014; 10:e1003911. [PMID: 25340788 PMCID: PMC4207469 DOI: 10.1371/journal.pcbi.1003911] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 09/16/2014] [Indexed: 12/21/2022] Open
Abstract
Cell membranes are complex multicomponent systems, which are highly heterogeneous in the lipid distribution and composition. To date, most molecular simulations have focussed on relatively simple lipid compositions, helping to inform our understanding of in vitro experimental studies. Here we describe on simulations of complex asymmetric plasma membrane model, which contains seven different lipids species including the glycolipid GM3 in the outer leaflet and the anionic lipid, phosphatidylinositol 4,5-bisphophate (PIP2), in the inner leaflet. Plasma membrane models consisting of 1500 lipids and resembling the in vivo composition were constructed and simulations were run for 5 µs. In these simulations the most striking feature was the formation of nano-clusters of GM3 within the outer leaflet. In simulations of protein interactions within a plasma membrane model, GM3, PIP2, and cholesterol all formed favorable interactions with the model α-helical protein. A larger scale simulation of a model plasma membrane containing 6000 lipid molecules revealed correlations between curvature of the bilayer surface and clustering of lipid molecules. In particular, the concave (when viewed from the extracellular side) regions of the bilayer surface were locally enriched in GM3. In summary, these simulations explore the nanoscale dynamics of model bilayers which mimic the in vivo lipid composition of mammalian plasma membranes, revealing emergent nanoscale membrane organization which may be coupled both to fluctuations in local membrane geometry and to interactions with proteins. Cell membranes play important roles in vivo both in shielding the cell interior from the surrounding environment and in cell function through lipid components of the membrane having roles in controlling protein function, cell signaling etc. We employ molecular dynamics simulations to explore the behavior of biologically realistic membrane models. Our simulations reveal nano-domain clustering of the glycolipid GM3 and to a lesser extent of the anionic lipid phosphatidylinositol 4,5-bisphophate (PIP2). When including transmembrane proteins we are able to observe preferential interactions of known regulatory lipids (e.g. GM3, PIP2 and cholesterol) with the proteins. Membrane curvature is shown to be coupled to the local lipid composition, suggestive of a link between lipid nano-domains and membrane geometry.
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Affiliation(s)
- Heidi Koldsø
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - David Shorthouse
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Jean Hélie
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- * E-mail:
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Doshi U, Hamelberg D. Towards fast, rigorous and efficient conformational sampling of biomolecules: Advances in accelerated molecular dynamics. Biochim Biophys Acta Gen Subj 2014; 1850:878-888. [PMID: 25153688 DOI: 10.1016/j.bbagen.2014.08.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 08/12/2014] [Accepted: 08/13/2014] [Indexed: 02/06/2023]
Abstract
BACKGROUND Accelerated molecular dynamics (aMD) has been proven to be a powerful biasing method for enhanced sampling of biomolecular conformations on general-purpose computational platforms. Biologically important long timescale events that are beyond the reach of standard molecular dynamics can be accessed without losing the detailed atomistic description of the system in aMD. Over other biasing methods, aMD offers the advantages of tuning the level of acceleration to access the desired timescale without any advance knowledge of the reaction coordinate. SCOPE OF REVIEW Recent advances in the implementation of aMD and its applications to small peptides and biological macromolecules are reviewed here along with a brief account of all the aMD variants introduced in the last decade. MAJOR CONCLUSIONS In comparison to the original implementation of aMD, the recent variant in which all the rotatable dihedral angles are accelerated (RaMD) exhibits faster convergence rates and significant improvement in statistical accuracy of retrieved thermodynamic properties. RaMD in conjunction with accelerating diffusive degrees of freedom, i.e. dual boosting, has been rigorously tested for the most difficult conformational sampling problem, protein folding. It has been shown that RaMD with dual boosting is capable of efficiently sampling multiple folding and unfolding events in small fast folding proteins. GENERAL SIGNIFICANCE RaMD with the dual boost approach opens exciting possibilities for sampling multiple timescales in biomolecules. While equilibrium properties can be recovered satisfactorily from aMD-based methods, directly obtaining dynamics and kinetic rates for larger systems presents a future challenge. This article is part of a Special Issue entitled Recent developments of molecular dynamics.
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Affiliation(s)
- Urmi Doshi
- Department of Chemistry and the Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30302-3965, United States
| | - Donald Hamelberg
- Department of Chemistry and the Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30302-3965, United States.
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