1
|
Patra S, Biswas P, Karmakar S, Biswas K. Repression of resistance mechanisms of Pseudomonas aeruginosa: implications of the combination of antibiotics and phytoconstituents. Arch Microbiol 2024; 206:294. [PMID: 38850339 DOI: 10.1007/s00203-024-04012-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/17/2024] [Accepted: 05/19/2024] [Indexed: 06/10/2024]
Abstract
Antimicrobial resistance is a prevalent problem witnessed globally and creating an alarming situation for the treatment of infections caused by resistant pathogens. Available armaments such as antibiotics often fail to exhibit the intended action against resistant pathogens, leading to failure in the treatments that are causing mortality. New antibiotics or a new treatment approach is necessary to combat this situation. P. aeruginosa is an opportunistic drug resistant pathogen and is the sixth most common cause of nosocomial infections. P. aeruginosa due to its genome organization and other factors are exhibiting resistance against drugs. Bacterial biofilm formation, low permeability of outer membrane, the production of the beta-lactamase, and the production of several efflux systems limits the antibacterial potential of several classes of antibiotics. Combination of phytoconstituents with antibiotics is a promising strategy to combat multidrug resistant P. aeruginosa. Phytoconstituents such as flavonoids, terpenoids, alkaloids, polypeptides, phenolics, and essential oils are well known antibacterial agents. In this review, the activity of combination of the phytoconstituents and antibiotics, and their corresponding mechanism of action was discussed elaborately. The combination of antibiotics and plant-derived compounds exhibited better efficacy compared to antibiotics alone against the antibiotic resistance P. aeruginosa infections.
Collapse
Affiliation(s)
- Susmita Patra
- Eminent College of Pharmaceutical Technology, Barbaria, Barasat, North 24 Parganas, Kolkata, West Bengal, 700126, India
| | - Poulomi Biswas
- Eminent College of Pharmaceutical Technology, Barbaria, Barasat, North 24 Parganas, Kolkata, West Bengal, 700126, India
| | - Sanmoy Karmakar
- Department of Pharmaceutical Technology, Jadavpur University, Jadavpur, Kolkata, West Bengal, 700032, India
| | - Kaushik Biswas
- Eminent College of Pharmaceutical Technology, Barbaria, Barasat, North 24 Parganas, Kolkata, West Bengal, 700126, India.
| |
Collapse
|
2
|
Ceccarelli M, Milenkovic S, Bodrenko IV. The Effect of Lipopolysaccharides on the Electrostatic Properties of Gram-Negative General Porins from Enterobacteriaceae. Chemphyschem 2024:e202400147. [PMID: 38625051 DOI: 10.1002/cphc.202400147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 04/17/2024]
Abstract
We investigated, by using all-atom molecular dynamics simulations, the effect of the outer membrane of Gram-negative bacteria, composed in the outer leaflet by polar/charged lipopolysaccharides (LPS), on the electrostatic properties of general porins from the Enterobacteriaceae family. General porins constitute the main path for the facilitated diffusion of polar antibiotics through the outer membrane. As model system we selected OmpK36 from Klebsiella pneumoniae, the ortholog of OmpC from Escherichia coli. This species presents high variability of amino acid composition of porins, with the effect to increase its resistance to the penetration of antibiotics. The various properties we analyzed seem to indicate that LPS acts as an independent layer without affecting the internal electrostatic properties of OmpK36. The only apparent effect on the microsecond time scale we sampled is the appearance of calcium ions, when present at moderate concentration in solution, inside the pore. However, we noticed increased fluctuations of the polarization density and only minor changes on its average value.
Collapse
Affiliation(s)
- Matteo Ceccarelli
- Department of Physics, University of Cagliari, Cittadella Universitaria, 09042, Monserrato, IT
| | - Stefan Milenkovic
- Department of Physics, University of Cagliari, Cittadella Universitaria, 09042, Monserrato, IT
| | - Igor V Bodrenko
- Istituto Nanoscienze, CNR, piazza San Silvestro 12, 56127, Pisa, Italy
- Lab NEST, Scuola Normale Superiore, piazza San Silvestro 12, 56127, Pisa, Italy
| |
Collapse
|
3
|
Sharma P, Vaiwala R, Gopinath AK, Chockalingam R, Ayappa KG. Structure of the Bacterial Cell Envelope and Interactions with Antimicrobials: Insights from Molecular Dynamics Simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:7791-7811. [PMID: 38451026 DOI: 10.1021/acs.langmuir.3c03474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Bacteria have evolved over 3 billion years, shaping our intrinsic and symbiotic coexistence with these single-celled organisms. With rising populations of drug-resistant strains, the search for novel antimicrobials is an ongoing area of research. Advances in high-performance computing platforms have led to a variety of molecular dynamics simulation strategies to study the interactions of antimicrobial molecules with different compartments of the bacterial cell envelope of both Gram-positive and Gram-negative species. In this review, we begin with a detailed description of the structural aspects of the bacterial cell envelope. Simulations concerned with the transport and associated free energy of small molecules and ions through the outer membrane, peptidoglycan, inner membrane and outer membrane porins are discussed. Since surfactants are widely used as antimicrobials, a section is devoted to the interactions of surfactants with the cell wall and inner membranes. The review ends with a discussion on antimicrobial peptides and the insights gained from the molecular simulations on the free energy of translocation. Challenges involved in developing accurate molecular models and coarse-grained strategies that provide a trade-off between atomic details with a gain in sampling time are highlighted. The need for efficient sampling strategies to obtain accurate free energies of translocation is also discussed. Molecular dynamics simulations have evolved as a powerful tool that can potentially be used to design and develop novel antimicrobials and strategies to effectively treat bacterial infections.
Collapse
Affiliation(s)
- Pradyumn Sharma
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka, India, 560012
| | - Rakesh Vaiwala
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka, India, 560012
| | - Amar Krishna Gopinath
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka, India, 560012
| | - Rajalakshmi Chockalingam
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka, India, 560012
| | - K Ganapathy Ayappa
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka, India, 560012
| |
Collapse
|
4
|
Manrique PD, Leus IV, López CA, Mehla J, Malloci G, Gervasoni S, Vargiu AV, Kinthada RK, Herndon L, Hengartner NW, Walker JK, Rybenkov VV, Ruggerone P, Zgurskaya HI, Gnanakaran S. Predicting permeation of compounds across the outer membrane of P. aeruginosa using molecular descriptors. Commun Chem 2024; 7:84. [PMID: 38609430 PMCID: PMC11015012 DOI: 10.1038/s42004-024-01161-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
The ability Gram-negative pathogens have at adapting and protecting themselves against antibiotics has increasingly become a public health threat. Data-driven models identifying molecular properties that correlate with outer membrane (OM) permeation and growth inhibition while avoiding efflux could guide the discovery of novel classes of antibiotics. Here we evaluate 174 molecular descriptors in 1260 antimicrobial compounds and study their correlations with antibacterial activity in Gram-negative Pseudomonas aeruginosa. The descriptors are derived from traditional approaches quantifying the compounds' intrinsic physicochemical properties, together with, bacterium-specific from ensemble docking of compounds targeting specific MexB binding pockets, and all-atom molecular dynamics simulations in different subregions of the OM model. Using these descriptors and the measured inhibitory concentrations, we design a statistical protocol to identify predictors of OM permeation/inhibition. We find consistent rules across most of our data highlighting the role of the interaction between the compounds and the OM. An implementation of the rules uncovered in our study is shown, and it demonstrates the accuracy of our approach in a set of previously unseen compounds. Our analysis sheds new light on the key properties drug candidates need to effectively permeate/inhibit P. aeruginosa, and opens the gate to similar data-driven studies in other Gram-negative pathogens.
Collapse
Affiliation(s)
- Pedro D Manrique
- Physics Department, George Washington University, Washington, 20052, DC, USA.
| | - Inga V Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, 73019, OK, USA
| | - César A López
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, 87545, NM, USA
| | - Jitender Mehla
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, 73019, OK, USA
| | - Giuliano Malloci
- Department of Physics, University of Cagliari, Monserrato, 20052, CA, Italy
| | - Silvia Gervasoni
- Department of Physics, University of Cagliari, Monserrato, 20052, CA, Italy
| | - Attilio V Vargiu
- Department of Physics, University of Cagliari, Monserrato, 20052, CA, Italy
| | - Rama K Kinthada
- Department of Pharmacology and Physiology, Saint Louis University, St. Louis, 63103, MO, USA
| | - Liam Herndon
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, 87545, NM, USA
| | - Nicolas W Hengartner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, 87545, NM, USA
| | - John K Walker
- Department of Pharmacology and Physiology, Saint Louis University, St. Louis, 63103, MO, USA
| | - Valentin V Rybenkov
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, 73019, OK, USA
| | - Paolo Ruggerone
- Department of Physics, University of Cagliari, Monserrato, 20052, CA, Italy
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, 73019, OK, USA
| | - S Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, 87545, NM, USA.
| |
Collapse
|
5
|
Nguyen HL, Nguyen TQ, Li MS. SARS-CoV-2 Omicron Subvariants Do Not Differ Much in Binding Affinity to Human ACE2: A Molecular Dynamics Study. J Phys Chem B 2024; 128:3340-3349. [PMID: 38564480 PMCID: PMC11017248 DOI: 10.1021/acs.jpcb.3c06270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 03/12/2024] [Accepted: 03/12/2024] [Indexed: 04/04/2024]
Abstract
The emergence of the variant of concern Omicron (B.1.1.529) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exacerbates the COVID-19 pandemic due to its high contagious ability. Studies have shown that the Omicron binds human ACE2 more strongly than the wild type. The prevalence of Omicron in new cases of COVID-19 promotes novel lineages with improved receptor binding affinity and immune evasion. To shed light on this open problem, in this work, we investigated the binding free energy of the receptor binding domain of the Omicron lineages BA.2, BA.2.3.20, BA.3, BA4/BA5, BA.2.75, BA.2.75.2, BA.4.6, XBB.1, XBB.1.5, BJ.1, BN.1, BQ.1.1, and CH.1.1 to human ACE2 using all-atom molecular dynamics simulation and the molecular mechanics Poisson-Boltzmann surface area method. The results show that these lineages have increased binding affinity compared to the BA.1 lineage, and BA.2.75 and BA.2.75.2 subvariants bind ACE2 more strongly than others. However, in general, the binding affinities of the Omicron lineages do not differ significantly from each other. The electrostatic force dominates over the van der Waals force in the interaction between Omicron lineages and human cells. Based on our results, we argue that viral evolution does not further improve the affinity of SARS-CoV-2 for ACE2 but may increase immune evasion.
Collapse
Affiliation(s)
- Hoang Linh Nguyen
- Institute
of Fundamental and Applied Sciences, Duy
Tan University, Ho Chi Minh City 700000, Vietnam
- Faculty
of Environmental and Natural Sciences, Duy
Tan University, Da Nang 550000, Vietnam
| | - Thai Quoc Nguyen
- Faculty
of Physics, VNU University of Science, Vietnam
National University, 334 Nguyen Trai, Hanoi 100000, Vietnam
- Dong
Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh
City, Dong Thap 81000, Vietnam
| | - Mai Suan Li
- Institute
of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, Warsaw 02-668, Poland
| |
Collapse
|
6
|
Vaiwala R, Ayappa KG. Martini-3 Coarse-Grained Models for the Bacterial Lipopolysaccharide Outer Membrane of Escherichia coli. J Chem Theory Comput 2024; 20:1704-1716. [PMID: 37676287 DOI: 10.1021/acs.jctc.3c00471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
The outer lipopolysaccharide (LPS) membrane of Gram-negative bacteria forms the main barrier for transport of antimicrobial molecules into the bacterial cell. In this study we develop coarse-grained models for the outer membrane of Escherichia coli in the Martini-3 framework. The coarse-grained model force field was parametrized and validated using all-atom simulations of symmetric membranes of lipid A and rough LPS as well as a complete asymmetric membrane of LPS with the O-antigen. The bonded parameters were obtained using an iterative refinement procedure with target bonded distributions obtained from all-atom simulations. The membrane thickness, area of the LPS, and density distributions for the different regions as well as the water and ion densities in Martini-3 simulations show excellent agreement with the all-atom data. Additionally the solvent accessible surface area for individual molecules in water was found to be in good agreement. The binding of calcium ions with phosphate and carboxylate moieties of LPS is accurately captured in the Martini-3 model, indicative of the integrity of the highly negatively charged LPS molecules in the outer membranes of Gram-negative bacteria. The melting transition of the coarse-grained lipid A membrane model was found to occur between 300 and 310 K, and the model captured variations in area per LPS, order parameter, and membrane thickness across the melting transition. Our study reveals that the proposed Martini-3 models for LPS are able to capture the physicochemical balance of the complex sugar architecture of the outer membrane of Escherichia coli. The coarse-grained models developed in this study would be useful for determining membrane protein interactions and permeation of potential antimicrobials through bacterial membranes at mesoscopic spatial and temporal scales.
Collapse
Affiliation(s)
- Rakesh Vaiwala
- Department of Chemical Engineering, Indian Institute of Science, Bangalore 560012, India
| | - K Ganapathy Ayappa
- Department of Chemical Engineering, Indian Institute of Science, Bangalore 560012, India
| |
Collapse
|
7
|
Pritchard MF, Powell LC, Adams JYM, Menzies G, Khan S, Tøndervik A, Sletta H, Aarstad O, Skjåk-Bræk G, McKenna S, Buurma NJ, Farnell DJJ, Rye PD, Hill KE, Thomas DW. Structure-Activity Relationships of Low Molecular Weight Alginate Oligosaccharide Therapy against Pseudomonas aeruginosa. Biomolecules 2023; 13:1366. [PMID: 37759766 PMCID: PMC10527064 DOI: 10.3390/biom13091366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/26/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023] Open
Abstract
Low molecular weight alginate oligosaccharides have been shown to exhibit anti-microbial activity against a range of multi-drug resistant bacteria, including Pseudomonas aeruginosa. Previous studies suggested that the disruption of calcium (Ca2+)-DNA binding within bacterial biofilms and dysregulation of quorum sensing (QS) were key factors in these observed effects. To further investigate the contribution of Ca2+ binding, G-block (OligoG) and M-block alginate oligosaccharides (OligoM) with comparable average size DPn 19 but contrasting Ca2+ binding properties were prepared. Fourier-transform infrared spectroscopy demonstrated prolonged binding of alginate oligosaccharides to the pseudomonal cell membrane even after hydrodynamic shear treatment. Molecular dynamics simulations and isothermal titration calorimetry revealed that OligoG exhibited stronger interactions with bacterial LPS than OligoM, although this difference was not mirrored by differential reductions in bacterial growth. While confocal laser scanning microscopy showed that both agents demonstrated similar dose-dependent reductions in biofilm formation, OligoG exhibited a stronger QS inhibitory effect and increased potentiation of the antibiotic azithromycin in minimum inhibitory concentration and biofilm assays. This study demonstrates that the anti-microbial effects of alginate oligosaccharides are not purely influenced by Ca2+-dependent processes but also by electrostatic interactions that are common to both G-block and M-block structures.
Collapse
Affiliation(s)
- Manon F. Pritchard
- Advanced Therapies Group, School of Dentistry, Cardiff University, Cardiff CF14 4XY, UK; (L.C.P.); (J.Y.M.A.); (S.K.); (S.M.); (D.J.J.F.); (K.E.H.); (D.W.T.)
| | - Lydia C. Powell
- Advanced Therapies Group, School of Dentistry, Cardiff University, Cardiff CF14 4XY, UK; (L.C.P.); (J.Y.M.A.); (S.K.); (S.M.); (D.J.J.F.); (K.E.H.); (D.W.T.)
- Microbiology and Infectious Disease Group, Swansea University Medical School, Swansea SA2 8PP, UK
| | - Jennifer Y. M. Adams
- Advanced Therapies Group, School of Dentistry, Cardiff University, Cardiff CF14 4XY, UK; (L.C.P.); (J.Y.M.A.); (S.K.); (S.M.); (D.J.J.F.); (K.E.H.); (D.W.T.)
| | - Georgina Menzies
- School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK;
| | - Saira Khan
- Advanced Therapies Group, School of Dentistry, Cardiff University, Cardiff CF14 4XY, UK; (L.C.P.); (J.Y.M.A.); (S.K.); (S.M.); (D.J.J.F.); (K.E.H.); (D.W.T.)
| | - Anne Tøndervik
- Department of Bioprocess Technology, SINTEF Materials and Chemistry, N-7465 Trondheim, Norway; (A.T.); (H.S.)
| | - Håvard Sletta
- Department of Bioprocess Technology, SINTEF Materials and Chemistry, N-7465 Trondheim, Norway; (A.T.); (H.S.)
| | - Olav Aarstad
- Department of Biotechnology, Norwegian University of Science and Technology, N-7491 Trondheim, Norway; (O.A.); (G.S.-B.)
| | - Gudmund Skjåk-Bræk
- Department of Biotechnology, Norwegian University of Science and Technology, N-7491 Trondheim, Norway; (O.A.); (G.S.-B.)
| | - Stephen McKenna
- Advanced Therapies Group, School of Dentistry, Cardiff University, Cardiff CF14 4XY, UK; (L.C.P.); (J.Y.M.A.); (S.K.); (S.M.); (D.J.J.F.); (K.E.H.); (D.W.T.)
| | - Niklaas J. Buurma
- Physical Organic Chemistry Centre, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK;
| | - Damian J. J. Farnell
- Advanced Therapies Group, School of Dentistry, Cardiff University, Cardiff CF14 4XY, UK; (L.C.P.); (J.Y.M.A.); (S.K.); (S.M.); (D.J.J.F.); (K.E.H.); (D.W.T.)
| | - Philip D. Rye
- AlgiPharma AS, Industriveien 33, N-1337 Sandvika, Norway;
| | - Katja E. Hill
- Advanced Therapies Group, School of Dentistry, Cardiff University, Cardiff CF14 4XY, UK; (L.C.P.); (J.Y.M.A.); (S.K.); (S.M.); (D.J.J.F.); (K.E.H.); (D.W.T.)
| | - David W. Thomas
- Advanced Therapies Group, School of Dentistry, Cardiff University, Cardiff CF14 4XY, UK; (L.C.P.); (J.Y.M.A.); (S.K.); (S.M.); (D.J.J.F.); (K.E.H.); (D.W.T.)
| |
Collapse
|
8
|
Santos DS, De Nicola A, dos Santos VF, Milano G, Soares TA. Exploring the Molecular Dynamics of a Lipid-A Vesicle at the Atom Level: Morphology and Permeation Mechanism. J Phys Chem B 2023; 127:6694-6702. [PMID: 37467380 PMCID: PMC10405212 DOI: 10.1021/acs.jpcb.3c02848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/18/2023] [Indexed: 07/21/2023]
Abstract
Lipid-A was previously shown to spontaneously aggregate into a vesicle via the hybrid particle field approach. We assess the validity of the proposed vesiculation mechanism by simulating the resulting lipid-A vesicle at the atom level. The spatial confinement imposed by the vesicle geometry on the conformation and packing of lipid-A induces significant heterogeneity of physical properties in the inner and outer leaflets. It also induces tighter molecular packing and lower acyl chain order compared to the lamellar arrangement. Around 5% of water molecules passively permeates the vesicle membrane inward and outward. The permeation is facilitated by interactions with water molecules that are transported across the membrane by a network of electrostatic interactions with the hydrogen bond donors/acceptors in the N-acetylglucosamine ring and upper region of the acyl chains of lipid-A. The permeation process takes place at low rates but still at higher frequencies than observed for the lamellar arrangement of lipid-A. These findings not only substantiate the proposed lipid-A vesiculation mechanism but also reveal the complex structural dynamics of an important nonlamellar arrangement of lipid-A.
Collapse
Affiliation(s)
- Denys
E. S. Santos
- Departmento
de Química Fundamental, Universidade
Federal de Pernambuco, Recife 50740-560, Brazil
| | - Antonio De Nicola
- Scuola
Superiore Meridionale, Largo S. Marcellino 10, Napoli 80138, Italy
- Graduate
School of Organic Materials Science, Yamagata
University, Yonezawa 992-8510, Yamagata, Japan
| | - Vinicius F. dos Santos
- Departamento
de Química, Faculdade de Filosofia, Ciências e Letras
de Ribeirão Preto, Universidade de
São Paulo, Ribeirão
Preto 14040-901, Brazil
| | - Giuseppe Milano
- Department
of Chemical, Materials and Production Engineering, University of Naples Federico II, Piazzale Tecchio 80, Napoli 80125, Italy
| | - Thereza A. Soares
- Departamento
de Química, Faculdade de Filosofia, Ciências e Letras
de Ribeirão Preto, Universidade de
São Paulo, Ribeirão
Preto 14040-901, Brazil
- Hylleraas
Centre for Quantum Molecular Sciences, University
of Oslo, Oslo 0315, Norway
| |
Collapse
|
9
|
Pirhadi E, Vanegas JM, Farin M, Schertzer JW, Yong X. Effect of Local Stress on Accurate Modeling of Bacterial Outer Membranes Using All-Atom Molecular Dynamics. J Chem Theory Comput 2023; 19:363-372. [PMID: 36579901 DOI: 10.1021/acs.jctc.2c01026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Biological membranes are fundamental components of living organisms that play an undeniable role in their survival. Molecular dynamics (MD) serves as an essential computational tool for studying biomembranes on molecular and atomistic scales. The status quo of MD simulations of biomembranes studies a nanometer-sized membrane patch periodically extended under periodic boundary conditions (PBCs). In nature, membranes are usually composed of different lipids in their two layers (referred to as leaflets). This compositional asymmetry imposes a fixed ratio of lipid numbers between the two leaflets in a periodically constrained membrane, which needs to be set appropriately. The widely adopted methods of defining a leaflet lipid ratio suffer from the lack of control over the mechanical tension of each leaflet, which could significantly influence research findings. In this study, we investigate the role of membrane-building protocol and the resulting initial stress state on the interaction between small molecules and asymmetric membranes. We model the outer membrane of Pseudomonas aeruginosa bacteria using two different building protocols and probe their interactions with the Pseudomonas quinolone signal (PQS). Our results show that differential stress could shift the position of free energy minimum for the PQS molecule between the two leaflets of the asymmetric membrane. This work provides critical insights into the relationship between the initial per-leaflet tension and the spontaneous intercalation of PQS.
Collapse
Affiliation(s)
- Emad Pirhadi
- Department of Mechanical Engineering, Binghamton University, Binghamton, New York 13902-6000, United States
| | - Juan M Vanegas
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331-4003, United States
| | - Mithila Farin
- Department of Mechanical Engineering, Binghamton University, Binghamton, New York 13902-6000, United States
| | - Jeffrey W Schertzer
- Department of Biological Sciences, Binghamton University, Binghamton, New York 13902-6000, United States
| | - Xin Yong
- Department of Mechanical Engineering, Binghamton University, Binghamton, New York 13902-6000, United States
| |
Collapse
|
10
|
Manrique PD, López CA, Gnanakaran S, Rybenkov VV, Zgurskaya HI. New understanding of multidrug efflux and permeation in antibiotic resistance, persistence, and heteroresistance. Ann N Y Acad Sci 2023; 1519:46-62. [PMID: 36344198 PMCID: PMC9839546 DOI: 10.1111/nyas.14921] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Antibiotics effective against Gram-negative ESKAPE pathogens are a critical area of unmet need. Infections caused by these pathogens are not only difficult to treat but finding new therapies to overcome Gram-negative resistance is also a challenge. There are not enough antibiotics in development that target the most dangerous pathogens and there are not enough novel drugs in the pipeline. The major obstacle in the antibiotic discovery pipeline is the lack of understanding of how to breach antibiotic permeability barriers of Gram-negative pathogens. These barriers are created by active efflux pumps acting across both the inner and the outer membranes. Overproduction of efflux pumps alone or together with either modification of the outer membrane or antibiotic-inactivating enzymes and target mutations contribute to clinical levels of antibiotics resistance. Recent efforts have generated significant advances in the rationalization of compound efflux and permeation across the cell envelopes of Gram-negative pathogens. Combined with earlier studies and novel mathematical models, these efforts have led to a multilevel understanding of how antibiotics permeate these barriers and how multidrug efflux and permeation contribute to the development of antibiotic resistance and heteroresistance. Here, we discuss the new developments in this area.
Collapse
Affiliation(s)
- Pedro D. Manrique
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, United States
- Present address: Physics Department, George Washington University, Washington D.C. 20052, United States
| | - Cesar A. López
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, United States
| | - S. Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, United States
| | - Valentin V. Rybenkov
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019, United States
| | - Helen I. Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019, United States
| |
Collapse
|
11
|
Powell LC, Cullen JK, Boyle GM, De Ridder T, Yap PY, Xue W, Pierce CJ, Pritchard MF, Menzies GE, Abdulkarim M, Adams JYM, Stokniene J, Francis LW, Gumbleton M, Johns J, Hill KE, Jones AV, Parsons PG, Reddell P, Thomas DW. Topical, immunomodulatory epoxy-tiglianes induce biofilm disruption and healing in acute and chronic skin wounds. Sci Transl Med 2022; 14:eabn3758. [DOI: 10.1126/scitranslmed.abn3758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The management of antibiotic-resistant, bacterial biofilm infections in chronic skin wounds is an increasing clinical challenge. Despite advances in diagnosis, many patients do not derive benefit from current anti-infective/antibiotic therapies. Here, we report a novel class of naturally occurring and semisynthetic epoxy-tiglianes, derived from the Queensland blushwood tree (
Fontainea picrosperma)
, and demonstrate their antimicrobial activity (modifying bacterial growth and inducing biofilm disruption), with structure/activity relationships established against important human pathogens. In vitro, the lead candidate EBC-1013 stimulated protein kinase C (PKC)–dependent neutrophil reactive oxygen species (ROS) induction and NETosis and increased expression of wound healing–associated cytokines, chemokines, and antimicrobial peptides in keratinocytes and fibroblasts. In vivo, topical EBC-1013 induced rapid resolution of infection with increased matrix remodeling in acute thermal injuries in calves. In chronically infected diabetic mouse wounds, treatment induced cytokine/chemokine production, inflammatory cell recruitment, and complete healing (in six of seven wounds) with ordered keratinocyte differentiation. These results highlight a nonantibiotic approach involving contrasting, orthogonal mechanisms of action combining targeted biofilm disruption and innate immune induction in the treatment of chronic wounds.
Collapse
Affiliation(s)
- Lydia C. Powell
- Advanced Therapies Group, Cardiff University School of Dentistry, Cardiff CF14 4XY, UK
- Centre for Nanohealth, Swansea University Medical School, Swansea University, Swansea SA2 8PP, UK
| | - Jason K. Cullen
- Drug Discovery Group, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Glen M. Boyle
- Drug Discovery Group, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Tom De Ridder
- QBiotics Group Limited Yungaburra, Queensland 4884, Australia
| | - Pei-Yi Yap
- Drug Discovery Group, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Wenya Xue
- Advanced Therapies Group, Cardiff University School of Dentistry, Cardiff CF14 4XY, UK
| | - Carly J. Pierce
- Drug Discovery Group, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Manon F. Pritchard
- Advanced Therapies Group, Cardiff University School of Dentistry, Cardiff CF14 4XY, UK
| | | | - Muthanna Abdulkarim
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff CF10 3NB, UK
| | - Jennifer Y. M. Adams
- Advanced Therapies Group, Cardiff University School of Dentistry, Cardiff CF14 4XY, UK
| | - Joana Stokniene
- Advanced Therapies Group, Cardiff University School of Dentistry, Cardiff CF14 4XY, UK
| | - Lewis W. Francis
- Centre for Nanohealth, Swansea University Medical School, Swansea University, Swansea SA2 8PP, UK
| | - Mark Gumbleton
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff CF10 3NB, UK
| | - Jenny Johns
- Drug Discovery Group, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Katja E. Hill
- Advanced Therapies Group, Cardiff University School of Dentistry, Cardiff CF14 4XY, UK
| | - Adam V. Jones
- Oral Pathology, Cardiff and Vale University Health Board , Cardiff CF14 4XY, UK
| | - Peter G. Parsons
- Drug Discovery Group, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Paul Reddell
- QBiotics Group Limited Yungaburra, Queensland 4884, Australia
| | - David W. Thomas
- Advanced Therapies Group, Cardiff University School of Dentistry, Cardiff CF14 4XY, UK
| |
Collapse
|
12
|
Santos DES, Coutinho K, Soares TA. Surface Assessment via Grid Evaluation (SuAVE) for Every Surface Curvature and Cavity Shape. J Chem Inf Model 2022; 62:4690-4701. [PMID: 35946873 PMCID: PMC9554907 DOI: 10.1021/acs.jcim.2c00673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The surface assessment via grid evaluation
(SuAVE)
software was developed to account for the effect of curvature in the
calculations of structural properties of chemical interfaces regardless
of the chemical composition, asymmetry, and level of atom coarseness.
It employs differential geometry techniques, enabling the representation
of chemical surfaces as fully differentiable. In this article, we
present novel developments of SuAVE to treat closed surfaces and complex
cavity shapes. These developments expand the repertoire of curvature-dependent
analyses already available in the previous version of SuAVE (e.g., area per lipid, density profiles, membrane thickness,
deuterium-order parameters, volume per lipid, and surface curvature
angle) to include new functionalities applicable to soft matter (e.g., sphericity, average radius, principal moment of inertia,
and roundness) and crystalline porous materials (e.g., pore diameter, internal void volume, total area, and the total
void volume of the unit cell structure). SuAVE can accurately handle
chemical systems with high and low atom density as demonstrated for
two distinct chemical systems: the lipid A vesicle and a set of selected
metal–organic frameworks. The SuAVE software v2.0 is fully
parallel and benefits from a compiler that supports OpenMP. SuAVE
is freely available from https://github.com/SuAVE-Software/source and https://www.biomatsite.net/.
Collapse
Affiliation(s)
- Denys E S Santos
- Departamento de Química Fundamental, Universidade Federal de Pernambuco, Cidade Universitária, Recife 50740-560, Brazil
| | - Kaline Coutinho
- Instituto de Física, Universidade de São Paulo, Cidade Universitária, São Paulo 05508-090, Brazil
| | - Thereza A Soares
- Instituto de Física, Universidade de São Paulo, Cidade Universitária, São Paulo 05508-090, Brazil.,Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, 0315 Oslo, Norway
| |
Collapse
|
13
|
Abstract
Glycoscience assembles all the scientific disciplines involved in studying various molecules and macromolecules containing carbohydrates and complex glycans. Such an ensemble involves one of the most extensive sets of molecules in quantity and occurrence since they occur in all microorganisms and higher organisms. Once the compositions and sequences of these molecules are established, the determination of their three-dimensional structural and dynamical features is a step toward understanding the molecular basis underlying their properties and functions. The range of the relevant computational methods capable of addressing such issues is anchored by the specificity of stereoelectronic effects from quantum chemistry to mesoscale modeling throughout molecular dynamics and mechanics and coarse-grained and docking calculations. The Review leads the reader through the detailed presentations of the applications of computational modeling. The illustrations cover carbohydrate-carbohydrate interactions, glycolipids, and N- and O-linked glycans, emphasizing their role in SARS-CoV-2. The presentation continues with the structure of polysaccharides in solution and solid-state and lipopolysaccharides in membranes. The full range of protein-carbohydrate interactions is presented, as exemplified by carbohydrate-active enzymes, transporters, lectins, antibodies, and glycosaminoglycan binding proteins. A final section features a list of 150 tools and databases to help address the many issues of structural glycobioinformatics.
Collapse
Affiliation(s)
- Serge Perez
- Centre de Recherche sur les Macromolecules Vegetales, University of Grenoble-Alpes, Centre National de la Recherche Scientifique, Grenoble F-38041, France
| | - Olga Makshakova
- FRC Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, Kazan 420111, Russia
| |
Collapse
|
14
|
Nguyen H, Thai NQ, Nguyen PH, Li MS. SARS-CoV-2 Omicron Variant Binds to Human Cells More Strongly than the Wild Type: Evidence from Molecular Dynamics Simulation. J Phys Chem B 2022; 126:4669-4678. [PMID: 35723978 PMCID: PMC9235043 DOI: 10.1021/acs.jpcb.2c01048] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 06/06/2022] [Indexed: 12/12/2022]
Abstract
The emergence of the variant of concern Omicron (B.1.1.529) of the severe acute respiratory syndrome coronavirus 2 has aggravated the Covid-19 pandemic due to its very contagious ability. The high infection rate may be due to the high binding affinity of Omicron to human cells, but both experimental and computational studies have yielded conflicting results on this issue. Some studies have shown that the Omicron variant binds to human angiotensin-converting enzyme 2 (hACE2) more strongly than the wild type (WT), but other studies have reported comparable binding affinities. To shed light on this open problem, in this work, we calculated the binding free energy of the receptor binding domain (RBD) of the WT and Omicron spike protein to hACE2 using all-atom molecular dynamics simulation and the molecular mechanics Poisson-Boltzmann surface area method. We showed that Omicron binds to human cells more strongly than the WT due to increased RBD charge, which enhances electrostatic interaction with negatively charged hACE2. N440K, T478K, E484A, Q493R, and Q498R mutations in the RBD have been found to play a critical role in the stability of the RBD-hACE2 complex. The effect of homogeneous and heterogeneous models of glycans coating the viral RBD and the peptidyl domain of hACE2 was examined. Although the total binding free energy is not sensitive to the glycan model, the distribution of per-residue interaction energies depends on it. In addition, glycans have a little effect on the binding affinity of the WT RBD to hACE2.
Collapse
Affiliation(s)
- Hoang
Linh Nguyen
- Life
Science Lab, Institute for Computational
Science and Technology, Quang Trung
Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh
City 700000, Vietnam
- Ho
Chi Minh City University of Technology (HCMUT), Ho Chi Minh City 700000, Vietnam
- Vietnam
National University, Ho Chi Minh
City 700000, Vietnam
| | - Nguyen Quoc Thai
- Life
Science Lab, Institute for Computational
Science and Technology, Quang Trung
Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh
City 700000, Vietnam
- Dong
Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh
City, Dong Thap 8100, Vietnam
| | - Phuong H. Nguyen
- CNRS,
Universit́e de Paris, UPR9080, Laboratoire de Biochimie Th́eorique,
Paris, France; Institut de Biologie Physico-Chimique, FondationEdmond
de Rothschild, PSL Research University, Paris 75006, France
| | - Mai Suan Li
- Institute
of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, Warsaw 02-668, Poland
| |
Collapse
|
15
|
Ginez LD, Osorio A, Vázquez-Ramírez R, Arenas T, Mendoza L, Camarena L, Poggio S. Changes in fluidity of the E. coli outer membrane in response to temperature, divalent cations and polymyxin-B show two different mechanisms of membrane fluidity adaptation. FEBS J 2022; 289:3550-3567. [PMID: 35038363 DOI: 10.1111/febs.16358] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/23/2021] [Accepted: 01/13/2022] [Indexed: 12/28/2022]
Abstract
The outer membrane (OM) is an essential component of the Gram-negative bacterial cell envelope. Restricted diffusion of integral OM proteins and lipopolysaccharide (LPS) that constitute the outer leaflet of the OM support a model in which the OM is in a semi-crystalline state. The low fluidity of the OM has been suggested to be an important property of this membrane that even contributes to cell rigidity. The LPS characteristics strongly determine the properties of the OM and the LPS layer fluidity has been measured using different techniques that require specific conditions or are technically challenging. Here, we characterize the Escherichia coli LPS fluidity by evaluating the lateral diffusion of the styryl dye FM4-64FX in fluorescence recovery after photobleaching experiments. This technique allowed us to determine the effect of different conditions and genetic backgrounds on the LPS fluidity. Our results show that a fraction of the LPS can slowly diffuse and that the fluidity of the LPS layer adapts by modifying the diffusion of the LPS and the fraction of mobile LPS molecules.
Collapse
Affiliation(s)
- Luis David Ginez
- Departamento Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México
| | - Aurora Osorio
- Departamento Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México
| | - Ricardo Vázquez-Ramírez
- Departamento Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México
| | - Thelma Arenas
- Departamento Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México
| | - Luis Mendoza
- Departamento Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México
| | - Laura Camarena
- Departamento Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México
| | - Sebastian Poggio
- Departamento Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México
| |
Collapse
|
16
|
Abstract
AbstractThe complex composition of bacterial membranes has a significant impact on the understanding of pathogen function and their development towards antibiotic resistance. In addition to the inherent complexity and biosafety risks of studying biological pathogen membranes, the continual rise of antibiotic resistance and its significant economical and clinical consequences has motivated the development of numerous in vitro model membrane systems with tuneable compositions, geometries, and sizes. Approaches discussed in this review include liposomes, solid-supported bilayers, and computational simulations which have been used to explore various processes including drug-membrane interactions, lipid-protein interactions, host–pathogen interactions, and structure-induced bacterial pathogenesis. The advantages, limitations, and applicable analytical tools of all architectures are summarised with a perspective for future research efforts in architectural improvement and elucidation of resistance development strategies and membrane-targeting antibiotic mechanisms.
Collapse
|
17
|
Paracini N, Schneck E, Imberty A, Micciulla S. Lipopolysaccharides at Solid and Liquid Interfaces: Models for Biophysical Studies of the Gram-negative Bacterial Outer Membrane. Adv Colloid Interface Sci 2022; 301:102603. [PMID: 35093846 DOI: 10.1016/j.cis.2022.102603] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 01/14/2022] [Accepted: 01/15/2022] [Indexed: 11/18/2022]
Abstract
Lipopolysaccharides (LPSs) are a constitutive element of the cell envelope of Gram-negative bacteria, representing the main lipid in the external leaflet of their outer membrane (OM) lipid bilayer. These unique surface-exposed glycolipids play a central role in the interactions of Gram-negative organisms with their surrounding environment and represent a key element for protection against antimicrobials and the development of antibiotic resistance. The biophysical investigation of a wide range of different types of in vitro model membranes containing reconstituted LPS has revealed functional and structural properties of these peculiar membrane lipids, providing molecular-level details of their interaction with antimicrobial compounds. LPS assemblies reconstituted at interfaces represent a versatile tool to study the properties of the Gram-negative OM by exploiting several surface-sensitive techniques, in particular X-ray and neutron scattering, which can probe the structure of thin films with sub-nanometer resolution. This review provides an overview of different approaches employed to investigate structural and biophysical properties of LPS, focusing on studies on Langmuir monolayers of LPS at the air/liquid interface and a range of supported LPS-containing model membranes reconstituted at solid/liquid interfaces.
Collapse
Affiliation(s)
| | - Emanuel Schneck
- Physics Departent, Technische Universität Darmstadt, Darmstadt, Germany
| | - Anne Imberty
- Université Grenoble Alpes, CNRS, CERMAV, Grenoble, France
| | | |
Collapse
|
18
|
Messias A, Santos DES, Pontes FJS, Soares TA. The tug of war between Al 3+ and Na + for order-disorder transitions in lipid-A membranes. Phys Chem Chem Phys 2021; 23:15127-15137. [PMID: 34254086 DOI: 10.1039/d1cp02173g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cations play a critical role in the stability and morphology of lipid-A aggregates by neutralizing, hydrating and cross-linking these glycolipid molecules. Monophosphorylated lipid-A is the major immunostimulatory principle in commercially available adjuvants containing Al3+ such as adjuvant system 04 (AS04). The antagonist/agonist immunomodulatory properties of lipid-A are associated with chemical variations (e.g. the number of acyl chains and phosphate groups) and their aggregate arrangements (e.g. lamellar, nonlamellar or mixed). Therefore, the identification of the active form of lipid-A can provide valuable guidance in the development of vaccine adjuvants capable of boosting the immune system with decreased reactogenicity. Although the effect of mono and divalent cations on the structural polymorphism and endotoxicity of LPS has been previously investigated, much less is known about the effect of trivalent cations. We have investigated the effect of NaCl and AlCl3 salt solutions on the structural dynamics and stability of mono and diphosphorylated lipid-A membranes via atomistic MD simulations. The Al3+ ion exerts two major effects on the structural dynamics of lipid-A membranes. It acts as an efficient cross-linker of mono or diphosphorylated lipid-A molecules, thus stabilizing the lamellar arrangement of these glycolipids. It also alters the lipid-A packing and membrane fluidity, inducing disorder → order structural transitions of the membrane. This effect is promptly reversed upon the addition of NaCl solution, which promotes a nearly threefold increase in the amount of water in the carbohydrate moiety of the Al3+-containing lipid-A membranes. The exchange dynamics and residence times of cation-coordinated water molecules in these membranes provide insights into the molecular mechanism for the Na+-induced transition from a densely packed ordered phase to a disordered one. Al3+ counter-ions favor ordered lamellar aggregates, which has been previously associated with the lack of endotoxic activity and cytokine-inducing action. The resulting microscopic understanding of the structure and dynamics of lipid-A aggregates in the presence of Al3+ and Na+ salts can provide valuable guidance in the development of vaccine adjuvants capable of boosting the immune system with decreased reactogenicity.
Collapse
Affiliation(s)
- Andresa Messias
- Department of Fundamental Chemistry, Universidade Federal de Pernambuco, 50740-560 Recife, Brazil.
| | - Denys E S Santos
- Department of Fundamental Chemistry, Universidade Federal de Pernambuco, 50740-560 Recife, Brazil.
| | - Frederico J S Pontes
- Department of Fundamental Chemistry, Universidade Federal de Pernambuco, 50740-560 Recife, Brazil.
| | - Thereza A Soares
- Department of Fundamental Chemistry, Universidade Federal de Pernambuco, 50740-560 Recife, Brazil. and Instituto de Fisica, Universidade de São Paulo, 05508-090 São Paulo, Brazil
| |
Collapse
|
19
|
Marzuoli I, Cruz CHB, Lorenz CD, Fraternali F. Nanocapsule designs for antimicrobial resistance. NANOSCALE 2021; 13:10342-10355. [PMID: 34137751 DOI: 10.1039/d0nr08146a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The pressing need of new antimicrobial products is growing stronger, particularly because of widespread antimicrobial resistance, endangering our ability to treat common infections. The recent coronavirus pandemic has dramatically highlighted the necessity of effective antibacterial and antiviral protection. This work explores at the molecular level the mechanism of action of antibacterial nanocapsules assembled in virus-like particles, their stability and their interaction with mammal and antimicrobial model membranes. We use Molecular Dynamics with force-fields of different granularity and protein design strategies to study the stability, self-assembly and membrane poration properties of these nanocapsules.
Collapse
Affiliation(s)
- Irene Marzuoli
- Randall Centre for Cell and Molecular Biology, King's College London, London, UK.
| | - Carlos H B Cruz
- Randall Centre for Cell and Molecular Biology, King's College London, London, UK.
| | | | - Franca Fraternali
- Randall Centre for Cell and Molecular Biology, King's College London, London, UK.
| |
Collapse
|
20
|
Shearer J, Marzinek JK, Bond PJ, Khalid S. Molecular dynamics simulations of bacterial outer membrane lipid extraction: Adequate sampling? J Chem Phys 2021; 153:044122. [PMID: 32752683 DOI: 10.1063/5.0017734] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The outer membrane of Gram-negative bacteria is almost exclusively composed of lipopolysaccharide in its outer leaflet, whereas the inner leaflet contains a mixture of phospholipids. Lipopolysaccharide diffuses at least an order of magnitude slower than phospholipids, which can cause issues for molecular dynamics simulations in terms of adequate sampling. Here, we test a number of simulation protocols for their ability to achieve convergence with reasonable computational effort using the MARTINI coarse-grained force-field. This is tested in the context both of potential of mean force (PMF) calculations for lipid extraction from membranes and of lateral mixing within the membrane phase. We find that decoupling the cations that cross-link the lipopolysaccharide headgroups from the extracted lipid during PMF calculations is the best approach to achieve convergence comparable to that for phospholipid extraction. We also show that lateral lipopolysaccharide mixing/sorting is very slow and not readily addressable even with Hamiltonian replica exchange. We discuss why more sorting may be unrealistic for the short (microseconds) timescales we simulate and provide an outlook for future studies of lipopolysaccharide-containing membranes.
Collapse
Affiliation(s)
- Jonathan Shearer
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Jan K Marzinek
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (ASTAR), 30 Biopolis Street, Matrix #07-01, 138671, Singapore
| | - Peter J Bond
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (ASTAR), 30 Biopolis Street, Matrix #07-01, 138671, Singapore
| | - Syma Khalid
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| |
Collapse
|
21
|
Tong C, Chen T, Chen Z, Wang H, Wang X, Liu F, Dai H, Wang X, Li X. Forsythiaside a plays an anti-inflammatory role in LPS-induced mastitis in a mouse model by modulating the MAPK and NF-κB signaling pathways. Res Vet Sci 2021; 136:390-395. [PMID: 33799169 DOI: 10.1016/j.rvsc.2021.03.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 02/22/2021] [Accepted: 03/23/2021] [Indexed: 11/29/2022]
Abstract
Forsythiaside A, a major bioactive component extracted from Forsythiae fructus, possesses multiple biological properties, especially anti-inflammatory properties. In the present study, the anti-inflammatory effect of forsythiaside A was investigated in lipopolysaccharide (LPS)-induced acute mastitis in mice. Our results showed that the expression levels of IL-1β, IL-6, TNF-α, p38 MAPK, IκBα, and NF-κB p65 in the LPS group were all up-regulated, and obvious pathological changes were observed by sectioning. Compared with those in the LPS group, the expression levels of the above factors were significantly reduced, and the inflammation symptoms were also significantly reduced by section observation after forsythiaside A intervention. These results indicated that forsythiaside A effectively inhibited LPS-induced mammary inflammation in mice by attenuating the activation of the NF-κB and p38 MAPK signaling pathways.
Collapse
Affiliation(s)
- Chao Tong
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450000, Henan province, PR China; Wuhu Overseas Student Pioneer Park, Wuhu 241006, China
| | - Tong Chen
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450000, Henan province, PR China
| | - Zewen Chen
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450000, Henan province, PR China
| | - Hao Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450000, Henan province, PR China
| | - Xuefang Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450000, Henan province, PR China; Biotechnology Developing Center of Henan Academy of Sciences, Henan Academy of sciences, Zhengzhou 450002, Henan Province, PR China
| | - Fang Liu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450000, Henan province, PR China
| | - Hongyu Dai
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450000, Henan province, PR China
| | - Xuebing Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450000, Henan province, PR China; Key Laboratory for Animal-Derived Food Safety of Henan province, Zhengzhou 450000, Henan Province, PR China.
| | - Xiao Li
- Biotechnology Developing Center of Henan Academy of Sciences, Henan Academy of sciences, Zhengzhou 450002, Henan Province, PR China.
| |
Collapse
|
22
|
Foroozani Behbahani A, Harmandaris V. Gradient of Segmental Dynamics in Stereoregular Poly(Methyl Methacrylate) Melts Confined between Pristine or Oxidized Graphene Sheets. Polymers (Basel) 2021; 13:polym13050830. [PMID: 33800419 PMCID: PMC7962820 DOI: 10.3390/polym13050830] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/27/2021] [Accepted: 03/02/2021] [Indexed: 12/03/2022] Open
Abstract
Segmental dynamics in unentangled isotactic, syndiotactic, and atactic poly(methyl methacrylate) (i-, a-, and s-PMMA) melts confined between pristine graphene, reduced graphene oxide, RGO, or graphene oxide, GO, sheets is studied at various temperatures, well above glass transition temperature, via atomistic molecular dynamics simulations. The model RGO and GO sheets have different degrees of oxidization. The segmental dynamics is studied through the analysis of backbone torsional motions. In the vicinity of the model nanosheets (distances less than ≈2 nm), the dynamics slows down; the effect becomes significantly stronger with increasing the concentration of the surface functional groups, and hence increasing polymer/surface specific interactions. Upon decreasing temperature, the ratios of the interfacial segmental relaxation times to the respective bulk relaxation times increase, revealing the stronger temperature dependence of the interfacial segmental dynamics relative to the bulk dynamics. This heterogeneity in temperature dependence leads to the shortcoming of the time-temperature superposition principle for describing the segmental dynamics of the model confined melts. The alteration of the segmental dynamics at different distances, d, from the surfaces is described by a temperature shift, ΔTseg(d) (roughly speaking, shift of a characteristic temperature). Next, to a given nanosheet, i-PMMA has a larger value of ΔTseg than a-PMMA and s-PMMA. This trend correlates with the better interfacial packing and longer trains of i-PMMA chains. The backbone torsional autocorrelation functions are shown in the frequency domain and are qualitatively compared to the experimental dielectric loss spectra for the segmental α-relaxation in polymer nanocomposites. The εT″(f) (analogous of dielectric loss, ε″(f), for torsional motion) curves of the model confined melts are broader (toward lower frequencies) and have lower amplitudes relative to the corresponding bulk curves; however, the peak frequencies of the εT″(f) curves are only slightly affected.
Collapse
Affiliation(s)
- Alireza Foroozani Behbahani
- Institute of Applied and Computational Mathematics, Foundation for Research and Technology-Hellas, GR-71110 Heraklion, Greece
- Correspondence: (A.F.B.); (V.H.)
| | - Vagelis Harmandaris
- Institute of Applied and Computational Mathematics, Foundation for Research and Technology-Hellas, GR-71110 Heraklion, Greece
- Department of Mathematics and Applied Mathematics, University of Crete, GR-70013 Heraklion, Greece
- Computation-Based Science and Technology Research Center, The Cyprus Institute, 2121 Nicosia, Cyprus
- Correspondence: (A.F.B.); (V.H.)
| |
Collapse
|
23
|
Abstract
Antibiotic-resistant bacteria rapidly spread in clinical and natural environments and challenge our modern lifestyle. A major component of defense against antibiotics in Gram-negative bacteria is a drug permeation barrier created by active efflux across the outer membrane. We identified molecular determinants defining the propensity of small peptidomimetic molecules to avoid and inhibit efflux pumps in Pseudomonas aeruginosa, a human pathogen notorious for its antibiotic resistance. Combining experimental and computational protocols, we mapped the fate of the compounds from structure-activity relationships through their dynamic behavior in solution, permeation across both the inner and outer membranes, and interaction with MexB, the major efflux transporter of P. aeruginosa We identified predictors of efflux avoidance and inhibition and demonstrated their power by using a library of traditional antibiotics and compound series and by generating new inhibitors of MexB. The identified predictors will enable the discovery and optimization of antibacterial agents suitable for treatment of P. aeruginosa infections.IMPORTANCE Efflux pump avoidance and inhibition are desired properties for the optimization of antibacterial activities against Gram-negative bacteria. However, molecular and physicochemical interactions defining the interface between compounds and efflux pumps remain poorly understood. We identified properties that correlate with efflux avoidance and inhibition, are predictive of similar features in structurally diverse compounds, and allow researchers to distinguish between efflux substrates, inhibitors, and avoiders in P. aeruginosa The developed predictive models are based on the descriptors representative of different clusters comprising a physically intuitive combination of properties. Molecular shape (represented by acylindricity), amphiphilicity (anisotropic polarizability), aromaticity (number of aromatic rings), and the partition coefficient (LogD) are physicochemical predictors of efflux inhibitors, whereas interactions with Pro668 and Leu674 residues of MexB distinguish between inhibitors/substrates and efflux avoiders. The predictive models and efflux rules are applicable to compounds with unrelated chemical scaffolds and pave the way for development of compounds with the desired efflux interface properties.
Collapse
|
24
|
Rusu VH, Santos DES, Poleto MD, Galheigo MM, Gomes ATA, Verli H, Soares TA, Lins RD. Rotational Profiler: A Fast, Automated, and Interactive Server to Derive Torsional Dihedral Potentials for Classical Molecular Simulations. J Chem Inf Model 2020; 60:5923-5927. [PMID: 33213140 DOI: 10.1021/acs.jcim.0c01168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Rotational Profiler provides an analytical algorithm to compute sets of classical torsional dihedral parameters by fitting an empirical energy profile to a reference one that can be obtained experimentally or by quantum-mechanical methods. The resulting profiles are compatible with the functional forms in the most widely used biomolecular force fields (e.g., GROMOS, AMBER, OPLS, and CHARMM). The linear least-squares regression method is used to generate sets of parameters that best satisfy the fitting. Rotational Profiler is free to use, analytical, and force field/package independent. The formalism is herein described, and its usage, in an interactive and automated manner, is made available as a Web server at http://rotprof.lncc.br.
Collapse
Affiliation(s)
- Victor H Rusu
- Swiss National Supercomputing Centre, Lugano, Ticino 6900, Switzerland
| | - Denys E S Santos
- Department of Fundamental Chemistry, Federal University of Pernambuco, Recife, Pernambuco 50740-640, Brazil
| | - Marcelo D Poleto
- Department of General Biology, Federal University of Viçosa, Viçosa, Minas Gerais 36570-000, Brazil
| | - Marcelo M Galheigo
- Brazilian National Scientific Computing Laboratory, Petrópolis, Rio de Janeiro 25651-075, Brazil
| | - Antônio T A Gomes
- Brazilian National Scientific Computing Laboratory, Petrópolis, Rio de Janeiro 25651-075, Brazil
| | - Hugo Verli
- Center for Biotechnology, Federal University of Rio Grande do Sul, Rio Grande do Sul 91500-970, Brazil
| | - Thereza A Soares
- Department of Fundamental Chemistry, Federal University of Pernambuco, Recife, Pernambuco 50740-640, Brazil
| | - Roberto D Lins
- Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, Pernambuco 50740-465, Brazil
| |
Collapse
|
25
|
Out of Sight, Out of Mind: The Effect of the Equilibration Protocol on the Structural Ensembles of Charged Glycolipid Bilayers. Molecules 2020; 25:molecules25215120. [PMID: 33158044 PMCID: PMC7663769 DOI: 10.3390/molecules25215120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/28/2020] [Accepted: 10/30/2020] [Indexed: 11/16/2022] Open
Abstract
Molecular dynamics (MD) simulations represent an essential tool in the toolbox of modern chemistry, enabling the prediction of experimental observables for a variety of chemical systems and processes and majorly impacting the study of biological membranes. However, the chemical diversity of complex lipids beyond phospholipids brings new challenges to well-established protocols used in MD simulations of soft matter and requires continuous assessment to ensure simulation reproducibility and minimize unphysical behavior. Lipopolysaccharides (LPS) are highly charged glycolipids whose aggregation in a lamellar arrangement requires the binding of numerous cations to oppositely charged groups deep inside the membrane. The delicate balance between the fully hydrated carbohydrate region and the smaller hydrophobic core makes LPS membranes very sensitive to the choice of equilibration protocol. In this work, we show that the protocol successfully used to equilibrate phospholipid bilayers when applied to complex lipopolysaccharide membranes occasionally leads to a small expansion of the simulation box very early in the equilibration phase. Although the use of a barostat algorithm controls the system dimension and particle distances according to the target pressure, fluctuation in the fleeting pressure occasionally enables a few water molecules to trickle into the hydrophobic region of the membrane, with spurious solvent buildup. We show that this effect stems from the initial steps of NPT equilibration, where initial pressure can be fairly high. This can be solved with the use of a stepwise-thermalization NVT/NPT protocol, as demonstrated for atomistic MD simulations of LPS/DPPE and lipid-A membranes in the presence of different salts using an extension of the GROMOS forcefield within the GROMACS software. This equilibration protocol should be standard procedure for the generation of consistent structural ensembles of charged glycolipids starting from atomic coordinates not previously pre-equilibrated. Although different ways to deal with this issue can be envisioned, we investigated one alternative that could be readily available in major MD engines with general users in mind.
Collapse
|
26
|
Scherbinina SI, Toukach PV. Three-Dimensional Structures of Carbohydrates and Where to Find Them. Int J Mol Sci 2020; 21:E7702. [PMID: 33081008 PMCID: PMC7593929 DOI: 10.3390/ijms21207702] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 02/06/2023] Open
Abstract
Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology. Despite being a challenging task, development of computational methods for efficient treatment and management of spatial (3D) structural features of carbohydrates breaks new ground in modern glycoscience. This review is dedicated to approaches of chemo- and glyco-informatics towards 3D structural data generation, deposition and processing in regard to carbohydrates and their derivatives. Databases, molecular modeling and experimental data validation services, and structure visualization facilities developed for last five years are reviewed.
Collapse
Affiliation(s)
- Sofya I. Scherbinina
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky prospect 47, 119991 Moscow, Russia
- Higher Chemical College, D. Mendeleev University of Chemical Technology of Russia, Miusskaya Square 9, 125047 Moscow, Russia
| | - Philip V. Toukach
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky prospect 47, 119991 Moscow, Russia
| |
Collapse
|
27
|
Horne JE, Brockwell DJ, Radford SE. Role of the lipid bilayer in outer membrane protein folding in Gram-negative bacteria. J Biol Chem 2020; 295:10340-10367. [PMID: 32499369 PMCID: PMC7383365 DOI: 10.1074/jbc.rev120.011473] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 06/03/2020] [Indexed: 01/09/2023] Open
Abstract
β-Barrel outer membrane proteins (OMPs) represent the major proteinaceous component of the outer membrane (OM) of Gram-negative bacteria. These proteins perform key roles in cell structure and morphology, nutrient acquisition, colonization and invasion, and protection against external toxic threats such as antibiotics. To become functional, OMPs must fold and insert into a crowded and asymmetric OM that lacks much freely accessible lipid. This feat is accomplished in the absence of an external energy source and is thought to be driven by the high thermodynamic stability of folded OMPs in the OM. With such a stable fold, the challenge that bacteria face in assembling OMPs into the OM is how to overcome the initial energy barrier of membrane insertion. In this review, we highlight the roles of the lipid environment and the OM in modulating the OMP-folding landscape and discuss the factors that guide folding in vitro and in vivo We particularly focus on the composition, architecture, and physical properties of the OM and how an understanding of the folding properties of OMPs in vitro can help explain the challenges they encounter during folding in vivo Current models of OMP biogenesis in the cellular environment are still in flux, but the stakes for improving the accuracy of these models are high. OMP folding is an essential process in all Gram-negative bacteria, and considering the looming crisis of widespread microbial drug resistance it is an attractive target. To bring down this vital OMP-supported barrier to antibiotics, we must first understand how bacterial cells build it.
Collapse
Affiliation(s)
- Jim E Horne
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| |
Collapse
|
28
|
Kamalul Aripin NF, Heap JM, Piñol R, Manickam-Achari V, Martinez-Felipe A. Unveiling the hydrogen bonding network in liquid crystalline natural-based glycosides containing polymeric complexes: Experimental and theoretical assessment. Colloids Surf A Physicochem Eng Asp 2020. [DOI: 10.1016/j.colsurfa.2020.124685] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
29
|
Martinotti C, Ruiz-Perez L, Deplazes E, Mancera RL. Molecular Dynamics Simulation of Small Molecules Interacting with Biological Membranes. Chemphyschem 2020; 21:1486-1514. [PMID: 32452115 DOI: 10.1002/cphc.202000219] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/22/2020] [Indexed: 12/12/2022]
Abstract
Cell membranes protect and compartmentalise cells and their organelles. The semi-permeable nature of these membranes controls the exchange of solutes across their structure. Characterising the interaction of small molecules with biological membranes is critical to understanding of physiological processes, drug action and permeation, and many biotechnological applications. This review provides an overview of how molecular simulations are used to study the interaction of small molecules with biological membranes, with a particular focus on the interactions of water, organic compounds, drugs and short peptides with models of plasma cell membrane and stratum corneum lipid bilayers. This review will not delve on other types of membranes which might have different composition and arrangement, such as thylakoid or mitochondrial membranes. The application of unbiased molecular dynamics simulations and enhanced sampling methods such as umbrella sampling, metadynamics and replica exchange are described using key examples. This review demonstrates how state-of-the-art molecular simulations have been used successfully to describe the mechanism of binding and permeation of small molecules with biological membranes, as well as associated changes to the structure and dynamics of these membranes. The review concludes with an outlook on future directions in this field.
Collapse
Affiliation(s)
- Carlo Martinotti
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and, Curtin Institute for Computation, Curtin University, Perth, WA 6845, Australia
| | - Lanie Ruiz-Perez
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and, Curtin Institute for Computation, Curtin University, Perth, WA 6845, Australia
| | - Evelyne Deplazes
- School of Life Sciences, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Ricardo L Mancera
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and, Curtin Institute for Computation, Curtin University, Perth, WA 6845, Australia
| |
Collapse
|
30
|
Abstract
Gram-negative bacteria are protected by a multicompartmental molecular architecture known as the cell envelope that contains two membranes and a thin cell wall. As the cell envelope controls influx and efflux of molecular species, in recent years both experimental and computational studies of such architectures have seen a resurgence due to the implications for antibiotic development. In this article we review recent progress in molecular simulations of bacterial membranes. We show that enormous progress has been made in terms of the lipidic and protein compositions of bacterial systems. The simulations have moved away from the traditional setup of one protein surrounded by a large patch of the same lipid type toward a more bio-logically representative viewpoint. Simulations with multiple cell envelope components are also emerging. We review some of the key method developments that have facilitated recent progress, discuss some current limitations, and offer a perspective on future directions.
Collapse
Affiliation(s)
- Wonpil Im
- Departments of Biological Sciences and Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, USA
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, Republic of Korea
| | - Syma Khalid
- School of Chemistry, University of Southampton, Southampton S017 1BJ, United Kingdom
| |
Collapse
|
31
|
Rahnamoun A, Kim K, Pedersen JA, Hernandez R. Ionic Environment Affects Bacterial Lipopolysaccharide Packing and Function. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:3149-3158. [PMID: 32069057 DOI: 10.1021/acs.langmuir.9b03162] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The interaction of lipopolysaccharides (LPS) with metal cations strongly affects the stability and function of the Gram-negative bacterial outer membrane. The sensitivity of deep rough (Re) LPS packing and function to the ionic environment, as affected by cation valency and ionic radius, has been determined using molecular dynamics simulations and Langmuir balance experiments. The degree of LPS aggregation within the LPS models in the presence of different cations is assessed by measuring the effective mean molecular area (Âm) of each LPS molecule projected onto the interfacial plane at the end of the equilibration. These results are compared to the LPS mean molecular area from experimental measurements in which the LPS monolayers are assembled at the air-water interface using a Langmuir film balance. We found that packing of the LPS arrays is sensitive to the ionic radius and ion valency of the cations present in solution during LPS array packing. Using enhanced sampling of the free energy for the intercalation of oligo(allylamine HCl) (OAH) into deep rough Salmonella enterica LPS bilayers, we obtained the affinity of the core section of LPS to OAH as a function of the nature of the metal cations present in solution. We found that packing of the solvated LPS bilayer models is sensitive to ionic radius and ion valency of the neutralizing cations. This further suggests that ion bridging and steric barriers rather than charge shielding are important factors in mitigating ligand intercalation under conditions with low ionic concentrations.
Collapse
Affiliation(s)
- Ali Rahnamoun
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Kyoungtea Kim
- Molecular and Environmental Toxicology Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Joel A Pedersen
- Molecular and Environmental Toxicology Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Departments of Soil Science, Chemistry, Civil & Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Rigoberto Hernandez
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| |
Collapse
|
32
|
Molecular characterization of the outer membrane of Pseudomonas aeruginosa. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183151. [DOI: 10.1016/j.bbamem.2019.183151] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 10/28/2019] [Accepted: 12/06/2019] [Indexed: 01/07/2023]
|
33
|
Rice A, Rooney MT, Greenwood AI, Cotten ML, Wereszczynski J. Lipopolysaccharide Simulations Are Sensitive to Phosphate Charge and Ion Parameterization. J Chem Theory Comput 2020; 16:1806-1815. [PMID: 32023054 DOI: 10.1021/acs.jctc.9b00868] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The high proportion of lipopolysaccharide (LPS) molecules in the outer membrane of Gram-negative bacteria makes it a highly effective barrier to small molecules, antibiotic drugs, and other antimicrobial agents. Given this vital role in protecting bacteria from potentially hostile environments, simulations of LPS bilayers and outer membrane systems represent a critical tool for understanding the mechanisms of bacterial resistance and the development of new antibiotic compounds that circumvent these defenses. The basis of these simulations is parameterizations of LPS, which have been developed for all major molecular dynamics force fields. However, these parameterizations differ in both the protonation state of LPS and how LPS membranes behave in the presence of various ion species. To address these discrepancies and understand the effects of phosphate charge on bilayer properties, simulations were performed for multiple distinct LPS chemotypes with different ion parameterizations in both protonated or deprotonated lipid A states. These simulations show that bilayer properties, such as the area per lipid and inter-lipid hydrogen bonding, are highly influenced by the choice of phosphate group charges, cation type, and ion parameterization, with protonated LPS and monovalent cations with modified nonbonded parameters providing the best match to the experiments. Additionally, alchemical free energy simulations were performed to determine theoretical pKa values for LPS and subsequently validated by 31P solid-state nuclear magnetic resonance experiments. Results from these complementary computational and experimental studies demonstrate that the protonated state dominates at physiological pH, contrary to the deprotonated form modeled by many LPS force fields. Overall, these results highlight the sensitivity of LPS simulations to phosphate charge and ion parameters while offering recommendations for how existing models should be updated for consistency between force fields as well as to best match experiments.
Collapse
Affiliation(s)
- Amy Rice
- Department of Physics and Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - Mary T Rooney
- Department of Applied Science, College of William and Mary, Williamsburg, Virginia 23185, United States
| | - Alexander I Greenwood
- Department of Applied Science, College of William and Mary, Williamsburg, Virginia 23185, United States.,Department of Physics, College of William and Mary, Williamsburg, Virginia 23185, United States
| | - Myriam L Cotten
- Department of Applied Science, College of William and Mary, Williamsburg, Virginia 23185, United States
| | - Jeff Wereszczynski
- Department of Physics and Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| |
Collapse
|
34
|
Aggregation of Lipid A Variants: A Hybrid Particle-Field Model. Biochim Biophys Acta Gen Subj 2020; 1865:129570. [PMID: 32105775 DOI: 10.1016/j.bbagen.2020.129570] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/10/2020] [Accepted: 02/19/2020] [Indexed: 12/23/2022]
Abstract
Lipid A is one of the three components of bacterial lipopolysaccharides constituting the outer membrane of Gram-negative bacteria, and is recognized to have an important biological role in the inflammatory response of mammalians. Its biological activity is modulated by the number of acyl-chains that are present in the lipid and by the dielectric medium, i.e., the type of counter-ions, through electrostatic interactions. In this paper, we report on a coarse-grained model of chemical variants of Lipid A based on the hybrid particle-field/molecular dynamics approach (hPF-MD). In particular, we investigate the stability of Lipid A bilayers for two different hexa- and tetra-acylated structures. Comparing particle density profiles along bilayer cross-sections, we find good agreement between the hPF-MD model and reference all-atom simulation for both chemical variants of Lipid A. hPF-MD models of constituted bilayers composed by hexa-acylated Lipid A in water are stable within the simulation time. We further validate our model by verifying that the phase behavior of Lipid A/counterion/water mixtures is correctly reproduced. In particular, hPF-MD simulations predict the correct self-assembly of different lamellar and micellar phases from an initially random distribution of Lipid A molecules with counterions in water. Finally, it is possible to observe the spontaneous formation and stability of Lipid A vesicles by fusion of micellar aggregates.
Collapse
|
35
|
Domínguez-Medina CC, Pérez-Toledo M, Schager AE, Marshall JL, Cook CN, Bobat S, Hwang H, Chun BJ, Logan E, Bryant JA, Channell WM, Morris FC, Jossi SE, Alshayea A, Rossiter AE, Barrow PA, Horsnell WG, MacLennan CA, Henderson IR, Lakey JH, Gumbart JC, López-Macías C, Bavro VN, Cunningham AF. Outer membrane protein size and LPS O-antigen define protective antibody targeting to the Salmonella surface. Nat Commun 2020; 11:851. [PMID: 32051408 PMCID: PMC7015928 DOI: 10.1038/s41467-020-14655-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 01/23/2020] [Indexed: 11/28/2022] Open
Abstract
Lipopolysaccharide (LPS) O-antigen (O-Ag) is known to limit antibody binding to surface antigens, although the relationship between antibody, O-Ag and other outer-membrane antigens is poorly understood. Here we report, immunization with the trimeric porin OmpD from Salmonella Typhimurium (STmOmpD) protects against infection. Atomistic molecular dynamics simulations indicate this is because OmpD trimers generate footprints within the O-Ag layer sufficiently sized for a single IgG Fab to access. While STmOmpD differs from its orthologue in S. Enteritidis (SEn) by a single amino-acid residue, immunization with STmOmpD confers minimal protection to SEn. This is due to the OmpD-O-Ag interplay restricting IgG binding, with the pairing of OmpD with its native O-Ag being essential for optimal protection after immunization. Thus, both the chemical and physical structure of O-Ag are key for the presentation of specific epitopes within proteinaceous surface-antigens. This enhances combinatorial antigenic diversity in Gram-negative bacteria, while reducing associated fitness costs. The O-antigen of LPS is known to limit the binding of antibody to bacterial surface antigens. Here the AUs show that the chemical and physical structure of the O-antigen are central factors in limiting the exposure of surface antigens to antibodies during Salmonella infection, thus defining their protective qualities.
Collapse
Affiliation(s)
- C Coral Domínguez-Medina
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK.,Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Marisol Pérez-Toledo
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK.,Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK.,Medical Research Unit on Immunochemistry, Specialties Hospital, National Medical Centre "Siglo XXI" Mexican Institute for Social Security, Mexico City, Mexico
| | - Anna E Schager
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK.,Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Jennifer L Marshall
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK
| | - Charlotte N Cook
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK.,Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Saeeda Bobat
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK.,Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Hyea Hwang
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta GA, 30332, USA
| | - Byeong Jae Chun
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta GA, 30332, USA
| | - Erin Logan
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Anzio Road, Cape Town, Western Cape, 7925, South Africa
| | - Jack A Bryant
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Will M Channell
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK
| | - Faye C Morris
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Sian E Jossi
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK
| | - Areej Alshayea
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK
| | - Amanda E Rossiter
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Paul A Barrow
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire, LE12 5RD, UK
| | - William G Horsnell
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Anzio Road, Cape Town, Western Cape, 7925, South Africa
| | - Calman A MacLennan
- Jenner Institute, Nuffield Department of Medicine, Old Road Campus Research Building, Roosevelt Drive, University of Oxford, Oxford, OX3 7DQ, UK
| | - Ian R Henderson
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Jeremy H Lakey
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, NE2 4HH, UK
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Constantino López-Macías
- Medical Research Unit on Immunochemistry, Specialties Hospital, National Medical Centre "Siglo XXI" Mexican Institute for Social Security, Mexico City, Mexico
| | - Vassiliy N Bavro
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK.
| | - Adam F Cunningham
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK. .,Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK.
| |
Collapse
|
36
|
Guo J, Chia GW, Berezhnoy NV, Cazenave-Gassiot A, Kjelleberg S, Hinks J, Mu Y, Seviour T. Bacterial lipopolysaccharide core structures mediate effects of butanol ingress. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183150. [DOI: 10.1016/j.bbamem.2019.183150] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 11/07/2019] [Accepted: 12/06/2019] [Indexed: 12/13/2022]
|
37
|
Zhang H, Kai ELJ, Lu L. Investigating the stability of dengue virus envelope protein dimer using well-tempered metadynamics simulations. Proteins 2019; 88:643-653. [PMID: 31697409 DOI: 10.1002/prot.25844] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/24/2019] [Accepted: 11/03/2019] [Indexed: 12/21/2022]
Abstract
We explored the stability of the dengue virus envelope (E) protein dimer since it is widely assumed that the E protein dimer is stabilized by drug ligands or antibodies in an acidic environment, neutralizing the virus's ability to fuse with human cells. During this process, a large conformational change of the E protein dimer is required. We performed Molecular Dynamics simulations to mimic the conformational change and stability of the dimer in neutral and acidic conditions with the well-tempered metadynamics method. Furthermore, as a few neutralizing antibodies discovered from dengue patients were reported, we used the same simulation method to examine the influence of a selected antibody on the dimer stability in both neutral and acidic conditions. We also investigated the antibody's influence on a point-mutated E protein that had been reported to interrupt the protein-antibody interaction and result in more than 95% loss of the antibody's binding ability. Our simulation results are highly consistent with the experimental conclusion that binding of the antibody to the E protein dimer neutralizes the virus, especially in a low pH condition, while the mutation of W101A or N153A significantly reduces the antibody's ability in stabilizing the E protein dimer. We demonstrate that well-tempered metadynamics can be used to accurately explore the antibody's interaction on large protein complexes such as the E protein dimer, and the computational approach in this work is promising in future antibody development.
Collapse
Affiliation(s)
- Haiping Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institutes of Advanced Technology, Shenzhen, Guangdong Province, People's Republic of China
| | - Eric L J Kai
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Lanyuan Lu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| |
Collapse
|
38
|
Bouvier B. Curvature as a Collective Coordinate in Enhanced Sampling Membrane Simulations. J Chem Theory Comput 2019; 15:6551-6561. [DOI: 10.1021/acs.jctc.9b00716] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Benjamin Bouvier
- Laboratoire de Glycochimie, des Antimicrobiens et des Agroressources, CNRS UMR7378/Université de Picardie Jules Verne, 10, rue Baudelocque, 80039 Amiens Cedex, France
| |
Collapse
|
39
|
Behbahani AF, Motlagh GH, Vaez Allaei SM, Harmandaris VA. Structure and Conformation of Stereoregular Poly(methyl methacrylate) Chains Adsorbed on Graphene Oxide and Reduced Graphene Oxide via Atomistic Simulations. Macromolecules 2019. [DOI: 10.1021/acs.macromol.9b00574] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Alireza F. Behbahani
- Institute of Applied and Computational Mathematics, Foundation for Research and Technology—Hellas, Heraklion GR-71110, Greece
- Advanced Polymer Materials and Processing Lab, School of Chemical Engineering, College of Engineering, University of Tehran, Tehran 11155-4563, Iran
| | - G. Hashemi Motlagh
- Advanced Polymer Materials and Processing Lab, School of Chemical Engineering, College of Engineering, University of Tehran, Tehran 11155-4563, Iran
| | - S. Mehdi Vaez Allaei
- Department of Physics, University of Tehran, Tehran 14395-547, Iran
- School of Physics, Institute for Research in Fundamental Sciences (IPM), Tehran 19395-5531, Iran
| | - Vagelis A. Harmandaris
- Institute of Applied and Computational Mathematics, Foundation for Research and Technology—Hellas, Heraklion GR-71110, Greece
- Department of Mathematics and Applied Mathematics, University of Crete, Heraklion GR-71110, Greece
| |
Collapse
|
40
|
Marrink SJ, Corradi V, Souza PC, Ingólfsson HI, Tieleman DP, Sansom MS. Computational Modeling of Realistic Cell Membranes. Chem Rev 2019; 119:6184-6226. [PMID: 30623647 PMCID: PMC6509646 DOI: 10.1021/acs.chemrev.8b00460] [Citation(s) in RCA: 408] [Impact Index Per Article: 81.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Indexed: 12/15/2022]
Abstract
Cell membranes contain a large variety of lipid types and are crowded with proteins, endowing them with the plasticity needed to fulfill their key roles in cell functioning. The compositional complexity of cellular membranes gives rise to a heterogeneous lateral organization, which is still poorly understood. Computational models, in particular molecular dynamics simulations and related techniques, have provided important insight into the organizational principles of cell membranes over the past decades. Now, we are witnessing a transition from simulations of simpler membrane models to multicomponent systems, culminating in realistic models of an increasing variety of cell types and organelles. Here, we review the state of the art in the field of realistic membrane simulations and discuss the current limitations and challenges ahead.
Collapse
Affiliation(s)
- Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Valentina Corradi
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Paulo C.T. Souza
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Helgi I. Ingólfsson
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - D. Peter Tieleman
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Mark S.P. Sansom
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
| |
Collapse
|
41
|
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.
Collapse
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
| |
Collapse
|
42
|
Jefferies D, Shearer J, Khalid S. Role of O-Antigen in Response to Mechanical Stress of the E. coli Outer Membrane: Insights from Coarse-Grained MD Simulations. J Phys Chem B 2019; 123:3567-3575. [DOI: 10.1021/acs.jpcb.8b12168] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Damien Jefferies
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
| | - Jonathan Shearer
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
| | - Syma Khalid
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
| |
Collapse
|
43
|
Rice A, Wereszczynski J. Atomistic Scale Effects of Lipopolysaccharide Modifications on Bacterial Outer Membrane Defenses. Biophys J 2019; 114:1389-1399. [PMID: 29590596 DOI: 10.1016/j.bpj.2018.02.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 02/02/2018] [Accepted: 02/06/2018] [Indexed: 12/20/2022] Open
Abstract
Lipopolysaccharides (LPS) are a main constituent of the outer membrane of Gram-negative bacteria. Salmonella enterica, like many other bacterial species, are able to chemically modify the structure of their LPS molecules through the PhoPQ pathway as a defense mechanism against the host immune response. These modifications make the outer membrane more resistant to antimicrobial peptides (AMPs), large lipophilic drugs, and cation depletion, and are crucial for survival within a host organism. It is believed that these LPS modifications prevent the penetration of large molecules and AMPs through a strengthening of lateral interactions between neighboring LPS molecules. Here, we performed a series of long-timescale molecular dynamics simulations to study how each of three key S. enterica lipid A modifications affect bilayer properties, with a focus on membrane structural characteristics, lateral interactions, and the divalent cation bridging network. Our results discern the unique impact each modification has on strengthening the bacterial outer membrane through effects such as increased hydrogen bonding and tighter lipid packing. Additionally, one of the modifications studied shifts Ca2+ from the lipid A region, replacing it as a major cross-linking agent between adjacent lipids and potentially making bacteria less susceptible to AMPs that competitively displace cations from the membrane surface. These results further improve our understanding of outer membrane chemical properties and help elucidate how outer membrane modification systems, such as PhoPQ in S. enterica, are able to alter bacterial virulence.
Collapse
Affiliation(s)
- Amy Rice
- Department of Physics and The Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, Illinois
| | - Jeff Wereszczynski
- Department of Physics and The Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, Illinois.
| |
Collapse
|
44
|
Shearer J, Jefferies D, Khalid S. Outer Membrane Proteins OmpA, FhuA, OmpF, EstA, BtuB, and OmpX Have Unique Lipopolysaccharide Fingerprints. J Chem Theory Comput 2019; 15:2608-2619. [PMID: 30848905 DOI: 10.1021/acs.jctc.8b01059] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The outer membrane of Gram-negative bacteria has a highly complex asymmetrical architecture, containing a mixture of phospholipids in the inner leaflet and almost exclusively lipopolysaccharide (LPS) molecules in the outer leaflet. In E. coli, the outer membrane contains a wide range of proteins with a β barrel architecture, that vary in size from the smallest having eight strands to larger barrels composed of 22 strands. Here we report coarse-grained molecular dynamics simulations of six proteins from the E. coli outer membrane OmpA, OmpX, BtuB, FhuA, OmpF, and EstA in a range of membrane environments, which are representative of the in vivo conditions for different strains of E. coli. We show that each protein has a unique pattern of interaction with the surrounding membrane, which is influenced by the composition of the protein, the level of LPS in the outer leaflet, and the differing mobilities of the lipids in the two leaflets of the membrane. Overall we present analyses from over 200 μs of simulation for each protein.
Collapse
Affiliation(s)
- Jonathan Shearer
- School of Chemistry , University of Southampton, Highfield , Southampton , SO17 1BJ United Kingdom
| | - Damien Jefferies
- School of Chemistry , University of Southampton, Highfield , Southampton , SO17 1BJ United Kingdom
| | - Syma Khalid
- School of Chemistry , University of Southampton, Highfield , Southampton , SO17 1BJ United Kingdom
| |
Collapse
|
45
|
Baltoumas FA, Hamodrakas SJ, Iconomidou VA. The gram‐negative outer membrane modeler: Automated building of lipopolysaccharide‐rich bacterial outer membranes in four force fields. J Comput Chem 2019; 40:1727-1734. [DOI: 10.1002/jcc.25823] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/18/2019] [Accepted: 03/03/2019] [Indexed: 01/11/2023]
Affiliation(s)
- Fotis A. Baltoumas
- Section of Cell Biology and Biophysics, Department of Biology, School of SciencesNational and Kapodistrian University of Athens Panepistimiopolis, 15701, Athens Greece
| | - Stavros J. Hamodrakas
- Section of Cell Biology and Biophysics, Department of Biology, School of SciencesNational and Kapodistrian University of Athens Panepistimiopolis, 15701, Athens Greece
| | - Vassiliki A. Iconomidou
- Section of Cell Biology and Biophysics, Department of Biology, School of SciencesNational and Kapodistrian University of Athens Panepistimiopolis, 15701, Athens Greece
| |
Collapse
|
46
|
Corradi V, Sejdiu BI, Mesa-Galloso H, Abdizadeh H, Noskov SY, Marrink SJ, Tieleman DP. Emerging Diversity in Lipid-Protein Interactions. Chem Rev 2019; 119:5775-5848. [PMID: 30758191 PMCID: PMC6509647 DOI: 10.1021/acs.chemrev.8b00451] [Citation(s) in RCA: 245] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Membrane
lipids interact with proteins in a variety of ways, ranging
from providing a stable membrane environment for proteins to being
embedded in to detailed roles in complicated and well-regulated protein
functions. Experimental and computational advances are converging
in a rapidly expanding research area of lipid–protein interactions.
Experimentally, the database of high-resolution membrane protein structures
is growing, as are capabilities to identify the complex lipid composition
of different membranes, to probe the challenging time and length scales
of lipid–protein interactions, and to link lipid–protein
interactions to protein function in a variety of proteins. Computationally,
more accurate membrane models and more powerful computers now enable
a detailed look at lipid–protein interactions and increasing
overlap with experimental observations for validation and joint interpretation
of simulation and experiment. Here we review papers that use computational
approaches to study detailed lipid–protein interactions, together
with brief experimental and physiological contexts, aiming at comprehensive
coverage of simulation papers in the last five years. Overall, a complex
picture of lipid–protein interactions emerges, through a range
of mechanisms including modulation of the physical properties of the
lipid environment, detailed chemical interactions between lipids and
proteins, and key functional roles of very specific lipids binding
to well-defined binding sites on proteins. Computationally, despite
important limitations, molecular dynamics simulations with current
computer power and theoretical models are now in an excellent position
to answer detailed questions about lipid–protein interactions.
Collapse
Affiliation(s)
- Valentina Corradi
- Centre for Molecular Simulation and Department of Biological Sciences , University of Calgary , 2500 University Drive NW , Calgary , Alberta T2N 1N4 , Canada
| | - Besian I Sejdiu
- Centre for Molecular Simulation and Department of Biological Sciences , University of Calgary , 2500 University Drive NW , Calgary , Alberta T2N 1N4 , Canada
| | - Haydee Mesa-Galloso
- Centre for Molecular Simulation and Department of Biological Sciences , University of Calgary , 2500 University Drive NW , Calgary , Alberta T2N 1N4 , Canada
| | - Haleh Abdizadeh
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Nijenborgh 7 , 9747 AG Groningen , The Netherlands
| | - Sergei Yu Noskov
- Centre for Molecular Simulation and Department of Biological Sciences , University of Calgary , 2500 University Drive NW , Calgary , Alberta T2N 1N4 , Canada
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Nijenborgh 7 , 9747 AG Groningen , The Netherlands
| | - D Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences , University of Calgary , 2500 University Drive NW , Calgary , Alberta T2N 1N4 , Canada
| |
Collapse
|
47
|
Binding from Both Sides: TolR and Full-Length OmpA Bind and Maintain the Local Structure of the E. coli Cell Wall. Structure 2019; 27:713-724.e2. [PMID: 30713026 DOI: 10.1016/j.str.2019.01.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/12/2018] [Accepted: 12/31/2018] [Indexed: 12/23/2022]
Abstract
We present a molecular modeling and simulation study of the E. coli cell envelope, with a particular focus on the role of TolR, a native protein of the E. coli inner membrane, in interactions with the cell wall. TolR has been proposed to bind to peptidoglycan, but the only structure of this protein thus far is in a conformation in which the putative peptidoglycan binding domain is not accessible. We show that a model of the extended conformation of the protein in which this domain is exposed binds peptidoglycan largely through electrostatic interactions. Non-covalent interactions of TolR and OmpA with the cell wall, from the inner membrane and outer membrane sides, respectively, maintain the position of the cell wall even in the absence of Braun's lipoprotein. The charged residues that mediate the cell-wall interactions of TolR in our simulations are conserved across a number of species of gram-negative bacteria.
Collapse
|
48
|
Li A, Schertzer JW, Yong X. Molecular dynamics modeling of Pseudomonas aeruginosa outer membranes. Phys Chem Chem Phys 2018; 20:23635-23648. [PMID: 30191217 DOI: 10.1039/c8cp04278k] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Pseudomonas aeruginosa is a common Gram-negative bacterium and opportunistic human pathogen. The distinctive structure of its outer membrane (OM) and outer membrane vesicles (OMVs) plays a fundamental role in bacterial virulence, colonization ability, and antibiotic resistance. To provide critical insights into OM and OMV functionality, we conducted an all-atom molecular dynamics study of asymmetric membranes that are biologically relevant to P. aeruginosa. We hybridized a GLYCAM06-based lipopolysaccharides force field with the Stockholm lipids force field (Slipids) to model bilayer membranes with Lipid A molecules in one leaflet and physiologically relevant phospholipid molecules in the other, including 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine (DPPE), 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE), 1,2-dipalmitoyl-sn-glycero-3-phosphoglycerol (DPPG), and 1,2-dioleoyl-sn-glycero-3-phosphoglycerol (DOPG). In particular, a membrane with phospholipid composition representing the P. aeruginosa OM was constructed and modeled by mixing the physiologically dominant components. The detailed structure of membranes was characterized by area per lipid, transmembrane mass and charge densities, radial distribution function (RDF), deuterium order parameter (SCD) of acyl chains, and inclination angles of phosphates and disaccharide in Lipid A. The membrane fluidity in equilibrium and the hydration of functional groups were probed and characterized quantitatively. The consistent properties of the Lipid A leaflets in different membranes demonstrate its compatibility with various phospholipids present in the P. aeruginosa OM. The more ordered acyl chains of Lipid A compared to the cytoplasmic cell membrane contribute to the low permeability of bacterial outer membrane. The findings of this computational investigation of P. aeruginosa OM will further the understanding of microbial pathogenesis and enable future study of OMV biogenesis.
Collapse
Affiliation(s)
- Ao Li
- Department of Mechanical Engineering, Binghamton University, The State University of New York, Binghamton, New York 13902, USA.
| | | | | |
Collapse
|
49
|
Behbahani AF, Vaez Allaei SM, Motlagh GH, Eslami H, Harmandaris VA. Structure, Dynamics, and Apparent Glass Transition of Stereoregular Poly(methyl methacrylate)/Graphene Interfaces through Atomistic Simulations. Macromolecules 2018. [DOI: 10.1021/acs.macromol.8b01160] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Alireza F. Behbahani
- Advanced Polymer Materials and Processing Lab, School of Chemical Engineering, College of Engineering, University of Tehran, Tehran 11155-4563, Iran
- Institute of Applied and Computational Mathematics, Foundation for Research and Technology - Hellas, Heraklion GR-71110, Greece
| | - S. Mehdi Vaez Allaei
- Department of Physics, University of Tehran, Tehran 14395-547, Iran
- School of Physics, Institute for Research in Fundamental Sciences (IPM), Tehran 19395-5531, Iran
| | - Ghodratollah H. Motlagh
- Advanced Polymer Materials and Processing Lab, School of Chemical Engineering, College of Engineering, University of Tehran, Tehran 11155-4563, Iran
| | - Hossein Eslami
- Department of Chemistry, College of Sciences, Persian Gulf University, Boushehr 75168, Iran
| | - Vagelis A. Harmandaris
- Institute of Applied and Computational Mathematics, Foundation for Research and Technology - Hellas, Heraklion GR-71110, Greece
- Department of Mathematics and Applied Mathematics, University of Crete, Heraklion GR-71110, Greece
| |
Collapse
|
50
|
Ma H, Khan A, Nangia S. Dynamics of OmpF Trimer Formation in the Bacterial Outer Membrane of Escherichia coli. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:5623-5634. [PMID: 29166022 DOI: 10.1021/acs.langmuir.7b02653] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The self-assembly of outer membrane protein F (OmpF) in the outer membrane of Escherichia coli Gram-negative bacteria was studied using multiscale molecular dynamics simulations. To accommodate the long time scale required for protein assembly, coarse-grained parametrization of E. coli outer membrane lipids was first developed. The OmpF monomers formed stable dimers at specific protein-protein interactions sites irrespective of the lipid membrane environment. The dimer intermediate was asymmetric but provided a template to form a symmetric trimer. Superposition analysis of the self-assembled trimer with the X-ray crystal structure of the trimer available in the protein data bank showed excellent agreement with global root-mean-square deviation of less than 2.2 Å. The free energy change associated with dimer formation was -26 ± 1 kcal mol-1, and for a dimer to bind to a monomer and to form a trimer yielded -56 ± 4 kcal mol-1. Based on thermodynamic data, an alternate path to trimer formation via interaction of two dimers is also presented.
Collapse
Affiliation(s)
- Huilin Ma
- Department of Biomedical and Chemical Engineering , Syracuse University , Syracuse , New York 13244 , United States
| | - Aliza Khan
- Department of Biomedical and Chemical Engineering , Syracuse University , Syracuse , New York 13244 , United States
| | - Shikha Nangia
- Department of Biomedical and Chemical Engineering , Syracuse University , Syracuse , New York 13244 , United States
| |
Collapse
|