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Krishna NB, Roopa L, Pravin Kumar R, S GT. Computational studies on the catalytic potential of the double active site for enzyme engineering. Sci Rep 2024; 14:17892. [PMID: 39095391 DOI: 10.1038/s41598-024-60824-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/27/2024] [Indexed: 08/04/2024] Open
Abstract
Proteins possessing double active sites have the potential to revolutionise enzyme design strategies. This study extensively explored an enzyme that contains both a natural active site (NAS) and an engineered active site (EAS), focusing on understanding its structural and functional properties. Metadynamics simulations were employed to investigate how substrates interacted with their respective active sites. The results revealed that both the NAS and EAS exhibited similar minimum energy states, indicating comparable binding affinities. However, it became apparent that the EAS had a weaker binding site for the substrate due to its smaller pocket and constrained conformation. Interestingly, the EAS also displayed dynamic behaviour, with the substrate observed to move outside the pocket, suggesting the possibility of substrate translocation. To gain further insights, steered molecular dynamics (SMD) simulations were conducted to study the conformational changes of the substrate and its interactions with catalytic residues. Notably, the substrate adopted distinct conformations, including near-attack conformations, in both the EAS and NAS. Nevertheless, the NAS demonstrated superior binding minima for the substrate compared to the EAS, reinforcing the observation that the engineered active site was less favourable for substrate binding due to its limitations. The QM/MM (Quantum mechanics and molecular mechanics) analyses highlight the energy disparity between NAS and EAS. Specifically, EAS exhibited elevated energy levels due to its engineered active site being located on the surface. This positioning exposes the substrate to solvents and water molecules, adding to the energy challenge. Consequently, the engineered enzyme did not provide a significant advantage in substrate binding over the single active site protein. Further, the investigation of internal channels and tunnels within the protein shed light on the pathways facilitating transport between the two active sites. By unravelling the complex dynamics and functional characteristics of this double-active site protein, this study offers valuable insights into novel strategies of enzyme engineering. These findings establish a solid foundation for future research endeavours aimed at harnessing the potential of double-active site proteins in diverse biotechnological applications.
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Affiliation(s)
- Naveen Banchallihundi Krishna
- Department of Computational Biology and AI, Kcat Enzymatic Private Limited, #16, Ramakrishnappa Road, Cox Town, Bangalore, 560005, India
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysuru, 570015, India
| | - Lalitha Roopa
- Department of Computational Biology and AI, Kcat Enzymatic Private Limited, #16, Ramakrishnappa Road, Cox Town, Bangalore, 560005, India
| | - R Pravin Kumar
- Department of Computational Biology and AI, Kcat Enzymatic Private Limited, #16, Ramakrishnappa Road, Cox Town, Bangalore, 560005, India.
| | - Gopenath T S
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysuru, 570015, India
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2
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Paulraj MS, Eringathodi S, Mollah AKMM, Alexis Thayaparan CT, Kuldeep SA, Subramanian PS, M I, Dhanaraj P. 2-[( E)-(2-carboxybenzylidene) amino] ethan ammonium-like amino acid zwitterions: crystal structure, functional studies and its molecular dynamic simulation study with drug target receptors. J Biomol Struct Dyn 2024; 42:6081-6090. [PMID: 37403277 DOI: 10.1080/07391102.2023.2230296] [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: 11/22/2022] [Accepted: 06/22/2023] [Indexed: 07/06/2023]
Abstract
The novel synthetic amino acid-like zwitterion containing imine bond ionic compound 2-[(E)-(2-carboxy benzylidene) amino] ethan ammonium salt, C10H12N2O2, was synthesized. Computational functional characterization is now being used to predict novel compounds. Here, we report on a titled combination that has been crystallizing in orthorhombic space group Pcc2 with Z = 4. The zwitterions form centrosymmetric dimers to polymeric supramolecular network via intermolecular N-H… O hydrogen bonds between the carboxylate groups and ammonium ion. The components are linked by ionic (N+-H-O-) and hydrogen bonds (N+-H-O), forming a complex three-dimensional supramolecular network. Further, molecular computational docking characterization study was performed with compound against multi-disease drug target biomolecule of anticancer target molecule of HDAC8 (PDB ID 1T69) receptor and antiviral molecular target protease (PDB ID 6LU7) to evaluate the interaction stability, conformational changes and to get insights into the natural dynamics on different timescales in solution. HighlightsThe novel zwitter ionic amino acid compound 2-[(E)-(2-carboxybenzylidene) amino] ethan ammonium salt, C10H12N2O2.The crystal structure determined for this compound illustrates the presence of intermolecular ionic N+-H-O- and N+-H-O hydrogen bonds between the carboxylate groups and ammonium ion, which influence the formation of a complex three-dimensional supramolecular polymeric network.Molecular docking studies helps to understand the conformational stability and interaction stabilityThe novel molecule can be considered for anticancer treatment.
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Affiliation(s)
| | - Suresh Eringathodi
- Analytical and Environmental Science Division and Centralized Instrument Facility, CSIR - Central Salt & Marine Chemicals Research Institute, Bhavnagar, Gujarat, India
| | | | | | | | - Palani Sivagnana Subramanian
- Inorganic Materials and Catalysis Division, CSIR - Central Salt & Marine Chemicals Research Institute, Bhavnagar, Gujarat, India
| | - Indiraleka M
- Department of Biotechnology, Mepco Schlenk Engineering College, Sivakasi, Tamil Nadu, India
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3
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Al-Soud YA, Al-Sawakhnah SO, Al-Qawasmeh RA, Al-Masoudi NA, Al-Ahmad AH, Al-Maliki L, van Geelen L, Kalscheuer R, Saeed BA, Shtaiwi A, Stark H. Novel 4-nitroimidazole analogues: synthesis, in vitro biological evaluation, in silico studies, and molecular dynamics simulation. Z NATURFORSCH C 2024; 79:61-71. [PMID: 38578162 DOI: 10.1515/znc-2023-0146] [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: 11/02/2023] [Accepted: 03/20/2024] [Indexed: 04/06/2024]
Abstract
A new series of 4-nitroimidazole bearing aryl piperazines 7-16, tetrazole 17 and 1,3,4-thiadiazole 18 derivatives was synthesized. All derivatives were screened for their anticancer activity against eight diverse human cancer cell lines (Capan-1, HCT-116, LN229, NCI-H460, DND-41, HL-60, K562, and Z138). Compound 17 proved the most potent compound of the series inhibiting proliferation of most of the selected human cancer cell lines with IC50 values in the low micromolar range. In addition, compound 11 exhibited IC50 values ranging 8.60-64.0 μM against a selection of cancer cell lines. These findings suggest that derivative 17 can potentially be a new lead compound for further development of novel antiproliferative agents. Additionally, 17-18 were assessed for their antibacterial and antituberculosis activity. Derivatives 17 and 18 were the most potent compounds of this series against both Staphylococcus aureus strain Wichita and a methicillin resistant strain of S. aureus (MRSA), as well as against Mycobacterium tuberculosis strain mc26230. The antiviral activity of 7-18 was also evaluated against diverse viruses, but no activity was detected. The docking study of compound 17 with putative protein targets in acute myeloid leukemia had been studied. Furthermore, the molecular dynamics simulation of 17 and 18 had been investigated.
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Affiliation(s)
- Yaseen A Al-Soud
- Department of Chemistry, College of Science, University of Al al-Bayt, Al-Mafraq, Jordan
| | - Sondos O Al-Sawakhnah
- Department of Chemistry, College of Science, University of Al al-Bayt, Al-Mafraq, Jordan
| | - Raed A Al-Qawasmeh
- Department of Chemistry, Pure and Applied Chemistry Group, College of Science, University of Sharjah, Sharjah 27272, UAE
| | - Najim A Al-Masoudi
- Department of Chemistry, College of Science, University of Basrah, Basrah, Iraq
| | - Ala'a H Al-Ahmad
- Department of Chemistry, College of Science, University of Al al-Bayt, Al-Mafraq, Jordan
| | - Lamiaa Al-Maliki
- Department of Molecular and Medical Biotechnology, Al-Nahrain University, Baghdad, Iraq
| | - Lasse van Geelen
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich - Heine - University Düsseldorf, Duesseldorf 40225, Germany
| | - Rainer Kalscheuer
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich - Heine - University Düsseldorf, Duesseldorf 40225, Germany
| | - Bahjat A Saeed
- Department of Chemistry, College of Education for Pure Science, University of Basrah, Basrah, Iraq
| | - Amneh Shtaiwi
- Faculty of Pharmacy, Middle East University, Queen Alia Airport Street, 11610, Amman, Jordan
| | - Holger Stark
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich - Heine - University Düsseldorf, Universitaetsstr. 1, 40225 Duesseldorf, Germany
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4
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Biswal S, Agmon N. Collagen Structured Hydration. Biomolecules 2023; 13:1744. [PMID: 38136615 PMCID: PMC10742079 DOI: 10.3390/biom13121744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023] Open
Abstract
Collagen is a triple-helical protein unique to the extracellular matrix, conferring rigidity and stability to tissues such as bone and tendon. For the [(PPG)10]3 collagen-mimetic peptide at room temperature, our molecular dynamics simulations show that these properties result in a remarkably ordered first hydration layer of water molecules hydrogen bonded to the backbone carbonyl (bb-CO) oxygen atoms. This originates from the following observations. The radius of gyration attests that the PPG triplets are organized along a straight line, so that all triplets (excepting the ends) are equivalent. The solvent-accessible surface area (SASA) for the bb-CO oxygens shows a repetitive regularity for every triplet. This leads to water occupancy of the bb-CO sites following a similar regularity. In the crystal-phase X-ray data, as well as in our 100 K simulations, we observe a 0-2-1 water occupancy in the P-P-G triplet. Surprisingly, a similar (0-1.7-1) regularity is maintained in the liquid phase, in spite of the sub-nsec water exchange rates, because the bb-CO sites rarely remain vacant. The manifested ordered first-shell water molecules are expected to produce a cylindrical electrostatic potential around the peptide, to be investigated in future work.
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Affiliation(s)
| | - Noam Agmon
- The Fritz Haber Research Center, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel;
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5
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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.
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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
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Jamal QMS, Alharbi AH. Molecular docking and dynamics studies of cigarette smoke carcinogens interacting with acetylcholinesterase and butyrylcholinesterase enzymes of the central nervous system. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:61972-61992. [PMID: 34382170 DOI: 10.1007/s11356-021-15269-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 06/28/2021] [Indexed: 06/13/2023]
Abstract
The free radicals produced by cigarette smoking are responsible for tissue damage, heart and lung diseases, and carcinogenesis. The effect of tobacco on the central nervous system (CNS) has received increased attention nowadays in research. Therefore, to explore the molecular interaction of cigarette smoke carcinogens (CSC) 4-(methylnitrosamine)-1-(3-pyridyl)-1-butanol (NNAL), 4-(methylnitrosamine)-1-(3-pyridyl)-1-butanone (NNK), and N'-nitrosonornicotine (NNN) with well-known targets of CNS-related disorders, acetylcholinesterase (AChE), and butyrylcholinesterase (BuChE) enzymes, a cascade of the computational study was conducted including molecular docking and molecular dynamics simulations (MDS). The investigated results of NNAL+AChEcomplex, NNK+AChEcomplex, and NNK+BuChEcomplex based on intermolecular energies (∆G) were found to -8.57 kcal/mol, -8.21 kcal/mol, and -8.08 kcal/mol, respectively. MDS deviation and fluctuation plots of the NNAL and NNK interaction with AChE and BuChE have shown significant results. Further, Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) results shown the best total binding energy (Binding∆G) -87.381 (+/-13.119) kJ/mol during NNK interaction with AChE. Our study suggests that CSC is well capable of altering the normal biomolecular mechanism of CNS; thus, obtained data could be useful to design extensive wet laboratory experimentation to know the effects of CSC on human CNS.
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Affiliation(s)
- Qazi Mohammad Sajid Jamal
- Department of Health Informatics, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah, Saudi Arabia.
| | - Ali H Alharbi
- Department of Health Informatics, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah, Saudi Arabia
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Yuan H, Liu L, Zhou J, Zhang T, Daily JW, Park S. Bioactive Components of Houttuynia cordata Thunb and Their Potential Mechanisms Against COVID-19 Using Network Pharmacology and Molecular Docking Approaches. J Med Food 2022; 25:355-366. [PMID: 35438554 DOI: 10.1089/jmf.2021.k.0144] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
We investigated the molecular mechanism by which Houttuynia cordata Thunb (HCT) may intervene in coronavirus disease 2019 (COVID-19) and COVID-19-induced cytokine storms using network pharmacology and molecular docking approaches. Using the Traditional Chinese medicine Systems Pharmacology Database and Analysis Platform (TCMSP), a "component-target-pathway" topology map of HCT for COVID-19 treatment was constructed using Cytoscape. Core target genes were analyzed using the STRING database, and the signal pathway map and biological mechanism of COVID-19 therapy were obtained using cluster profilers. Active components of HCT were docked with severe respiratory syndrome coronavirus 2 (SARS-CoV-2) 3C-like protease (3CLpro) and RNA-dependent RNA polymerase (RdRp) using AutoDockTools. Data visualization and statistical analysis were conducted using the R program. A molecular dynamic simulation was carried out with the Groningen Machine for Chemical Simulation program. HCT had six active anti-COVID-19 ingredients and 45 molecular targets. Their crucial target proteins for COVID-19 treatment were the RELA (nuclear factor kappa B [NF-κB] p65 subunit), interleukin 6, and mitogen-activated protein kinase 1. In functional enrichment analysis, the potential molecular targets of active components of HCT for COVID-19 treatment belonged to 18 signaling pathways (adjusted P = 2.12E-11). Gene ontology obtained by Kyoto Encyclopedia of Genes and Genome enrichment screening showed that the primary mechanism of COVID-19 treatment was upregulation of protein kinase C followed by downregulations of T cell differentiation and proliferation and NF-κB signaling. Molecular docking showed that the active components of HCT (quercetin and kaempferol) had similar binding affinities for SARS-CoV-2 3CLpro and SARS-CoV-2 RdRp, primary COVID-19 target proteins as did clinically used drugs. These results were confirmed with molecular dynamics simulation. In conclusion, multiple components of HCT, especially quercetin and kaempferol, have the potential to treat COVID-19 infection and COVID-19-induced cytokine storm by targeting multiple proteins.
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Affiliation(s)
- Heng Yuan
- Department of Bio-Convergence System, Hoseo University, Asan, South Korea
| | - Liping Liu
- College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo, China
| | - Junyu Zhou
- Department of Bio-Convergence System, Hoseo University, Asan, South Korea
| | - Ting Zhang
- Department of Bio-Convergence System, Hoseo University, Asan, South Korea
| | - James W Daily
- Daily Manufacturing, Inc., Rockwell, North Carolina, USA
| | - Sunmin Park
- Department of Bio-Convergence System, Hoseo University, Asan, South Korea.,Department of Food and Nutrition, Obesity/Diabetes Research Center, Hoseo University, Asan, South Korea
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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.
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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
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Gao Y, Lee J, Smith IPS, Lee H, Kim S, Qi Y, Klauda JB, Widmalm G, Khalid S, Im W. CHARMM-GUI Supports Hydrogen Mass Repartitioning and Different Protonation States of Phosphates in Lipopolysaccharides. J Chem Inf Model 2021; 61:831-839. [PMID: 33442985 PMCID: PMC7902386 DOI: 10.1021/acs.jcim.0c01360] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Hydrogen mass repartitioning (HMR) that permits time steps of all-atom molecular dynamics simulation up to 4 fs by increasing the mass of hydrogen atoms has been used in protein and phospholipid bilayers simulations to improve conformational sampling. Molecular simulation input generation via CHARMM-GUI now supports HMR for diverse simulation programs. In addition, considering ambiguous pH at the bacterial outer membrane surface, different protonation states, either -2e or -1e, of phosphate groups in lipopolysaccharides (LPS) are also supported in CHARMM-GUI LPS Modeler. To examine the robustness of HMR and the influence of protonation states of phosphate groups on LPS bilayer properties, eight different LPS-type all-atom systems with two phosphate protonation states are modeled and simulated utilizing both OpenMM 2-fs (standard) and 4-fs (HMR) schemes. Consistency in the conformational space sampled by standard and HMR simulations shows the reliability of HMR even in LPS, one of the most complex biomolecules. For systems with different protonation states, similar conformations are sampled with a PO41- or PO42- group, but different phosphate protonation states make slight impacts on lipid packing and conformational properties of LPS acyl chains. Systems with PO41- have a slightly smaller area per lipid and thus slightly more ordered lipid A acyl chains compared to those with PO42-, due to more electrostatic repulsion between PO42- even with neutralizing Ca2+ ions. HMR and different protonation states of phosphates of LPS available in CHARMM-GUI are expected to be useful for further investigations of biological systems of diverse origin.
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Affiliation(s)
- Ya Gao
- School of Mathematics, Physics and Statistics, Shanghai University of Engineering Science, Shanghai 201620, China
| | - Jumin Lee
- Department of Biological Sciences, Department of Chemistry, Department of Bioengineering, and Department of Computer Science and Engineering, Lehigh University, Bethlehem, PA 18015, USA
| | | | - Hwayoung Lee
- Department of Biological Sciences, Department of Chemistry, Department of Bioengineering, and Department of Computer Science and Engineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Seonghoon Kim
- Department of Biological Sciences, Department of Chemistry, Department of Bioengineering, and Department of Computer Science and Engineering, Lehigh University, Bethlehem, PA 18015, USA
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, Republic of Korea
| | - Yifei Qi
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
| | - Jeffery B. Klauda
- Department of Chemical and Biomolecular Engineering and the Biophysics Program, University of Maryland College Park, Maryland 20742, USA
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
| | - Syma Khalid
- School of Chemistry, University of Southampton, Southampton, S017 1BJ, UK
| | - Wonpil Im
- Department of Biological Sciences, Department of Chemistry, Department of Bioengineering, and Department of Computer Science and Engineering, Lehigh University, Bethlehem, PA 18015, USA
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