201
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Huang S, Croy A, Bezugly V, Cuniberti G. Stabilization of aqueous graphene dispersions utilizing a biocompatible dispersant: a molecular dynamics study. Phys Chem Chem Phys 2019; 21:24007-24016. [DOI: 10.1039/c9cp04742e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Investigation of the high efficiency of flavin mononucleotide sodium salt (FMNS) for the stabilization of aqueous graphene dispersions using all-atom molecular dynamics simulations.
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Affiliation(s)
- Shirong Huang
- Institute for Materials Science and Max Bergmann Center for Biomaterials
- Technische Universität Dresden
- 01062 Dresden
- Germany
| | - Alexander Croy
- Institute for Materials Science and Max Bergmann Center for Biomaterials
- Technische Universität Dresden
- 01062 Dresden
- Germany
| | - Viktor Bezugly
- Institute for Materials Science and Max Bergmann Center for Biomaterials
- Technische Universität Dresden
- 01062 Dresden
- Germany
- Life Science Inkubator Sachsen GmbH & Co. KG
| | - Gianaurelio Cuniberti
- Institute for Materials Science and Max Bergmann Center for Biomaterials
- Technische Universität Dresden
- 01062 Dresden
- Germany
- Dresden Center for Computational Materials Science (DCMS)
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202
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A computational and experimental study to develop E-selectin targeted peptides for molecular imaging applications. Future Med Chem 2018; 10:2695-2711. [PMID: 30520324 DOI: 10.4155/fmc-2018-0244] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Aim: E-selectin is overexpressed on angiogenic and inflamed endothelium. Molecules binding to E-selectin with high affinity and specificity enable its use as a molecular imaging biomarker. Material & methods: The interactions of four different peptides (i.e., Ac-P1 [Acetyl-IELLQAR-CONH2], H2N-P2 [H2N-DITWDQLWDLMK-CONH2], H2N-P3A5 [H2N-YRNWAGRW-CONH2], and Ac-P4 [Acetyl-YRNWDGRW-CONH2]) with E-selectin were analyzed by computational methodologies, surface plasmon resonance and in vitro using activated human umbilical vein endothelial cells. Poly(butyl cyanoacrylate) microbubbles were functionalized with the best candidates and evaluated as molecular ultrasound probes in cultured cells and explanted carotid arteries. Results: H2N-P3A5 and Ac-P4 peptides bound stronger to E-selectin than Ac-P1 and H2N-P2, but with lower specificity. H2N-P2 bound with higher specificity and affinity than Ac-P1. Conclusion: H2N-P2 is a good candidate for designing E-selectin-targeted molecular imaging agents.
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203
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Han F, Liu Y, E J, Guan S, Han W, Shan Y, Wang S, Zhang H. Effects of Tyr555 and Trp678 on the processivity of cellobiohydrolase A from Ruminiclostridium thermocellum: A simulation study. Biopolymers 2018; 109:e23238. [PMID: 30484856 DOI: 10.1002/bip.23238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/21/2018] [Accepted: 10/01/2018] [Indexed: 12/12/2022]
Abstract
Cellobiohydrolase A from Ruminiclostridium thermocellum (Cbh9A) is a processive exoglucanase from family 9 and is an important cellobiohydrolase that hydrolyzes cello-oligosaccharide into cellobiose. Residues Tyr555 and Trp678 considerably affect catalytic activity, but their mechanisms are still unknown. To investigate how the Tyr555 and Trp678 affect the processivity of Cbh9A, conventional molecular dynamics, steered molecular dynamics, and free energy calculation were performed to simulate the processive process of wild type (WT)-Cbh9A, Y555S mutant, and W678G mutant. Analysis of simulation results suggests that the binding free energies between the substrate and WT-Cbh9A are lower than those of Y555S and W678G mutants. The pull forces and energy barrier in Y555S and W678G mutants also reduced significantly during the steered molecular dynamics (SMD) simulation compared with that of the WT-Cbh9A. And the potential mean force calculations showed that the pulling energy barrier of Y555S and W678G mutants is much lower than that of WT-Cbh9A.
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Affiliation(s)
- Fei Han
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, China
| | - Ye Liu
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, National Engineering Laboratory of AIDS Vaccine, College of Life Science, Jilin University, Changchun, China
| | - Jingwen E
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, China
| | - Shanshan Guan
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, National Engineering Laboratory of AIDS Vaccine, College of Life Science, Jilin University, Changchun, China
| | - Weiwei Han
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, National Engineering Laboratory of AIDS Vaccine, College of Life Science, Jilin University, Changchun, China
| | - Yaming Shan
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, National Engineering Laboratory of AIDS Vaccine, College of Life Science, Jilin University, Changchun, China
| | - Song Wang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, China
| | - Hao Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, China
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204
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Nogueira E, Sárria MP, Azoia NG, Antunes E, Loureiro A, Guimarães D, Noro J, Rollett A, Guebitz G, Cavaco-Paulo A. Internalization of Methotrexate Conjugates by Folate Receptor-α. Biochemistry 2018; 57:6780-6786. [DOI: 10.1021/acs.biochem.8b00607] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Eugénia Nogueira
- Centre of Biological Engineering, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
| | - Marisa P. Sárria
- Centre of Biological Engineering, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
| | - Nuno G. Azoia
- Centre of Biological Engineering, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
| | - Egipto Antunes
- Centre of Biological Engineering, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
| | - Ana Loureiro
- Centre of Biological Engineering, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
| | - Diana Guimarães
- Centre of Biological Engineering, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
| | - Jennifer Noro
- Centre of Biological Engineering, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
| | - Alexandra Rollett
- Institute for Environmental Biotechnology, University of Natural Resources and Life Sciences, Vienna, A-3430 Tulln, Austria
| | - Georg Guebitz
- Institute for Environmental Biotechnology, University of Natural Resources and Life Sciences, Vienna, A-3430 Tulln, Austria
| | - Artur Cavaco-Paulo
- Centre of Biological Engineering, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
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205
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Murcia Rios A, Vahidi S, Dunn SD, Konermann L. Evidence for a Partially Stalled γ Rotor in F 1-ATPase from Hydrogen-Deuterium Exchange Experiments and Molecular Dynamics Simulations. J Am Chem Soc 2018; 140:14860-14869. [PMID: 30339028 DOI: 10.1021/jacs.8b08692] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
F1-ATPase uses ATP hydrolysis to drive rotation of the γ subunit. The γ C-terminal helix constitutes the rotor tip that is seated in an apical bearing formed by α3β3. It remains uncertain to what extent the γ conformation during rotation differs from that seen in rigid crystal structures. Existing models assume that the entire γ subunit participates in every rotation. Here we interrogated E. coli F1-ATPase by hydrogen-deuterium exchange (HDX) mass spectrometry. Rotation of γ caused greatly enhanced deuteration in the γ C-terminal helix. The HDX kinetics implied that most F1 complexes operate with an intact rotor at any given time, but that the rotor tip is prone to occasional unfolding. A molecular dynamics (MD) strategy was developed to model the off-axis forces acting on γ. MD runs showed stalling of the rotor tip and unfolding of the γ C-terminal helix. MD-predicted H-bond opening events coincided with experimental HDX patterns. Our data suggest that in vitro operation of F1-ATPase is associated with significant rotational resistance in the apical bearing. These conditions cause the γ C-terminal helix to get "stuck" (and unfold) sporadically while the remainder of γ continues to rotate. This scenario contrasts the traditional "greasy bearing" model that envisions smooth rotation of the γ C-terminal helix. The fragility of the apical rotor tip in F1-ATPase is attributed to the absence of a c10 ring that stabilizes the rotation axis in intact FoF1. Overall, the MD/HDX strategy introduced here appears well suited for interrogating the inner workings of molecular motors.
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Affiliation(s)
- Angela Murcia Rios
- Departments of Chemistry and Biochemistry , The University of Western Ontario , London , Ontario N6A 5B7 , Canada
| | - Siavash Vahidi
- Departments of Chemistry and Biochemistry , The University of Western Ontario , London , Ontario N6A 5B7 , Canada
| | - Stanley D Dunn
- Departments of Chemistry and Biochemistry , The University of Western Ontario , London , Ontario N6A 5B7 , Canada
| | - Lars Konermann
- Departments of Chemistry and Biochemistry , The University of Western Ontario , London , Ontario N6A 5B7 , Canada
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206
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Fuentes D, Muñoz NM, Guo C, Polak U, Minhaj AA, Allen WJ, Gustin MC, Cressman ENK. A molecular dynamics approach towards evaluating osmotic and thermal stress in the extracellular environment. Int J Hyperthermia 2018; 35:559-567. [PMID: 30303437 DOI: 10.1080/02656736.2018.1512161] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/13/2018] [Accepted: 08/12/2018] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVE A molecular dynamics approach to understanding fundamental mechanisms of combined thermal and osmotic stress induced by thermochemical ablation (TCA) is presented. METHODS Structural models of fibronectin and fibronectin bound to its integrin receptor provide idealized models for the effects of thermal and osmotic stress in the extracellular matrix. Fibronectin binding to integrin is known to facilitate cell survival. The extracellular environment produced by TCA at the lesion boundary was modelled at 37 °C and 43 °C with added sodium chloride (NaCl) concentrations (0, 40, 80, 160, and 320 mM). Atomistic simulations of solvated proteins were performed using the GROMOS96 force field and TIP3P water model. Computational results were compared with the results of viability studies of human hepatocellular carcinoma (HCC) cell lines HepG2 and Hep3B under matching thermal and osmotic experimental conditions. RESULTS Cell viability was inversely correlated with hyperthermal and hyperosmotic stresses. Added NaCl concentrations were correlated with a root mean square fluctuation increase of the fibronectin arginylglycylaspartic acid (RGD) binding domain. Computed interaction coefficients demonstrate preferential hydration of the protein model and are correlated with salt-induced strengthening of hydrophobic interactions. Under the combined hyperthermal and hyperosmotic stress conditions (43 °C and 320 mM added NaCl), the free energy change required for fibronectin binding to integrin was less favorable than that for binding under control conditions (37 °C and 0 mM added NaCl). CONCLUSION Results quantify multiple measures of structural changes as a function of temperature increase and addition of NaCl to the solution. Correlations between cell viability and stability measures suggest that protein aggregates, non-functional proteins, and less favorable cell attachment conditions have a role in TCA-induced cell stress.
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Affiliation(s)
- David Fuentes
- a Department of Imaging Physics , M. D. Anderson Cancer Center, The University of Texas , Houston , TX , USA
| | - Nina M Muñoz
- b Department of Interventional Radiology , M. D. Anderson Cancer Center, The University of Texas, Houston , TX , USA
| | - Chunxiao Guo
- b Department of Interventional Radiology , M. D. Anderson Cancer Center, The University of Texas, Houston , TX , USA
| | - Urzsula Polak
- b Department of Interventional Radiology , M. D. Anderson Cancer Center, The University of Texas, Houston , TX , USA
| | - Adeeb A Minhaj
- b Department of Interventional Radiology , M. D. Anderson Cancer Center, The University of Texas, Houston , TX , USA
| | - William J Allen
- c Texas Advanced Computing Center , The University of Texas at Austin , Austin , TX , USA
| | - Michael C Gustin
- d Department of Biosciences , Rice University , Houston , TX , USA
| | - Erik N K Cressman
- b Department of Interventional Radiology , M. D. Anderson Cancer Center, The University of Texas, Houston , TX , USA
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207
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Mukhija A, Kishore N. Prevention and Disintegration of Human Serum Albumin Fibrils under Physiological Conditions: Biophysical Aspects. J Phys Chem B 2018; 122:9896-9906. [DOI: 10.1021/acs.jpcb.8b07140] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Achal Mukhija
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India
| | - Nand Kishore
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India
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208
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Kumar A, Tiwari A, Sharma A. Changing Paradigm from one Target one Ligand Towards Multi-target Directed Ligand Design for Key Drug Targets of Alzheimer Disease: An Important Role of In Silico Methods in Multi-target Directed Ligands Design. Curr Neuropharmacol 2018; 16:726-739. [PMID: 29542413 PMCID: PMC6080096 DOI: 10.2174/1570159x16666180315141643] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 04/01/2017] [Accepted: 05/01/2017] [Indexed: 12/14/2022] Open
Abstract
Alzheimer disease (AD) is now considered as a multifactorial neurodegenerative disorder and rapidly increasing to an alarming situation and causing higher death rate. One target one ligand hypothesis does not provide complete solution of AD due to multifactorial nature of the disease and one target one drug fails to provide better treatment against AD. Moreo-ver, currently available treatments are limited and most of the upcoming treatments under clinical trials are based on modulat-ing single target. So, the current AD drug discovery research is shifting towards a new approach for a better solution that simultaneously modulates more than one targets in the neurodegenerative cascade. This can be achieved by network pharma-cology, multi-modal therapies, multifaceted, and/or the more recently proposed term “multi-targeted designed drugs”. Drug discovery project is a tedious, costly and long-term project. Moreover, multi-target AD drug discovery added extra challeng-es such as the good binding affinity of ligands for multiple targets, optimal ADME/T properties, no/less off-target side effect and crossing of the blood-brain barrier. These hurdles may be addressed by insilico methods for an efficient solution in less time and cost as computational methods successfully applied to single target drug discovery project. Here, we are summariz-ing some of the most prominent and computationally explored single targets against AD and further, we discussed a success-ful example of dual or multiple inhibitors for same targets. Moreover, we focused on ligand and structure-based computa-tional approach to design MTDL against AD. However, it is not an easy task to balance dual activity in a single molecule but computational approach such as virtual screening docking, QSAR, simulation and free energy is useful in future MTDLs drug discovery alone or in combination with a fragment-based method. However, rational and logical implementations of computational drug designing methods are capable of assisting AD drug discovery and play an important role in optimizing multi-target drug discovery.
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Affiliation(s)
- Akhil Kumar
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow-226015, (U.P.), India
| | - Ashish Tiwari
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow-226015, (U.P.), India
| | - Ashok Sharma
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow-226015, (U.P.), India
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209
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Mathpati AC, Bhanage BM. Prediction of enantioselectivity of lipase catalyzed kinetic resolution using umbrella sampling. J Biotechnol 2018; 283:70-80. [DOI: 10.1016/j.jbiotec.2018.07.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/21/2018] [Accepted: 07/18/2018] [Indexed: 12/21/2022]
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210
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Si D, Xu Z, Nan N, Hu G. DNA Confined in a Nanodroplet: A Molecular Dynamics Study. J Phys Chem B 2018; 122:8812-8818. [PMID: 30180585 DOI: 10.1021/acs.jpcb.8b05056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
As a major genetic material, the configuration and the mechanical properties of a double-stranded DNA (dsDNA) molecule in confinement are crucial for the application of nanotechnology and biological engineering. In the present paper, molecular dynamics simulation is utilized to study the configuration of dsDNA in a nanodroplet on a graphene substrate. The results show that the semiflexible dsDNA molecule changes its configuration with radius of gyration ( Rg) of a few nanometers because of the confined space, that is, the Rg of the dsDNA molecule decreases with the reduction of the nanodroplet size. In comparison, the dsDNA in the bulk usually has a persistent length of tens of nanometers. Especially, if the nanodroplet is small enough, the dsDNA molecule might form a loop structure inside. The dsDNA molecule affects the wetting properties of the graphene substrate. It is found that the graphene becomes more hydrophilic in smaller systems containing the dsDNA molecule, whereas for larger droplets, the changes of the contact angles are not significant with the presence of dsDNA. Moreover, the results indicate that for larger droplets, the line tension of the droplet containing DNA is positive and greater than that without DNA; for smaller droplets, the line tension becomes negative because the dsDNA is compressed and bent in the confinement, and has the potential to expand outwards. The worm-like chain model is used to study the bending energy of a dsDNA molecule in a droplet. The results address that the bending energy of the non-loop-structured dsDNA decreases as the droplet becomes larger, and it is larger than that of loop-structured dsDNA, as the loop structure efficiently prevents the DNA from bending in the vertical direction.
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Affiliation(s)
- Dongqing Si
- Shanghai Institute of Applied Mathematics and Mechanics, Shanghai Key Laboratory of Mechanics in Energy Engineering , Shanghai University , Shanghai 200072 , China
| | - Zhen Xu
- School of Mechanical Engineering , Shanghai University of Engineering Science , Shanghai 201620 , China
| | - Nan Nan
- Shanghai Institute of Applied Mathematics and Mechanics, Shanghai Key Laboratory of Mechanics in Energy Engineering , Shanghai University , Shanghai 200072 , China
| | - Guohui Hu
- Shanghai Institute of Applied Mathematics and Mechanics, Shanghai Key Laboratory of Mechanics in Energy Engineering , Shanghai University , Shanghai 200072 , China
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211
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Zhou H, Yu H, Zhao X, Yang L, Huang X. Molecular dynamics simulations investigate the pathway of substrate entry active site of rhomboid protease. J Biomol Struct Dyn 2018; 37:3445-3455. [PMID: 30175657 DOI: 10.1080/07391102.2018.1517609] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Rhomboid proteases can catalyze peptide bond cleavage and participate in abundant biological processes encompassing all branches of life; however, the pathway for substrate entry into its active site remains ambiguous. Here, the two possible pathways are preliminarily determined through molecular dynamics: One pathway is between Tm2 and Tm5, and the other is between Loop3 and Loop5. Then, the umbrella sampling simulations are performed to investigate the more feasible pathway for substrate entry. The results show that free energy barriers along the two pathways are similar; in the pathway 1, Trp236 and Trp157 as pivotal residues are responsible for the rotation of substrate in the binding process; in the pathway 2, among some important residues, the residue His150 plays an important role in substrate entry. Further, combining with previous experiment results, it is concluded that the substrate is inclined to enter into the active site along pathway 2. Our results are important for further understanding the function and catalysis mechanism of rhomboid proteases. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hua Zhou
- a Institute of Theoretical Chemistry , Jilin University , Changchun , China
| | - Hui Yu
- b College of Chemistry and Biology , Beihua University , Jilin , China
| | - Xi Zhao
- a Institute of Theoretical Chemistry , Jilin University , Changchun , China
| | - Lianjuan Yang
- c The Fungal Reference Laboratory of Shanghai Dermatology Hospital , Shanghai , China
| | - Xuri Huang
- a Institute of Theoretical Chemistry , Jilin University , Changchun , China
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212
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Khatua P, Bandyopadhyay S. Understanding the microscopic origin behind heterogeneous properties of water confined in and around A β17-42 protofilaments. J Chem Phys 2018; 149:065101. [PMID: 30111136 DOI: 10.1063/1.5040672] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Aggregation of amyloid beta (Aβ) peptides in the brain is responsible for one of the most devastating neurodegenerative diseases, namely, Alzheimer's disease. In this study, we have carried out atomistic molecular dynamics simulations to explore the effects of non-uniform structural distortions of Aβ17-42 pre-fibrillar aggregates of different sizes on the microscopic structure and ordering of water molecules confined within their amphiphilic nanocores. The calculations revealed non-uniform peptide-water interactions resulting in simultaneous existence of both highly ordered and disordered water molecules within the spatially heterogeneous confined environment of the protofilament cores. It is found that the high degree of ordering originates from a sizable fraction of doubly coordinated core water molecules, while the randomly oriented ones are those that are coordinated with three neighbors in their first coordination shells. Furthermore, it is quantitatively demonstrated that relative fractions of these two types of water molecules are correlated with the protofilament core topology and the degree of confinement within that. It is proposed that the ordered core waters are likely to stabilize the Aβ protofilaments by screening the residue charges and favoring water-mediated salt bridge formations, while the randomly oriented ones can drive further growth of the protofilaments by being displaced easily during the docking of additional peptides. In that way, both types of core water molecules can play equally important roles in controlling the growth and stability of the Aβ-aggregates.
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Affiliation(s)
- Prabir Khatua
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
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213
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Kouza M, Banerji A, Kolinski A, Buhimschi I, Kloczkowski A. Role of Resultant Dipole Moment in Mechanical Dissociation of Biological Complexes. Molecules 2018; 23:molecules23081995. [PMID: 30103417 PMCID: PMC6222447 DOI: 10.3390/molecules23081995] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 08/07/2018] [Accepted: 08/08/2018] [Indexed: 12/25/2022] Open
Abstract
Protein-peptide interactions play essential roles in many cellular processes and their structural characterization is the major focus of current experimental and theoretical research. Two decades ago, it was proposed to employ the steered molecular dynamics (SMD) to assess the strength of protein-peptide interactions. The idea behind using SMD simulations is that the mechanical stability can be used as a promising and an efficient alternative to computationally highly demanding estimation of binding affinity. However, mechanical stability defined as a peak in force-extension profile depends on the choice of the pulling direction. Here we propose an uncommon choice of the pulling direction along resultant dipole moment (RDM) vector, which has not been explored in SMD simulations so far. Using explicit solvent all-atom MD simulations, we apply SMD technique to probe mechanical resistance of ligand-receptor system pulled along two different vectors. A novel pulling direction—when ligand unbinds along the RDM vector—results in stronger forces compared to commonly used ligand unbinding along center of masses vector. Our observation that RDM is one of the factors influencing the mechanical stability of protein-peptide complex can be used to improve the ranking of binding affinities by using mechanical stability as an effective scoring function.
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Affiliation(s)
- Maksim Kouza
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland;
- Battelle Center for Mathematical Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA;
- Correspondence: ; Tel.: +48-22-55-26-364
| | - Anirban Banerji
- Battelle Center for Mathematical Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA;
| | - Andrzej Kolinski
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland;
| | - Irina Buhimschi
- Center for Perinatal Research, Research Institute at Nationwide Children’s Hospital, Columbus, OH 43215, USA;
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43215, USA
| | - Andrzej Kloczkowski
- Battelle Center for Mathematical Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA;
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43215, USA
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214
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Dos Santos CBR, da Silva Ramos R, Ortiz BLS, da Silva GM, Giuliatti S, Balderas-Lopez JL, Navarrete A, Carvalho JCT. Oil from the fruits of Pterodon emarginatus Vog.: A traditional anti-inflammatory. Study combining in vivo and in silico. JOURNAL OF ETHNOPHARMACOLOGY 2018; 222:107-120. [PMID: 29723629 DOI: 10.1016/j.jep.2018.04.041] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/25/2018] [Accepted: 04/27/2018] [Indexed: 06/08/2023]
Abstract
ETHNOBOTANICAL RELEVANCE The oil obtained from the fruits of Pterodon emarginatus Vog. (OPe) is used orally and topically, in traditional medicine for some purposes, such as acute and chronic inflammatory states as rheumatoid arthritis. MATERIALS AND METHODS In this work, the anti-inflammatory activity of the OPe was demonstrated based on several animal models and presented an in silico study based on the 6α,7β-dihydroxy-vouacapan-17β-oic acid (DHVA) majority compound of the OPe to evaluate the interaction this compound, with cyclooxygenase-2 (COX-2) in 4COX (Mus musculus) and 5KIR (Homo sapiens) and molecular dynamics simulation. RESULTS The OPe (498 mg/kg, p.o) significantly inhibited (p < 0.05, Student t-test) the primary and secondary reactions of arthritis by Freund's Complete Adjuvant (FCA) and in dermatitis induced by croton oil in mice, OPe inhibited peak of edema. In vascular permeability test in rats, the treatment with OPe was able to block the response to PGE2, serotonin, and bradykinin (p < 0.05, Student t-test). In the writhing test in mice, the OPe at doses of 498 and 980 mg/kg (p.o) produced inhibition of 73% and 92%, respectively, and was not significantly effective in the hot plate test. In the evaluation of the potency in relation to gastric injury (gastric ulcer induced by stress) and combined assay in the assessment of anti-inflammatory potency and gastric damage, it was observed that indomethacin (10 mg/kg, p.o.) inhibited carrageenan edema by 51% and produced a higher number of gastric lesions when compared to the group treated with OPe, where only areas of hyperemia were observed, without the occurrence of ulcerative lesion, and which inhibited the edema by 47%. In the in silico study, it was found that the DHVA is capable of binding to two organisms (4COX - Mus musculus and 5KIR - Homo sapiens), however, with higher binding affinity to the organism Homo sapiens. CONCLUSIONS As expected, all tested ligands were capable of forming hydrogen interactions with residues at their respective binding sites, but the DHVA ligand was capable of creating slightly more hydrogen bonds when docked to either 4COX or 5KIR than the other tested ligands, thus demonstrating the participation of this compound in the anti-inflammatory and antialgic responses observed in the in vivo assays as a COX-2 inhibitor. Therefore, the results obtained support the traditional use of OPe for inflammatory and gastric problems.
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Affiliation(s)
- Cleydson Breno Rodrigues Dos Santos
- Laboratório de Pesquisa em Fármacos, Departamento de Ciências Biológicas e Saúde, Universidade Federal do Amapá (UNIFAP), Rodovia Juscelino Kubitschek, S/N, Campus Marco Zero, Macapá, AP CEP 68903-419, Brazil; Laboratório de Modelagem e Química Computacional (LMQC), Departamento de Ciências Biológicas e Saúde, Universidade Federal do Amapá (UNIFAP), Rodovia Juscelino Kubitschek, S/N, Campus Marco Zero, Macapá, AP CEP 68903-419, Brazil
| | - Ryan da Silva Ramos
- Laboratório de Modelagem e Química Computacional (LMQC), Departamento de Ciências Biológicas e Saúde, Universidade Federal do Amapá (UNIFAP), Rodovia Juscelino Kubitschek, S/N, Campus Marco Zero, Macapá, AP CEP 68903-419, Brazil
| | - Brenda Lorena Sánchez Ortiz
- Laboratório de Pesquisa em Fármacos, Departamento de Ciências Biológicas e Saúde, Universidade Federal do Amapá (UNIFAP), Rodovia Juscelino Kubitschek, S/N, Campus Marco Zero, Macapá, AP CEP 68903-419, Brazil; Programa de Pós-Graduação em Inovação Farmacêutica, Departamento de Ciências Biológicas e Saúde, Universidade Federal do Amapá (UNIFAP), Rodovia Juscelino Kubitschek, S/N, Campus Marco Zero, Macapá, AP CEP 68903-419, Brazil
| | - Gabriel Monteiro da Silva
- Grupo de Bioinformatica, Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (USP/RP), Avenida Bandeirantes 3900, Monte Alegre, Ribeirao Preto, Sao Paulo CEP 14049-900, Brazil
| | - Silvana Giuliatti
- Grupo de Bioinformatica, Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (USP/RP), Avenida Bandeirantes 3900, Monte Alegre, Ribeirao Preto, Sao Paulo CEP 14049-900, Brazil
| | - José Luis Balderas-Lopez
- Laboratorio de Farmacología de Productos Naturales, Facultad de Química, Departamento de Farmacia, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Andrés Navarrete
- Laboratorio de Farmacología de Productos Naturales, Facultad de Química, Departamento de Farmacia, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - José Carlos Tavares Carvalho
- Laboratório de Pesquisa em Fármacos, Departamento de Ciências Biológicas e Saúde, Universidade Federal do Amapá (UNIFAP), Rodovia Juscelino Kubitschek, S/N, Campus Marco Zero, Macapá, AP CEP 68903-419, Brazil; Programa de Pós-Graduação em Inovação Farmacêutica, Departamento de Ciências Biológicas e Saúde, Universidade Federal do Amapá (UNIFAP), Rodovia Juscelino Kubitschek, S/N, Campus Marco Zero, Macapá, AP CEP 68903-419, Brazil.
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215
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Galamba N, Pipolo S. On the Binding Free Energy and Molecular Origin of Sickle Cell Hemoglobin Aggregation. J Phys Chem B 2018; 122:7475-7483. [DOI: 10.1021/acs.jpcb.8b03708] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- N. Galamba
- Centro de Química e Bioquímica and Biosystems and Integrative Sciences Institute, Faculdade de Ciências da Universidade de Lisboa, Edifício C8, Campo Grande, 1749-016 Lisboa, Portugal
| | - Silvio Pipolo
- Université
de Lille, CNRS, Centrale Lille, ENSCL, Université d’
Artois UMR 8181 − UCCS Unité de Catalyse et Chimie du
Solide, F-59000, Lille, France
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216
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Influence of gauche effect on uncharged oxime reactivators for the reactivation of tabun-inhibited AChE: quantum chemical and steered molecular dynamics studies. J Comput Aided Mol Des 2018; 32:793-807. [DOI: 10.1007/s10822-018-0130-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 07/04/2018] [Indexed: 02/06/2023]
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217
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Pazos IM, Ma J, Mukherjee D, Gai F. Ultrafast Hydrogen-Bonding Dynamics in Amyloid Fibrils. J Phys Chem B 2018; 122:11023-11029. [PMID: 29883122 DOI: 10.1021/acs.jpcb.8b04642] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
While there are many studies on the subject of hydrogen-bonding dynamics in biological systems, few, if any, have investigated this fundamental process in amyloid fibrils. Herein, we seek to add insight into this topic by assessing the dynamics of a hydrogen bond buried in the dry interface of amyloid fibrils. To prepare a suitable model peptide system for this purpose, we introduce two mutations into the amyloid-forming Aβ16-22 peptide. The first one is a lysine analogue at position 19, which is used to help form structurally homogeneous fibrils, and the second one is an aspartic acid derivative (DM) at position 17, which is intended (1) to be used as a site-specific infrared probe and (2) to serve as a hydrogen-bond acceptor to lysine so that an inter-β-sheet hydrogen bond can be formed in the fibrils. Using both infrared spectroscopy and atomic force microscopy, we show that (1) this mutant peptide indeed forms well-defined fibrils, (2) when bulk solvent is removed, there is no detectable water present in the fibrils, (3) infrared results obtained with the DM probe are consistent with a protofibril structure that is composed of two antiparallel β-sheets stacked in a parallel fashion, leading to formation of the expected hydrogen bond. Using two-dimensional infrared spectroscopy, we further show that the dynamics of this hydrogen bond occur on a time scale of ∼2.3 ps, which is attributed to the rapid rotation of the -NH3+ group of lysine around its Cε-Nζ bond. Taken together, these results suggest that (1) DM is a useful infrared marker in facilitating structure determination of amyloid fibrils and (2) even in the tightly packed core of amyloid fibrils certain amino acid side chains can undergo ultrafast motions, hence contributing to the thermodynamic stability of the system.
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218
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Zhan S, Ahlquist MSG. Dynamics and Reactions of Molecular Ru Catalysts at Carbon Nanotube–Water Interfaces. J Am Chem Soc 2018; 140:7498-7503. [DOI: 10.1021/jacs.8b00433] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shaoqi Zhan
- Department of Theoretical Chemistry & Biology, School of Engineering Sciences in Chemistry Biotechnology and Health, KTH Royal Institute of Technology, 10691 Stockholm, Sweden
| | - Mårten S. G. Ahlquist
- Department of Theoretical Chemistry & Biology, School of Engineering Sciences in Chemistry Biotechnology and Health, KTH Royal Institute of Technology, 10691 Stockholm, Sweden
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219
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Insights into Stabilizing Forces in Amyloid Fibrils of Differing Sizes from Polarizable Molecular Dynamics Simulations. J Mol Biol 2018; 430:3819-3834. [PMID: 29782833 DOI: 10.1016/j.jmb.2018.05.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/27/2018] [Accepted: 05/09/2018] [Indexed: 11/23/2022]
Abstract
Pathological aggregation of amyloid-forming proteins is a hallmark of a number of human diseases, including Alzheimer's, type 2 diabetes, Parkinson's, and more. Despite having very different primary amino acid sequences, these amyloid proteins form similar supramolecular, fibril structures that are highly resilient to physical and chemical denaturation. To better understand the structural stability of disease-related amyloids and to gain a greater understanding of factors that stabilize functional amyloid assemblies, insights into tertiary and quaternary interactions are needed. We performed molecular dynamics simulations on human tau, amyloid-β, and islet amyloid polypeptide fibrils to determine key physicochemical properties that give rise to their unique characteristics and fibril structures. These simulations are the first of their kind in employing a polarizable force field to explore properties of local electric fields on dipole properties and other electrostatic forces that contribute to amyloid stability. Across these different amyloid fibrils, we focused on how the underlying forces stabilize fibrils to elucidate the driving forces behind the protein aggregation. The polarizable model allows for an investigation of how side-chain dipole moments, properties of structured water molecules in the fibril core, and the local environment around salt bridges contribute to the formation of interfaces essential for fibril stability. By systematically studying three amyloidogenic proteins of various fibril sizes for key structural properties and stabilizing forces, we shed light on properties of amyloid structures related to both diseased and functional states at the atomistic level.
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220
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Dey A, Kamat A, Nayak S, Danino D, Kesselman E, Dandekar P, Jain R. Role of proton balance in formation of self-assembled chitosan nanoparticles. Colloids Surf B Biointerfaces 2018; 166:127-134. [PMID: 29558703 DOI: 10.1016/j.colsurfb.2018.03.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 02/08/2018] [Accepted: 03/13/2018] [Indexed: 11/17/2022]
Abstract
Researchers have explored the ability of chitosan to form nanoparticles, to suit varying applications, ranging from wound-healing to gene delivery. Ionic gelation is a widely used method for formulating chitosan nanoparticles, where self-assembly plays a crucial role. This self-assembly is initially promoted by hydrophilic-hydrophobic parity amongst individual chitosan residues, along with electrostatic and Van der Waals interactions with the cross-linker. However, until now the intrinsic ability of chitosan to self-assemble is not widely studied; hence, we investigate the self-assembly of chitosan, based on proton balance between its protonated and deprotonated residues, to promote facile nanoparticle synthesis. This is one of the first reports that highlights subtle but critical influence of proton balance in the chitosan polymer on the formation of chitosan nanoparticles.
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Affiliation(s)
- Anomitra Dey
- Department of Chemical Engineering, Institute of Chemical Technology, Matunga, Mumbai 400019, India
| | - Aditya Kamat
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Matunga, Mumbai 400019, India
| | - Sonal Nayak
- Department of Chemical Engineering, Institute of Chemical Technology, Matunga, Mumbai 400019, India
| | - Dganit Danino
- Department of Biotechnology & Food Engineering, Technion - Israel Institute of Technology, Hafia 3200003, Israel
| | - Ellina Kesselman
- Department of Biotechnology & Food Engineering, Technion - Israel Institute of Technology, Hafia 3200003, Israel
| | - Prajakta Dandekar
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Matunga, Mumbai 400019, India.
| | - Ratnesh Jain
- Department of Chemical Engineering, Institute of Chemical Technology, Matunga, Mumbai 400019, India.
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221
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Huang H, Han F, Guan S, Qian M, Wan Y, Shan Y, Zhang H, Wang S. Insight into the process of product expulsion in cellobiohydrolase Cel6A from Trichoderma reesei by computational modeling. J Biomol Struct Dyn 2018. [PMID: 29519213 DOI: 10.1080/07391102.2018.1450164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Glycoside hydrolase cellulase family 6 from Trichoderma reesei (TrCel6A) is an important cellobiohydrolase to hydrolyze cellooligosaccharide into cellobiose. The knowledge of enzymatic mechanisms is critical for improving the conversion efficiency of cellulose into ethanol or other chemicals. However, the process of product expulsion, a key component of enzymatic depolymerization, from TrCel6A has not yet been described in detail. Here, conventional molecular dynamics and steered molecular dynamics (SMD) were applied to study product expulsion from TrCel6A. Tyr103 may be a crucial residue in product expulsion given that it exhibits two different posthydrolytic conformations. In one conformation, Tyr103 rotates to open the -3 subsite. However, Tyr103 does not rotate in the other conformation. Three different routes for product expulsion were proposed on the basis of the two different conformations. The total energy barriers of the three routes were calculated through SMD simulations. The total energy barrier of product expulsion through Route 1, in which Tyr103 does not rotate, was 22.2 kcal·mol-1. The total energy barriers of product expulsion through Routes 2 and 3, in which Tyr103 rotates to open the -3 subsite, were 10.3 and 14.4 kcal·mol-1, respectively. Therefore, Routes 2 and 3 have lower energy barriers than Route 1, and Route 2 is the thermodynamically optimal route for product expulsion. Consequently, the rotation of Tyr103 may be crucial for product release from TrCel6A. Results of this work have potential applications in cellulase engineering.
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Affiliation(s)
- Houhou Huang
- a Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry , Jilin University , Changchun 130023 , People's Republic of China
| | - Fei Han
- a Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry , Jilin University , Changchun 130023 , People's Republic of China
| | - Shanshan Guan
- a Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry , Jilin University , Changchun 130023 , People's Republic of China.,b National Engineering Laboratory for AIDS Vaccine, School of Life Sciences , Jilin University , Changchun 130012 , People's Republic of China
| | - Mengdan Qian
- c State Key Laboratory of Integrated Optoelectronics, College of Electronic Science and Engineering , Jilin University , Changchun , Jilin 130012 , People's Republic of China
| | - Yongfeng Wan
- a Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry , Jilin University , Changchun 130023 , People's Republic of China
| | - Yaming Shan
- b National Engineering Laboratory for AIDS Vaccine, School of Life Sciences , Jilin University , Changchun 130012 , People's Republic of China
| | - Hao Zhang
- a Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry , Jilin University , Changchun 130023 , People's Republic of China
| | - Song Wang
- a Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry , Jilin University , Changchun 130023 , People's Republic of China
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222
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Metwally H, Konermann L. Crown Ether Effects on the Location of Charge Carriers in Electrospray Droplets: Implications for the Mechanism of Protein Charging and Supercharging. Anal Chem 2018; 90:4126-4134. [DOI: 10.1021/acs.analchem.8b00099] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Haidy Metwally
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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223
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Farrokhpour H, Mansouri A, Rajabi AR, Najafi Chermahini A. The effect of the diameter of cyclic peptide nanotube on its chirality discrimination. J Biomol Struct Dyn 2018; 37:691-701. [DOI: 10.1080/07391102.2018.1436090] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Hossein Farrokhpour
- Department of Chemistry, Isfahan University of Technology , Isfahan, 84156-83111, Iran
| | - Alireza Mansouri
- Department of Chemistry, Isfahan University of Technology , Isfahan, 84156-83111, Iran
| | - Ahmad Reza Rajabi
- Department of Chemistry, Isfahan University of Technology , Isfahan, 84156-83111, Iran
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224
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Periole X, Huber T, Bonito-Oliva A, Aberg KC, van der Wel PCA, Sakmar TP, Marrink SJ. Energetics Underlying Twist Polymorphisms in Amyloid Fibrils. J Phys Chem B 2018; 122:1081-1091. [PMID: 29254334 PMCID: PMC5857390 DOI: 10.1021/acs.jpcb.7b10233] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Amyloid fibrils are highly ordered protein aggregates associated with more than 40 human diseases. The exact conditions under which the fibrils are grown determine many types of reported fibril polymorphism, including different twist patterns. Twist-based polymorphs display unique mechanical properties in vitro, and the relevance of twist polymorphism in amyloid diseases has been suggested. We present transmission electron microscopy images of Aβ42-derived (amyloid β) fibrils, which are associated with Alzheimer's disease, demonstrating the presence of twist variability even within a single long fibril. To better understand the molecular underpinnings of twist polymorphism, we present a structural and thermodynamics analysis of molecular dynamics simulations of the twisting of β-sheet protofilaments of a well-characterized cross-β model: the GNNQQNY peptide from the yeast prion Sup35. The results show that a protofilament model of GNNQQNY is able to adopt twist angles from -11° on the left-hand side to +8° on the right-hand side in response to various external conditions, keeping an unchanged peptide structure. The potential of mean force (PMF) of this cross-β structure upon twisting revealed that only ∼2kBT per peptide are needed to stabilize a straight conformation with respect to the left-handed free-energy minimum. The PMF also shows that the canonical structural core of β-sheets, i.e., the hydrogen-bonded backbone β-strands, favors the straight conformation. However, the concerted effects of the side chains contribute to twisting, which provides a rationale to correlate polypeptide sequence, environmental growth conditions and number of protofilaments in a fibril with twist polymorphisms.
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Affiliation(s)
- Xavier Periole
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Groningen 9747 AG, The Netherlands
| | - Thomas Huber
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University , 1230 York Avenue, New York, New York 10065, United States
| | - Alessandra Bonito-Oliva
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University , 1230 York Avenue, New York, New York 10065, United States
| | - Karina C Aberg
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University , 1230 York Avenue, New York, New York 10065, United States
| | - Patrick C A van der Wel
- Department of Structural Biology and Center for Protein Conformational Diseases, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States
| | - Thomas P Sakmar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University , 1230 York Avenue, New York, New York 10065, United States
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet , 141 57 Huddinge, Sweden
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Groningen 9747 AG, The Netherlands
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225
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Popinako A, Antonov M, Dibrova D, Chemeris A, Sokolova OS. Analysis of the interactions between GMF and Arp2/3 complex in two binding sites by molecular dynamics simulation. Biochem Biophys Res Commun 2018; 496:529-535. [PMID: 29339159 DOI: 10.1016/j.bbrc.2018.01.080] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 01/11/2018] [Indexed: 12/17/2022]
Abstract
The Arp2/3 complex plays a key role in nucleating actin filaments branching. The glia maturation factor (GMF) competes with activators for interacting with the Arp2/3 complex and initiates the debranching of actin filaments. In this study, we performed a comparative analysis of interactions between GMF and the Arp2/3 complex and identified new amino acid residues involved in GMF binding to the Arp2/3 complex at two separate sites, revealed by X-ray and single particle EM techniques. Using molecular dynamics simulations we demonstrated the quantitative and qualitative changes in hydrogen bonds upon binding with GMF. We identified the specific amino acid residues in GMF and Arp2/3 complex that stabilize the interactions and estimated the mean force profile for the GMF using umbrella sampling. Phylogenetic and structural analyses of the recently defined GMF binding site on the Arp3 subunit indicate a new mechanism for Arp2/3 complex inactivation that involves interactions between the Arp2/3 complex and GMF at two binding sites.
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Affiliation(s)
- A Popinako
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of RAS, 33 Leninsky Ave, bld. 2, Moscow, 119071, Russia
| | - M Antonov
- M.K. Ammosov North-Eastern Federal University, 58 Belinskiy str, suite 312, Yakutsk, 677980, Republic of Sakha (Yakutia), Russia
| | - D Dibrova
- Lomonosov Moscow State University, Faculty of Biology, 1 Leninskie gory, bld 12, Moscow, 119234, Russia
| | - A Chemeris
- Lomonosov Moscow State University, Faculty of Biology, 1 Leninskie gory, bld 12, Moscow, 119234, Russia
| | - O S Sokolova
- Lomonosov Moscow State University, Faculty of Biology, 1 Leninskie gory, bld 12, Moscow, 119234, Russia.
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226
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Wang B, Zhang J, Zhang Y, Mao Z, Lu N, Liu QH. The penetration of a charged peptide across a membrane under an external electric field: a coarse-grained molecular dynamics simulation. RSC Adv 2018; 8:41517-41525. [PMID: 35559300 PMCID: PMC9091862 DOI: 10.1039/c8ra07654e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 11/28/2018] [Indexed: 01/05/2023] Open
Abstract
The processes of single polyarginine (R8) peptide penetration through planar and vesicle membranes under an external electric field are simulated via a coarse-grained molecular dynamics (CGMD) simulation.
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Affiliation(s)
- Bin Wang
- Institute of Electromagnetics and Acoustics
- Department of Electronic Science
- Xiamen University
- Xiamen
- P. R. China
| | - Jianhua Zhang
- Institute of Electromagnetics and Acoustics
- Department of Electronic Science
- Xiamen University
- Xiamen
- P. R. China
| | - Youyu Zhang
- Institute of Electromagnetics and Acoustics
- Department of Electronic Science
- Xiamen University
- Xiamen
- P. R. China
| | - Zheng Mao
- Institute of Electromagnetics and Acoustics
- Department of Electronic Science
- Xiamen University
- Xiamen
- P. R. China
| | - Nan Lu
- Institute of Electromagnetics and Acoustics
- Department of Electronic Science
- Xiamen University
- Xiamen
- P. R. China
| | - Qing Huo Liu
- Department of Electrical and Computer Engineering
- Duke University
- Durham
- USA
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227
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Jin Y, Sun Y, Lei J, Wei G. Dihydrochalcone molecules destabilize Alzheimer's amyloid-β protofibrils through binding to the protofibril cavity. Phys Chem Chem Phys 2018; 20:17208-17217. [DOI: 10.1039/c8cp01631c] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Dihydrochalcone molecules destabilize Aβ17–42protofibrils by disrupting the N-terminal β1 region and the turn region through binding to the protofibril cavity.
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Affiliation(s)
- Yibo Jin
- Department of Physics
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education)
- Collaborative Innovation Center of Advanced Microstructures (Nanjing)
- Fudan University
| | - Yunxiang Sun
- Department of Physics
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education)
- Collaborative Innovation Center of Advanced Microstructures (Nanjing)
- Fudan University
| | - Jiangtao Lei
- Department of Physics
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education)
- Collaborative Innovation Center of Advanced Microstructures (Nanjing)
- Fudan University
| | - Guanghong Wei
- Department of Physics
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education)
- Collaborative Innovation Center of Advanced Microstructures (Nanjing)
- Fudan University
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228
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Kumar A, Sharma A. Computational Modeling of Multi-target-Directed Inhibitors Against Alzheimer’s Disease. NEUROMETHODS 2018. [DOI: 10.1007/978-1-4939-7404-7_19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
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229
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Xiang N, Lyu Y, Zhu X, Narsimhan G. Investigation of the interaction of amyloid β peptide (11–42) oligomers with a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) membrane using molecular dynamics simulation. Phys Chem Chem Phys 2018; 20:6817-6829. [PMID: 29299557 DOI: 10.1039/c7cp07148e] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The mechanism of pore formation in model neural cell membranes by β amyloid (Aβ) peptides was investigated using molecular dynamics simulation which indicated that Aβ oligomers of size equal or greater than 3 has a higher tendency for pore formation than monomers and that cholesterol tends to retard Aβ binding and insertion into the membrane.
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Affiliation(s)
- Ning Xiang
- Department of Agricultural and Biological Engineering
- Purdue University
- West Lafayette
- USA
| | - Yuan Lyu
- Department of Agricultural and Biological Engineering
- Purdue University
- West Lafayette
- USA
| | - Xiao Zhu
- ItaP
- Research Computing
- Rosen Center for Advanced Computing
- Purdue University
- West Lafayette
| | - Ganesan Narsimhan
- Department of Agricultural and Biological Engineering
- Purdue University
- West Lafayette
- USA
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230
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Liu X, Shi D, Zhou S, Liu H, Liu H, Yao X. Molecular dynamics simulations and novel drug discovery. Expert Opin Drug Discov 2017; 13:23-37. [DOI: 10.1080/17460441.2018.1403419] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Xuewei Liu
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
| | - Danfeng Shi
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
| | | | - Hongli Liu
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Huanxiang Liu
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Xiaojun Yao
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
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231
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Molecular dynamic studies of π + - π − stacked imidazolium/imidazolate ion pairs in chloroform solution. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.06.120] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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232
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Yesudhas D, Anwar MA, Panneerselvam S, Kim HK, Choi S. Evaluation of Sox2 binding affinities for distinct DNA patterns using steered molecular dynamics simulation. FEBS Open Bio 2017; 7:1750-1767. [PMID: 29123983 PMCID: PMC5666385 DOI: 10.1002/2211-5463.12316] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 08/14/2017] [Accepted: 09/05/2017] [Indexed: 11/29/2022] Open
Abstract
Transcription factors (TFs) are gene expression regulators that bind to DNA in a sequence‐specific manner and determine the functional characteristics of the gene. It is worthwhile to study the unique characteristics of such specific TF‐binding pattern in DNA. Sox2 recognizes a 6‐ to 7‐base pair consensus DNA sequence; the central four bases of the binding site are highly conserved, whereas the two to three flanking bases are variable. Here, we attempted to analyze the binding affinity and specificity of the Sox2 protein for distinct DNA sequence patterns via steered molecular dynamics, in which a pulling force is employed to dissociate Sox2 from Sox2–DNA during simulation to study the behavior of a complex under nonequilibrium conditions. The simulation results revealed that the first two stacking bases of the binding pattern have an exclusive impact on the binding affinity, with the corresponding mutant complexes showing greater binding and longer dissociation time than the experimental complexes do. In contrast, mutation of the conserved bases tends to reduce the affinity, and mutation of the complete conserved region disrupts the binding. It might pave the way to identify the most likely binding pattern recognized by Sox2 based on the affinity of each configuration. The α2‐helix of Sox2 was found to be the key player in the Sox2–DNA association. The characterization of Sox2's binding patterns for the target genes in the genome helps in understanding of its regulatory functions.
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Affiliation(s)
- Dhanusha Yesudhas
- Department of Molecular Science and Technology Ajou University Suwon Korea
| | | | | | - Han-Kyul Kim
- Department of Molecular Science and Technology Ajou University Suwon Korea
| | - Sangdun Choi
- Department of Molecular Science and Technology Ajou University Suwon Korea
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233
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Mechanistic principles underlying regulation of the actin cytoskeleton by phosphoinositides. Proc Natl Acad Sci U S A 2017; 114:E8977-E8986. [PMID: 29073094 DOI: 10.1073/pnas.1705032114] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The actin cytoskeleton powers membrane deformation during many cellular processes, such as migration, morphogenesis, and endocytosis. Membrane phosphoinositides, especially phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2], regulate the activities of many actin-binding proteins (ABPs), including profilin, cofilin, Dia2, N-WASP, ezrin, and moesin, but the underlying molecular mechanisms have remained elusive. Moreover, because of a lack of available methodology, the dynamics of membrane interactions have not been experimentally determined for any ABP. Here, we applied a combination of biochemical assays, photobleaching/activation approaches, and atomistic molecular dynamics simulations to uncover the molecular principles by which ABPs interact with phosphoinositide-rich membranes. We show that, despite using different domains for lipid binding, these proteins associate with membranes through similar multivalent electrostatic interactions, without specific binding pockets or penetration into the lipid bilayer. Strikingly, our experiments reveal that these proteins display enormous differences in the dynamics of membrane interactions and in the ranges of phosphoinositide densities that they sense. Profilin and cofilin display transient, low-affinity interactions with phosphoinositide-rich membranes, whereas F-actin assembly factors Dia2 and N-WASP reside on phosphoinositide-rich membranes for longer periods to perform their functions. Ezrin and moesin, which link the actin cytoskeleton to the plasma membrane, bind membranes with very high affinity and slow dissociation dynamics. Unlike profilin, cofilin, Dia2, and N-WASP, they do not require high "stimulus-responsive" phosphoinositide density for membrane binding. Moreover, ezrin can limit the lateral diffusion of PI(4,5)P2 along the lipid bilayer. Together, these findings demonstrate that membrane-interaction mechanisms of ABPs evolved to precisely fulfill their specific functions in cytoskeletal dynamics.
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234
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Perthold JW, Oostenbrink C. Simulation of Reversible Protein-Protein Binding and Calculation of Binding Free Energies Using Perturbed Distance Restraints. J Chem Theory Comput 2017; 13:5697-5708. [PMID: 28898077 PMCID: PMC5688412 DOI: 10.1021/acs.jctc.7b00706] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
Virtually
all biological processes depend on the interaction between
proteins at some point. The correct prediction of biomolecular binding
free-energies has many interesting applications in both basic and
applied pharmaceutical research. While recent advances in the field
of molecular dynamics (MD) simulations have proven the feasibility
of the calculation of protein–protein binding free energies,
the large conformational freedom of proteins and complex free energy
landscapes of binding processes make such calculations a difficult
task. Moreover, convergence and reversibility of resulting free-energy
values remain poorly described. In this work, an easy-to-use, yet
robust approach for the calculation of standard-state protein–protein
binding free energies using perturbed distance restraints is described.
In the binding process the conformations of the proteins were restrained,
as suggested earlier. Two approaches to avoid end-state problems upon
release of the conformational restraints were compared. The method
was evaluated by practical application to a small model complex of
ubiquitin and the very flexible ubiquitin-binding domain of human
DNA polymerase ι (UBM2). All computed free energy differences
were closely monitored for convergence, and the calculated binding
free energies had a mean unsigned deviation of only 1.4 or 2.5 kJ·mol–1 from experimental values. Statistical error estimates
were in the order of thermal noise. We conclude that the presented
method has promising potential for broad applicability to quantitatively
describe protein–protein and various other kinds of complex
formation.
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Affiliation(s)
- Jan Walther Perthold
- Institute for Molecular Modeling and Simulation, Department for Material Sciences and Process Engineering, University of Natural Resources and Life Sciences (BOKU) Vienna , Muthgasse 18, 1190 Vienna, Austria
| | - Chris Oostenbrink
- Institute for Molecular Modeling and Simulation, Department for Material Sciences and Process Engineering, University of Natural Resources and Life Sciences (BOKU) Vienna , Muthgasse 18, 1190 Vienna, Austria
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235
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Khatua P, Sinha SK, Bandyopadhyay S. Size-Dependent Conformational Features of Aβ17–42 Protofilaments from Molecular Simulation Studies. J Chem Inf Model 2017; 57:2378-2392. [DOI: 10.1021/acs.jcim.7b00407] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Prabir Khatua
- Molecular
Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Sudipta Kumar Sinha
- Department
of Chemistry, Indian Institute of Technology Ropar, Ropar 140001, India
| | - Sanjoy Bandyopadhyay
- Molecular
Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
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236
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Gupta R, Kashyap N, Rai B. Molecular mechanism of transdermal co-delivery of interferon-alpha protein with gold nanoparticle – a molecular dynamics study. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1367094] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Rakesh Gupta
- Physical Science Research Area, TCS Research, Tata Research Development and Design Centre, Pune, India
| | - Nishi Kashyap
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, India
| | - Beena Rai
- Physical Science Research Area, TCS Research, Tata Research Development and Design Centre, Pune, India
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237
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Pohjolainen E, Malola S, Groenhof G, Häkkinen H. Exploring Strategies for Labeling Viruses with Gold Nanoclusters through Non-equilibrium Molecular Dynamics Simulations. Bioconjug Chem 2017; 28:2327-2339. [DOI: 10.1021/acs.bioconjchem.7b00367] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Emmi Pohjolainen
- Department of Physics and ‡Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland FI-40014
| | - Sami Malola
- Department of Physics and ‡Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland FI-40014
| | - Gerrit Groenhof
- Department of Physics and ‡Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland FI-40014
| | - Hannu Häkkinen
- Department of Physics and ‡Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland FI-40014
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238
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Zolghadr AR, Heydari Dokoohaki M. How Does the P7C3-Series of Neuroprotective Small Molecules Prevent Membrane Disruption? J Chem Inf Model 2017; 57:2009-2019. [PMID: 28691805 DOI: 10.1021/acs.jcim.7b00151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Molecular dynamics (MD) simulations are conducted to suggest a mechanism of action for the aminopropyl dibromocarbazole derivative (P7C3) small molecule, which protects neurons from apoptotic cell death. At first, the influence of embedded Aβ42 stacks on the structure of membrane is studied. Then, the effect of P7C3 molecules on the Aβ42 fibril enriched membrane and Aβ42 fibril depleted membrane (when Aβ42 fibrils are originally dissolved in the aqueous phase) are evaluated. Also, the formation of an amyloid ion channel in the Aβ42 enriched membrane is examined by calculating deuterium order parameter, density profile, and surface thickness. For Aβ42 in the fully inserted state, ion channel-like structures are formed. The presence of P7C3 molecules in this case just postpones membrane destruction but could not prevent pore formation. In contrast, when both Aβ42 and P7C3 molecules are embedded in the aqueous solution, the P7C3 molecules are self-assembled at membrane/ionic aqueous solution interface and prevent the precipitation and deposition of Aβ42 fibrils into the membrane.
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239
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Nandy A, Saenz-Méndez P, Gorman AM, Samali A, Eriksson LA. Homology model of the human tRNA splicing ligase RtcB. Proteins 2017; 85:1983-1993. [PMID: 28707320 DOI: 10.1002/prot.25352] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 06/28/2017] [Accepted: 07/11/2017] [Indexed: 12/25/2022]
Abstract
RtcB is an essential human tRNA ligase required for ligating the 2',3'-cyclic phosphate and 5'-hydroxyl termini of cleaved tRNA halves during tRNA splicing and XBP1 fragments during endoplasmic reticulum stress. Activation of XBP1 has been implicated in various human tumors including breast cancer. Here we present, for the first time, a homology model of human RtcB (hRtcB) in complex with manganese and covalently bound GMP built from the Pyrococcus horikoshii RtcB (bRtcB) crystal structure, PDB ID 4DWQA. The structure is analyzed in terms of stereochemical quality, folding reliability, secondary structure similarity with bRtcB, druggability of the active site binding pocket and its metal-binding microenvironment. In comparison with bRtcB, loss of a manganese-coordinating water and movement of Asn226 (Asn202 in 4DWQA) to form metal-ligand coordination, demonstrates the uniqueness of the hRtcB model. Rotation of GMP leads to the formation of an additional metal-ligand coordination (Mn-O). Umbrella sampling simulations of Mn binding in wild type and the catalytically inactive C122A mutant reveal a clear reduction of Mn binding ability in the mutant, thus explaining the loss of activity therein. Our results furthermore clearly show that the GTP binding site of the enzyme is a well-defined pocket that can be utilized as target site for in silico drug discovery.
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Affiliation(s)
- Argha Nandy
- Apoptosis Research Center, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Patricia Saenz-Méndez
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Göteborg, Sweden.,Computational Chemistry and Biology Group, Facultad de Química, Universidad de la República, Montevideo, 11800, Uruguay
| | - Adrienne M Gorman
- Apoptosis Research Center, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Afshin Samali
- Apoptosis Research Center, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Leif A Eriksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Göteborg, Sweden
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240
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Dorosh L, Stepanova M. Probing oligomerization of amyloid beta peptide in silico. MOLECULAR BIOSYSTEMS 2017; 13:165-182. [PMID: 27844078 DOI: 10.1039/c6mb00441e] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Aggregation of amyloid β (Aβ) peptide is implicated in fatal Alzheimer's disease, for which no cure is available. Understanding the mechanisms responsible for this aggregation is required in order for therapies to be developed. In an effort to better understand the molecular mechanisms involved in spontaneous aggregation of Aβ peptide, extensive molecular dynamics simulations are reported, and the results are analyzed through a combination of structural biology tools and a novel essential collective dynamics method. Several model systems composed of ten or twelve Aβ17-42 chains in water are investigated, and the influence of metal ions is probed. The results suggest that Aβ monomers tend to aggregate into stable globular-like oligomers with 13-23% of β-sheet content. Two stages of oligomer formation have been identified: quick collapse within the first 40 ns of the simulation, characterized by a decrease in inter-chain separation and build-up of β-sheets, and the subsequent slow relaxation of the oligomer structure. The resulting oligomers comprise a stable, coherently moving sub-aggregate of 6-9 strongly inter-correlated chains. Cu2+ and Fe2+ ions have been found to develop coordination bonds with carboxylate groups of E22, D23 and A42, which remain stable during 200 ns simulations. The presence of Fe2+, and particularly Cu2+ ions, in negatively charged cavities has been found to cause significant changes in the structure and dynamics of the oligomers. The results indicate, in particular, that formation of non-fibrillar oligomers might be involved in early template-free aggregation of Aβ17-42 monomers, with charged species such as Cu2+ or Fe2+ ions playing an important role.
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Affiliation(s)
- L Dorosh
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, Canada. and National Research Council of Canada, Edmonton, Alberta, Canada
| | - M Stepanova
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, Canada. and National Research Council of Canada, Edmonton, Alberta, Canada and Department of Physics, Astronomy, and Materials Science, Missouri State University, Springfield, MO, USA
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241
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Bodnarchuk MS, Dini D, Heyes DM, Breakspear A, Chahine S. Molecular Dynamics Studies of Overbased Detergents on a Water Surface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:7263-7270. [PMID: 28665133 DOI: 10.1021/acs.langmuir.7b00827] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Molecular dynamics (MD) simulations are reported of model overbased detergent nanoparticles on a model water surface which mimic their behavior on a Langmuir trough or large water droplet in engine oil. The simulations predict that the structure of the nanoparticle on a water surface is different to when it is immersed in a bulk hydrophobic solvent. The surfactant tails are partly directed out of the water, while the carbonate core maximizes its extent of contact with the water. Umbrella sampling calculations of the potential of mean force between two particles showed that they are associated with varying degrees with a maximum binding free energy of ca. 10 kBT for the salicylate stabilized particle, ca. 8 kBT for a sulfurized alkyl phenate stabilized particle, and ca. 5 kBT for a sulfonate stabilized particle. The differences in the strength of attraction depend on the proximity of nearest approach and the energy penalty associated with the disruption of the hydration shell of water molecules around the calcium carbonate core when the two particles approach. This is greatest for the sulfonate particle, which partially loses the surfactant ions to the solution, and least for the salicylate, which forms the weakest water "cage". The particles are separated by a water hydration layer, even at the point of closest approach.
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Affiliation(s)
- M S Bodnarchuk
- Department of Mechanical Engineering, Imperial College London , Exhibition Road, London SW7 2AZ, United Kingdom
| | - D Dini
- Department of Mechanical Engineering, Imperial College London , Exhibition Road, London SW7 2AZ, United Kingdom
| | - D M Heyes
- Department of Mechanical Engineering, Imperial College London , Exhibition Road, London SW7 2AZ, United Kingdom
| | - A Breakspear
- BP Technology Centre, Whitchurch Hill, Pangbourne RG8 7QR, United Kingdom
| | - S Chahine
- BP Technology Centre, Whitchurch Hill, Pangbourne RG8 7QR, United Kingdom
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242
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Abstract
The 97 amino acid bitopic membrane protein M2 of influenza A forms a tetrameric bundle in which two of the monomers are covalently linked via a cysteine bridge. In its tetrameric assembly the protein conducts protons across the viral envelope and within intracellular compartments during the infectivity cycle of the virus. A key residue in the translocation of the protons is His-37 which forms a planar tetrad in the configuration of the bundle accepting and translocating the incoming protons from the N terminal side, exterior of the virus, to the C terminal side, inside the virus. With experimentally available data from NMR spectroscopy of the transmembrane domains of the tetrameric M2 bundle classical MD simulations are conducted with the protein bundle in different protonation stages in respect to His-37. A full correlation analysis (FCA) of the data sets with the His-37 tetrad either in a fully four times unprotonated or protonated state, assumed to mimic high and low pH in vivo, respectively, in both cases reveal asymmetric backbone dynamics. His-37 side chain rotation dynamics is increased at full protonation of the tetrad compared to the dynamics in the fully unprotonated state. The data suggest that proton translocation can be achieved by decoupled side chain or backbone dynamics. Graphical abstract Visualization of the tetrameric bundle of the transmembrane domains of M2 of influenza A after 200 ns of MD simulations (upper left). The four histidine residues 37 are either not protonated as in M20 or fully protonated is in M24+. The asymmetric dynamics of the backbones are shown after a full correlation analysis (FCA) in blue (lower left). The rotational dynamics of the χ2 dihedral angles of the histidines in M20 (upper right) are less than those in M24+ (lower right).
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Affiliation(s)
- Monoj Mon Kalita
- Institute of Biophotonics and Biophotonics & Molecular Imaging Research Center (BMIRC), School of Biomedical Science and Engineering, National Yang-Ming University, 155, Li-Nong St., Sec. 2, Taipei, 112, Taiwan
| | - Wolfgang B Fischer
- Institute of Biophotonics and Biophotonics & Molecular Imaging Research Center (BMIRC), School of Biomedical Science and Engineering, National Yang-Ming University, 155, Li-Nong St., Sec. 2, Taipei, 112, Taiwan.
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243
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Wu S, Li L, Li Q. Mechanism of NTP Binding to the Active Site of T7 RNA Polymerase Revealed by Free-Energy Simulation. Biophys J 2017; 112:2253-2260. [PMID: 28591598 PMCID: PMC5474740 DOI: 10.1016/j.bpj.2017.04.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 04/11/2017] [Accepted: 04/24/2017] [Indexed: 11/26/2022] Open
Abstract
In genetic transcription, molecular dynamic details and energetics of NTP binding to the active site of RNA polymerase (RNAP) are poorly understood. In this article, we investigated the NTP binding process in T7 RNAP using all-atom MD simulation combined with the umbrella sampling technique. Based on our simulations, a two-step mechanism was proposed to explain NTP binding: first, substrate NTP in aqueous solution, which carries a magnesium ion, diffuses through a secondary channel of RNAP to attain a pore region, where it undergoes conformational changes to give a correct orientation; next, the NTP establishes initial basepairing contacts with the template nucleoside (TN). Our free-energy calculations suggest that both steps are spontaneous. This mechanism can easily explain the problem of NTP binding with different orientations. Moreover, it is found that the nascent NTP:TN basepair is fragile and easily broken by thermal disturbance. Therefore, we speculate that the fingers domain will be triggered to close, so as to create a steady environment for the next chemical step. The observations from the work provide valuable information for comprehensively understanding the mechanism of the basic step in genetic transcription.
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Affiliation(s)
- Shaogui Wu
- College of Chemistry and Materials Science, Sichuan Normal University, Chengdu, China; State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, China.
| | - Laicai Li
- College of Chemistry and Materials Science, Sichuan Normal University, Chengdu, China
| | - Quan Li
- College of Chemistry and Materials Science, Sichuan Normal University, Chengdu, China
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244
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Kargar F, Emadi S, Fazli H. The molecular behavior of a single β-amyloid inside a dipalmitoylphosphatidylcholine bilayer at three different temperatures: An atomistic simulation study: Aβ interaction with DPPC: Atomistic simulation. Proteins 2017; 85:1298-1310. [PMID: 28342211 DOI: 10.1002/prot.25290] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 03/16/2017] [Accepted: 03/21/2017] [Indexed: 01/29/2023]
Abstract
The behavior of a single Aβ40 molecule within a dipalmitoylphosphatidylcholine (DPPC) bilayer was studied by all-atom molecular dynamics simulations. The effect of membrane structure was investigated on Aβ40 behavior, secondary structure, and insertion depth. Simulations were performed at three temperatures (323, 310, and 300 K) to probe three different bilayer fluidities. Results show that at all above temperatures, the peptide contains two short helices, coil, bend, and turn structures. At 300 K, the peptide contains a region with β structure in C-terminal region. Our results also show that Aβ decreases the bilayer thickness and the order of lipids in its vicinity which leads to water insertion into the bilayer and concomitant increase in the local fluidity. The peptide remains embedded in the bilayer at all temperatures, and become inserted into the bilayer up to several residues at 323 and 310 K. At 310 and 300 K, the dominant interaction energy between Aβ and bilayer changes from electrostatic to van der Waals. It can be proposed that at higher temperatures (e.g., 323 K), Lys28 and the C-terminal region of the peptide play the role of two anchors that keep Aβ inside the top leaflet. This study demonstrates that Aβ molecule can perturb the integrity of cellular membranes. Proteins 2017; 85:1298-1310. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Faezeh Kargar
- Department of Physics, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, 45137-66731, Iran
| | - Saeed Emadi
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, 45137-66731, Iran
| | - Hossein Fazli
- Department of Physics, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, 45137-66731, Iran.,Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, 45137-66731, Iran
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245
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Rodriguez RA, Chen LY, Plascencia-Villa G, Perry G. Elongation affinity, activation barrier, and stability of Aβ42 oligomers/fibrils in physiological saline. Biochem Biophys Res Commun 2017; 487:444-449. [PMID: 28427941 DOI: 10.1016/j.bbrc.2017.04.084] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 04/16/2017] [Indexed: 11/26/2022]
Abstract
Amyloid-beta (Aβ) peptides, Aβ40 and the more neurotoxic Aβ42, have been the subject of many research efforts for Alzheimer's disease. In two recent independent investigations, the atomistic structure of Aβ42 fibril has been clearly established in the S-shaped conformation consisting of three β-sheets stabilized by salt bridges formed between the Lys28 sidechain and the C-terminus of Ala42. This structure distinctively differs from the long-known structure of Aβ40 in the β-hairpin shaped conformation consisting of two β-sheets. Recent in silico investigations based on all-atom models have reached closer agreement with the in vitro measurements of Aβ40 thermodynamics. In this study, we present an in silico investigation of Aβ42 thermodynamics. Using the established force field parameters in seven sets of all-atom simulations, we examined the stability of small Aβ42 oligomers in physiological saline. We computed the elongation affinity of the S-shaped Aβ42 fibril, reaching agreement with the experimental data. We also estimated the Arrhenius activation barrier along the elongation pathway (from the disordered conformation of a free Aβ42 peptide to its S-shaped conformation on a fibril) that amounts to about 16 kcal/mol, which is consistent with the experimental data. Based on these quantitative agreements, we conclude that aggregation of Aβ42 peptides into fibrils is thermodynamically slow without precipitation by extrinsic factors such as heparan sulfate proteoglycan and highlight the possibility to prevent Aβ42 aggregation by eliminating some precipitation factors or by increasing competitive agents to capture and transport free Aβ42 peptides from the cerebrospinal fluid.
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Affiliation(s)
- Roberto A Rodriguez
- Department of Physics, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Liao Y Chen
- Department of Physics, University of Texas at San Antonio, San Antonio, TX 78249, USA.
| | | | - George Perry
- Department of Biology and Neurosciences Institute, University of Texas at San Antonio, San Antonio, TX 78249, USA
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246
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Licari G, Cwiklik L, Jungwirth P, Vauthey E. Exploring Fluorescent Dyes at Biomimetic Interfaces with Second Harmonic Generation and Molecular Dynamics. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:3373-3383. [PMID: 28314372 DOI: 10.1021/acs.langmuir.7b00403] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The adsorption of a DNA fluorescent probe belonging to the thiazole orange family at the dodecane/water and dodecane/phospholipid/water interfaces has been investigated using a combination of surface second harmonic generation (SSHG) and all-atomistic molecular dynamics (MD) simulations. Both approaches point to a high affinity of the cationic dye for the dodecane/water interface with a Gibbs free energy of adsorption on the order of -45 kJ/mol. Similar affinity was observed with a monolayer of negatively charged DPPG (1,2-dipalmitoyl-sn-glycero-3-phospho-rac-(1-glycerol)) lipids. On the other hand, no significant adsorption could be found with the zwitterionic DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) lipids. This was rationalized in terms of Coulombic interactions between the monolayer surface and the cationic dye. The similar affinity for the interface with and without DPPG, despite the favorable Coulombic attraction in the latter case, could be explained after investigating the interfacial orientation of the dye. In the absence of a monolayer, the dye adsorbs with its molecular plane almost flat at the interface, whereas in the presence of DPPG it has to intercalate into the monolayer and adopt a significantly different orientation to benefit from the electrostatic stabilization.
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Affiliation(s)
- Giuseppe Licari
- Department of Physical Chemistry, University of Geneva , 30 quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - Lukasz Cwiklik
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences , Dolejškova 2155/3, 182 23 Prague 8, Czech Republic
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences , Flemingovo nam. 2, 16610 Prague 6, Czech Republic
| | - Eric Vauthey
- Department of Physical Chemistry, University of Geneva , 30 quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
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247
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Wu S. Molecular dynamics simulation study of the “stay or leave” problem for two magnesium ions in gene transcription. Proteins 2017; 85:1002-1007. [DOI: 10.1002/prot.25268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 01/30/2017] [Accepted: 02/05/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Shaogui Wu
- College of Chemistry and Materials Science; Sichuan Normal University; Chengdu 610066 China
- State Key Laboratory of Theoretical Physics; Institute of Theoretical Physics, Chinese Academy of Sciences; Beijing 100190 China
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Ferreira MF, Franca EF, Leite FL. Unbinding pathway energy of glyphosate from the EPSPs enzyme binding site characterized by Steered Molecular Dynamics and Potential of Mean Force. J Mol Graph Model 2017; 72:43-49. [PMID: 28033555 DOI: 10.1016/j.jmgm.2016.11.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 11/13/2016] [Accepted: 11/14/2016] [Indexed: 10/20/2022]
Abstract
The quantification of herbicides in the environment, like glyphosate, is extremely important to prevent contamination. Nanobiosensors stands out in the quantization process, because of the high selectivity, sensitivity and short response time of the method. In order to emulate the detection of glyphosate using a specific nanobiossensor through an Atomic Force Microscope (AFM), this work carried out Steered Molecular Dynamics simulations (SMD) in which the herbicide was unbinded from the active site of the enzyme 5- enolpyruvylshikimate 3 phosphate synthase (EPSPS) along three different directions.After the simulations, Potential of Mean Force calculations were carried, from a cumulant expansion of Jarzynski's equation to obtain the profile of free energy of interaction between the herbicide and the active site of the enzyme in the presence of shikimate-3 substrate phosphate (S3P). The set of values for external work, had a Gaussian distribution. The PMF values ranged according to the directions of the unbindong pahway of each simulation, displaying energy values of 10.7, 14.7 and 19.5KJmol-1. The results provide a theoretical support in order to assist the construction of a specific nanobiossensor to quantify the glyphosate herbicide.
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Affiliation(s)
- Moacir F Ferreira
- Instituto de Química, Universidade Federal de Uberlândia, 38408-100, Uberlândia, MG, Brazil.
| | - Eduardo F Franca
- Instituto de Química, Universidade Federal de Uberlândia, 38408-100, Uberlândia, MG, Brazil
| | - Fábio L Leite
- Universidade Federal de São Carlos, 18052-780, Sorocaba, SP, Brazil
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249
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Majumdar S, Acharya A, Tomar SK, Prakash B. Disrupting domain-domain interactions is indispensable for EngA-ribosome interactions. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1865:289-303. [PMID: 27979707 DOI: 10.1016/j.bbapap.2016.12.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 12/06/2016] [Accepted: 12/10/2016] [Indexed: 11/24/2022]
Abstract
EngA consists of two tandem GTPase-domains-GD1 and GD2-followed by a KH-domain. EngA was considered to be a 50S assembly factor since it was shown to bind 50S and its deletion leads to the accumulation of immature 45S ribosomal subunits. Subsequently, we demonstrated an additional ribosome bound state of EngA bound to 50S, 30S, and 70S. While the former (50S binding) is achieved upon GTP binding at both GD1 and GD2, the latter is formed upon GTP hydrolysis at GD1, which is believed to trigger a large conformational change in the protein. The present study brings out two key aspects of EngA regulation: First, that distinctly stabilized GD1-KH interfaces allows EngA to exist in different ribosome bound states, and second is the importance of these states to ribosome assembly. Our analyses suggest that distinct inter-domain (GD-KH) interfaces are stabilized by interactions arising from unique sets of motifs, conserved across EngA homologues, and seem to be mechanistically linked to GTP/GDP binding. By experimentally measuring binding affinities for several interface mutants, we show that disrupting the interface interactions is necessary to realize EngA-ribosome binding. These findings are also supported by a recent cryo-EM structure of EngA bound to 50S, wherein the GD1-KH interface is completely disrupted leading to an 'extended' or 'open state' of the protein. Overall, it appears that the transition of EngA from a 'closed state' with GD1-KH forming a tight interface, to an 'open state' mediates interaction with ribosomal subunits.
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Affiliation(s)
- Soneya Majumdar
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Abhishek Acharya
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Sushil Kumar Tomar
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Balaji Prakash
- Department of Molecular Nutrition, CSIR-Central Food Technological Research Institute, Mysore 570020, India.
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250
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Structural and fluctuational difference between two ends of Aβ amyloid fibril: MD simulations predict only one end has open conformations. Sci Rep 2016; 6:38422. [PMID: 27934893 PMCID: PMC5146922 DOI: 10.1038/srep38422] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 11/08/2016] [Indexed: 02/02/2023] Open
Abstract
Aβ amyloid fibrils, which are related to Alzheimer’s disease, have a cross-β structure consisting of two β-sheets: β1 and β2. The Aβ peptides are thought to be serially arranged in the same molecular conformation along the fibril axis. However, to understand the amyloid extension mechanism, we must understand the amyloid fibril structure and fluctuation at the fibril end, which has not been revealed to date. Here, we reveal these features by all-atom molecular dynamics (MD) simulations of Aβ42 and Aβ40 fibrils in explicit water. The structure and fluctuation were observed to differ between the two ends. At the even end, the Aβ peptide always took a closed form wherein β1 and β2 were closely spaced. The Aβ peptide fluctuated more at the odd end and took an open form wherein the two β-sheets were well separated. The differences are attributed to the stronger β-sheet formation by the β1 exposed at the even end than the β2 exposed at the odd end. Along with the small fluctuations at the even end, these results explain why the fibril extends from one end only, as observed in experiments. Our MD results agree well with recent observations by high-speed atomic force microscopy.
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