1
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Bandyopadhyay S, Majumdar BB, Mondal J. Solvent's Role in Cavity-Ligand Recognition Would Depend on the Mode of Ligand Diffusion. J Phys Chem B 2022; 126:2952-2958. [PMID: 35436126 DOI: 10.1021/acs.jpcb.1c09645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Solvent is known to play crucial roles in dictating the thermodynamics and kinetics of the biomolecular recognition process. Here, we show that the extent of significance of water in modulating the ligand recognition process is critically contingent on the ligand diffusion and on the constraints introduced on it. Toward the end, we use a well-known prototypical system of spherical ligand diffusing freely toward a hydrophobic concave cavity in explicit water. We analyze a large series of adaptively sampled unbiased molecular dynamics simulation trajectories within the framework of time-structured independent component analysis (TICA). Our quantitative investigations reveal that water would play a significant role in the ligand recognition process, provided that the ligand is constricted to diffuse along a centro-symmetric fashion. On the contrary, water's contribution in the ligand recognition process would diminish to a negligible value if the ligand freely diffuses toward the pocket. A Markov state model (MSM) constructed using the simulated trajectories identifies a set of transiently populated metastable states comprising partially ligand-unbound macro states, alongside ligand-bound and ligand-unbound pose and gives rise to multiple transition paths of ligand in its way to the hydrophobic cavity. Lifting the restriction on ligand movement changes its binding pathway, time scales, and the extent of the role of solvent in modulating the recognition process.
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2
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Vangaveti S, Ranganathan SV, Agris PF. Physical Chemistry of a Single tRNA-Modified Nucleoside Regulates Decoding of the Synonymous Lysine Wobble Codon and Affects Type 2 Diabetes. J Phys Chem B 2022; 126:1168-1177. [PMID: 35119848 DOI: 10.1021/acs.jpcb.1c09053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The 2-methylthio-modification (ms2-) of N6-threonylcarbonyladenosine (t6A37) at position-37 (ms2t6A37) in tRNAUUULys3 provides the needed stability between the tRNA anticodon and the human insulin mRNA codon AAG during translation, as determined by molecular dynamics simulation. Single-nucleoside polymorphisms of the human gene for the enzyme, Cdkal1 that post-transcriptionally modifies t6A37 to ms2t6A37 in tRNAUUULys3, correlate with type 2 diabetes mellitus. Without the ms2-modification, tRNAUUULys3 is incapable of correctly translating the insulin mRNA AAG codon for lysine at the site of protease cleavage between the A-chain and the C-peptide. By enhancing anticodon/codon cross-strand stacking, the ms2-modification adds stability through van der Waals interactions and dehydration of the ASL loop and cavity of the anticodon/codon minihelix but does not add hydrogen bonding of any consequence. Thus, the modifying enzyme Cdkal1, by adding a crucial ms2-group to tRNAUUULys3-t6A37, facilitates the decoding of the AAG codon and enables human pancreatic islets to correctly translate insulin mRNA.
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Affiliation(s)
- Sweta Vangaveti
- The RNA Institute, University at Albany, Albany, New York 12222, United States
| | - Srivathsan V Ranganathan
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon 97210 United States
| | - Paul F Agris
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina 27710 United States
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3
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Biswas P, Sen D, Prasher M, Sarkar SK, Dasgupta K. Confinement driven anomalous freezing in nano porous spray dried microspheres. NANOTECHNOLOGY 2021; 32:385707. [PMID: 34116521 DOI: 10.1088/1361-6528/ac0ab6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/11/2021] [Indexed: 06/12/2023]
Abstract
One-step evaporative jamming of colloidal silica particles in contact-free spray droplets resulted in well-defined powder micro-granules with interstitial nanopores. This paper reports the anomalous freezing behaviour of confined water in the microspheres synthesized using spray drying. It has been revealed that the freezing point of water in these microspheres gets significantly lowered (∼-45 °C) owing to the confinement effect. Thermoporometry results are corroborated with the structural details obtained using complementary techniques of gas adsorption measurements and small-angle x-ray scattering.
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Affiliation(s)
- Priyanka Biswas
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai-400085, India
- Homi Bhabha National Institute, Mumbai-400094, India
| | - Debasis Sen
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai-400085, India
- Homi Bhabha National Institute, Mumbai-400094, India
| | - Meenu Prasher
- Materials Science Division, Bhabha Atomic Research Centre, Mumbai-400085, India
| | - Sudip Kumar Sarkar
- Materials Science Division, Bhabha Atomic Research Centre, Mumbai-400085, India
| | - Kinshuk Dasgupta
- Homi Bhabha National Institute, Mumbai-400094, India
- Glass and Advanced Materials Division, Materials Group, Bhabha Atomic Research Centre, Mumbai-400085, India
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4
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Yamini G, Kanchi S, Kalu N, Momben Abolfath S, Leppla SH, Ayappa KG, Maiti PK, Nestorovich EM. Hydrophobic Gating and 1/ f Noise of the Anthrax Toxin Channel. J Phys Chem B 2021; 125:5466-5478. [PMID: 34015215 DOI: 10.1021/acs.jpcb.0c10490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
"Pink" or 1/f noise is a natural phenomenon omnipresent in physics, economics, astrophysics, biology, and even music and languages. In electrophysiology, the stochastic activity of a number of biological ion channels and artificial nanopores could be characterized by current noise with a 1/f power spectral density. In the anthrax toxin channel (PA63), it appears as fast voltage-independent current interruptions between conducting and nonconducting states. This behavior hampers potential development of PA63 as an ion-channel biosensor. On the bright side, the PA63 flickering represents a mesmerizing phenomenon to investigate. Notably, similar 1/f fluctuations are observed in the channel-forming components of clostridial binary C2 and iota toxins, which share functional and structural similarities with the anthrax toxin channel. Similar to PA63, they are evolved to translocate the enzymatic components of the toxins into the cytosol. Here, using high-resolution single-channel lipid bilayer experiments and all-atom molecular dynamic simulations, we suggest that the 1/f noise in PA63 occurs as a result of "hydrophobic gating" at the ϕ-clamp region, the phenomenon earlier observed in several water-filled channels "fastened" inside by the hydrophobic belts. The ϕ-clamp is a narrow "hydrophobic ring" in the PA63 lumen formed by seven or eight phenylalanine residues at position 427, conserved in the C2 and iota toxin channels, which catalyzes protein translocation. Notably, the 1/f noise remains undetected in the F427A PA63 mutant. This finding can elucidate the functional purpose of 1/f noise and its possible role in the transport of the enzymatic components of binary toxins.
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Affiliation(s)
- Goli Yamini
- Department of Biology, The Catholic University of America, 620 Michigan Avenue, Washington D.C., 20064, United States
| | - Subbarao Kanchi
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru 560012, India.,Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bengaluru 560012, India
| | - Nnanya Kalu
- Department of Biology, The Catholic University of America, 620 Michigan Avenue, Washington D.C., 20064, United States
| | - Sanaz Momben Abolfath
- Department of Biology, The Catholic University of America, 620 Michigan Avenue, Washington D.C., 20064, United States
| | - Stephen H Leppla
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - K Ganapathy Ayappa
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru 560012, India
| | - Prabal K Maiti
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bengaluru 560012, India
| | - Ekaterina M Nestorovich
- Department of Biology, The Catholic University of America, 620 Michigan Avenue, Washington D.C., 20064, United States
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5
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Monroe JI, Jiao S, Davis RJ, Robinson Brown D, Katz LE, Shell MS. Affinity of small-molecule solutes to hydrophobic, hydrophilic, and chemically patterned interfaces in aqueous solution. Proc Natl Acad Sci U S A 2021; 118:e2020205118. [PMID: 33372161 PMCID: PMC7821046 DOI: 10.1073/pnas.2020205118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Performance of membranes for water purification is highly influenced by the interactions of solvated species with membrane surfaces, including surface adsorption of solutes upon fouling. Current efforts toward fouling-resistant membranes often pursue surface hydrophilization, frequently motivated by macroscopic measures of hydrophilicity, because hydrophobicity is thought to increase solute-surface affinity. While this heuristic has driven diverse membrane functionalization strategies, here we build on advances in the theory of hydrophobicity to critically examine the relevance of macroscopic characterizations of solute-surface affinity. Specifically, we use molecular simulations to quantify the affinities to model hydroxyl- and methyl-functionalized surfaces of small, chemically diverse, charge-neutral solutes represented in produced water. We show that surface affinities correlate poorly with two conventional measures of solute hydrophobicity, gas-phase water solubility and oil-water partitioning. Moreover, we find that all solutes show attraction to the hydrophobic surface and most to the hydrophilic one, in contrast to macroscopically based hydrophobicity heuristics. We explain these results by decomposing affinities into direct solute interaction energies (which dominate on hydroxyl surfaces) and water restructuring penalties (which dominate on methyl surfaces). Finally, we use an inverse design algorithm to show how heterogeneous surfaces, with multiple functional groups, can be patterned to manipulate solute affinity and selectivity. These findings, importantly based on a range of solute and surface chemistries, illustrate that conventional macroscopic hydrophobicity metrics can fail to predict solute-surface affinity, and that molecular-scale surface chemical patterning significantly influences affinity-suggesting design opportunities for water purification membranes and other engineered interfaces involving aqueous solute-surface interactions.
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Affiliation(s)
- Jacob I Monroe
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106
| | - Sally Jiao
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106
| | - R Justin Davis
- Department of Civil, Architectural and Environmental Engineering, University of Texas at Austin, Austin, TX 78712
| | - Dennis Robinson Brown
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106
| | - Lynn E Katz
- Department of Civil, Architectural and Environmental Engineering, University of Texas at Austin, Austin, TX 78712
| | - M Scott Shell
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106;
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6
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Stefanutti E, Bove LE, Alabarse FG, Lelong G, Bruni F, Ricci MA. Vibrational dynamics of confined supercooled water. J Chem Phys 2019; 150:224504. [PMID: 31202218 DOI: 10.1063/1.5094147] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The quest for a possible liquid-liquid coexistence line in supercooled water below its homogeneous nucleation temperature is faced by confining water within a porous silica substrate (MCM-41). This system is investigated by synchrotron radiation infrared spectroscopy, exploring both the intramolecular and the intermolecular vibrational dynamics, in the temperature range from ambient down to ∼120 K, along several isobaric paths between 0.7 kbar and 3.0 kbar. Upon lowering the temperature, the OH-stretching band shows that the intramolecular vibrational dynamics continuously evolves from predominantly liquidlike to predominantly icelike. An abrupt change in the line shape of the intermolecular vibrational band between 220 K and 240 K, depending on the pressure, is the signature of nucleation of ice within the MCM-41 pores. These findings do not support the presence of two liquid phases and provide evidence for the coexistence of liquid water and ice in water confined in MCM-41.
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Affiliation(s)
- E Stefanutti
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 4 Place Jussieu, 75005 Paris, France
| | - L E Bove
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 4 Place Jussieu, 75005 Paris, France
| | - F G Alabarse
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 4 Place Jussieu, 75005 Paris, France
| | - G Lelong
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 4 Place Jussieu, 75005 Paris, France
| | - F Bruni
- Dipartimento di Scienze, Università Degli Studi Roma Tre, Via della Vasca Navale 84, 00146 Roma, Italy
| | - M A Ricci
- Dipartimento di Scienze, Università Degli Studi Roma Tre, Via della Vasca Navale 84, 00146 Roma, Italy
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7
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Pradhan MR, Nguyen MN, Kannan S, Fox SJ, Kwoh CK, Lane DP, Verma CS. Characterization of Hydration Properties in Structural Ensembles of Biomolecules. J Chem Inf Model 2019; 59:3316-3329. [DOI: 10.1021/acs.jcim.8b00453] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Mohan R. Pradhan
- Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
- School of Computer Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798
| | - Minh N. Nguyen
- Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Srinivasaraghavan Kannan
- Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Stephen J. Fox
- Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Chee Keong Kwoh
- School of Computer Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798
| | - David P. Lane
- p53 Laboratory, A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove, #06-04/05, Neuros/Immunos, Singapore 138648
| | - Chandra S. Verma
- Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
- School of Biological Sciences, Nanyang Technological University, 50 Nanyang Drive, Singapore 637551
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
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8
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Collective Transformation of Water between Hyperactive Antifreeze Proteins: RiAFPs. CRYSTALS 2019. [DOI: 10.3390/cryst9040188] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We demonstrate, by molecular dynamics simulations, that water confined between a pair of insect hyperactive antifreeze proteins from the longhorn beetle Rhagium inquisitor is discontinuously expelled as the two proteins approach each other at a certain distance. The extensive striped hydrophobic–hydrophilic pattern on the surface, comprising arrays of threonine residues, enables water to form three independent ice channels through the assistance of hydroxyl groups, even at 300 K. The transformation is reminiscent of a freezing–melting transition rather than a drying transition and governs the stable protein–protein separation in the evaluation of the potential of mean force. The collectivity of water penetration or expulsion and the hysteresis in the time scale of ten nanoseconds predict a potential first-order phase transition at the limit of infinite size and provide a new framework for the water-mediated interaction between solutes.
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9
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Li W, Zuo X, Zhou X, Lu H. Effect of aggregated gas molecules on dewetting transition of water between nanoscale hydrophobic plates. J Chem Phys 2019; 150:104702. [PMID: 30876371 DOI: 10.1063/1.5082229] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Affiliation(s)
- Weijian Li
- College of Mathematics, Physics and Information Engineering, Zhejiang Normal University, Jinhua 321004, China
| | - Xiaoliang Zuo
- College of Mathematics, Physics and Information Engineering, Zhejiang Normal University, Jinhua 321004, China
| | - Xiaoyan Zhou
- College of Mathematics, Physics and Information Engineering, Zhejiang Normal University, Jinhua 321004, China
| | - Hangjun Lu
- College of Mathematics, Physics and Information Engineering, Zhejiang Normal University, Jinhua 321004, China
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10
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Samanta T, Biswas R, Banerjee S, Bagchi B. Study of distance dependence of hydrophobic force between two graphene-like walls and a signature of pressure induced structure formation in the confined water. J Chem Phys 2018; 149:044502. [PMID: 30068196 DOI: 10.1063/1.5025823] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We examine the separation distance dependence of the hydrophobic force by systematically varying the distance (d) between two walls. The hydrophobic force exhibits a distance mediated crossover from a liquid-like to a gas-like behavior at around d ∼ 12 Å for 1 atm pressure. The distance dependence can be fitted to a bi-exponential form, with the longer distance part displaying a correlation length of 20 Å. In addition, the crossover is found to be accompanied by a divergent-like growth of the local relative number fluctuation of the water molecules confined between the two surfaces. Furthermore, at a fixed separation (d = 20 Å), we observe a pressure induced structural modification of confined water at high pressure. The confined water is found to form an ordered structure at high pressure (10 000 atm) and room temperature, in agreement with the experimental study [G. Algara-Siller et al. Nature 519(7544), 443 (2015)].
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Affiliation(s)
- Tuhin Samanta
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Rajib Biswas
- Department of Chemistry, Indian Institute of Technology Tirupati, Tirupati 517506, India
| | - Saikat Banerjee
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
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11
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Computational discovery of chemically patterned surfaces that effect unique hydration water dynamics. Proc Natl Acad Sci U S A 2018; 115:8093-8098. [PMID: 30038028 DOI: 10.1073/pnas.1807208115] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The interactions of water with solid surfaces govern their apparent hydrophobicity/hydrophilicity, influenced at the molecular scale by surface coverage of chemical groups of varied nonpolar/polar character. Recently, it has become clear that the precise patterning of surface groups, and not simply average surface coverage, has a significant impact on the structure and thermodynamics of hydration layer water, and, in turn, on macroscopic interfacial properties. Here we show that patterning also controls the dynamics of hydration water, a behavior frequently thought to be leveraged by biomolecules to influence functional dynamics, but yet to be generalized. To uncover the role of surface heterogeneities, we couple a genetic algorithm to iterative molecular dynamics simulations to design the patterning of surface functional groups, at fixed coverage, to either minimize or maximize proximal water diffusivity. Optimized surface configurations reveal that clustering of hydrophilic groups increases hydration water mobility, while dispersing them decreases it, but only if hydrophilic moieties interact with water through directional, hydrogen-bonding interactions. Remarkably, we find that, across different surfaces, coverages, and patterns, both the chemical potential for inserting a methane-sized hydrophobe near the interface and, in particular, the hydration water orientational entropy serve as strong predictors for hydration water diffusivity, suggesting that these simple thermodynamic quantities encode the way surfaces control water dynamics. These results suggest a deep and intriguing connection between hydration water thermodynamics and dynamics, demonstrating that subnanometer chemical surface patterning is an important design parameter for engineering solid-water interfaces with applications spanning separations to catalysis.
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12
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Katyal N, Agarwal M, Sen R, Kumar V, Deep S. Paradoxical Effect of Trehalose on the Aggregation of α-Synuclein: Expedites Onset of Aggregation yet Reduces Fibril Load. ACS Chem Neurosci 2018; 9:1477-1491. [PMID: 29601727 DOI: 10.1021/acschemneuro.8b00056] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Aggregation of α-synuclein is closely connected to the pathology of Parkinson's disease. The phenomenon involves multiple steps, commenced by partial misfolding and eventually leading to mature amyloid fibril formation. Trehalose, a widely accepted osmolyte, has been shown previously to inhibit aggregation of various globular proteins owing to its ability to prevent the initial unfolding of protein. In this study, we have examined if it behaves in a similar fashion with intrinsically disordered protein α-synuclein and possesses the potential to act as therapeutic agent against Parkinson's disease. It was observed experimentally that samples coincubated with trehalose fibrillate faster compared to the case in its absence. Molecular dynamics simulations suggested that this initial acceleration is manifestation of trehalose's tendency to perturb the conformational transitions between different conformers of monomeric protein. It stabilizes the aggregation prone "extended" conformer of α-synuclein, by binding to its exposed acidic residues of the C terminus. It also favors the β-rich oligomers once formed. Interestingly, the total fibrils formed are still promisingly less since it accelerates the competing pathway toward formation of amorphous aggregates.
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Affiliation(s)
- Nidhi Katyal
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauz-Khas, New Delhi 110016, India
| | - Manish Agarwal
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauz-Khas, New Delhi 110016, India
| | - Raktim Sen
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauz-Khas, New Delhi 110016, India
| | - Vinay Kumar
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauz-Khas, New Delhi 110016, India
| | - Shashank Deep
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauz-Khas, New Delhi 110016, India
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13
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Physico-chemical properties of aqueous drug solutions: From the basic thermodynamics to the advanced experimental and simulation results. Int J Pharm 2018; 540:65-77. [PMID: 29412151 DOI: 10.1016/j.ijpharm.2018.01.042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 01/22/2018] [Accepted: 01/22/2018] [Indexed: 11/20/2022]
Abstract
The physical chemical properties of aqueous solutions of model compounds are illustrated in relation to hydration and solubility issues by using three perspectives: thermodynamic, spectroscopic and molecular dynamics simulations. The thermodynamic survey of the fundamental backgrounds of concentration dependence and experimental solubility results show some peculiar behavior of aqueous solutions with several types of similar solutes. Secondly, the use of a variety of experimental spectroscopic devices, operating under different experimental conditions of dimension and frequency, has produced a large amount of structural and dynamic data on aqueous solutions showing the richness of the information produced, depending on where and how the experiment is carried out. Finally, the use of molecular dynamics computational work is presented to highlight how the different types of solute functional groups and surface topologies organize adjacent water molecules differently. The highly valuable contribution of computer simulation studies in providing molecular explanations for experimental deductions, either of a thermodynamic or spectroscopic nature, is shown to have changed the current knowledge of many aqueous solution processes. While this paper is intended to provide a collective view on the latest literature results, still the presentation aims at a tutorial explanation of the potentials of the three methodologies in the field of aqueous solutions of pharmaceutical molecules.
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14
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Samanta T, Bagchi B. Temperature effects on the hydrophobic force between two graphene-like surfaces in liquid water. J CHEM SCI 2018. [DOI: 10.1007/s12039-018-1433-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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15
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Katyal N, Deep S. Inhibition of GNNQQNY prion peptide aggregation by trehalose: a mechanistic view. Phys Chem Chem Phys 2018; 19:19120-19138. [PMID: 28702592 DOI: 10.1039/c7cp02912h] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Deposition of amyloid fibrils is the seminal event in the pathogenesis of numerous neurodegenerative diseases. The formation of this amyloid assembly is the manifestation of a cascade of structural transitions including toxic oligomer formation in the early stages of aggregation. Thus a viable therapeutic strategy involves the use of small molecular ligands to interfere with this assembly. In this perspective, we have explored the kinetics of aggregate formation of the fibril forming GNNQQNY peptide fragment from the yeast prion protein SUP35 using multiple all atom MD simulations with explicit solvent and provided mechanistic insights into the way trehalose, an experimentally known aggregation inhibitor, modulates the aggregation pathway. The results suggest that the assimilation process is impeded by different barriers at smaller and larger oligomeric sizes: the initial one being easily surpassed at higher temperatures and peptide concentrations. The kinetic profile demonstrates that trehalose delays the aggregation process by increasing both these activation barriers, specifically the latter one. It increases the sampling of small-sized aggregates that lack the beta sheet conformation. Analysis reveals that the barrier in the growth of larger stable oligomers causes the formation of multiple stable small oligomers which then fuse together bimolecularly. The PCA of 26 properties was carried out to deconvolute the events within the temporary lag phases, which suggested dynamism in lags involving an increase in interchain contacts and burial of SASA. The predominant growth route is monomer addition, which changes to condensation on account of a large number of depolymerisation events in the presence of trehalose. The favourable interaction of trehalose specifically with the sidechain of the peptide promotes crowding of trehalose molecules in its vicinity - the combination of both these factors imparts the observed behaviour. Furthermore, increasing trehalose concentration leads to faster expulsion of water molecules than interpeptide interactions. These expelled water molecules have larger translational movement, suggesting an entropy factor to favor the assembly process. Different conformations observed under this condition suggest the role of water molecules in guiding the morphology of the aggregates as well. A similar scenario exists on increasing peptide concentration.
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Affiliation(s)
- Nidhi Katyal
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauzkhas, New Delhi, India.
| | - Shashank Deep
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauzkhas, New Delhi, India.
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16
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Bai L, Jang J, Zhang Z, Jang J. Dewetting transition of water confined between atomically rough surfaces: A lattice gas Monte Carlo simulation study. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.01.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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17
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Levy Y. Protein Assembly and Building Blocks: Beyond the Limits of the LEGO Brick Metaphor. Biochemistry 2017; 56:5040-5048. [PMID: 28809494 DOI: 10.1021/acs.biochem.7b00666] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Proteins, like other biomolecules, have a modular and hierarchical structure. Various building blocks are used to construct proteins of high structural complexity and diverse functionality. In multidomain proteins, for example, domains are fused to each other in different combinations to achieve different functions. Although the LEGO brick metaphor is justified as a means of simplifying the complexity of three-dimensional protein structures, several fundamental properties (such as allostery or the induced-fit mechanism) make deviation from it necessary to respect the plasticity, softness, and cross-talk that are essential to protein function. In this work, we illustrate recently reported protein behavior in multidomain proteins that deviates from the LEGO brick analogy. While earlier studies showed that a protein domain is often unaffected by being fused to another domain or becomes more stable following the formation of a new interface between the tethered domains, destabilization due to tethering has been reported for several systems. We illustrate that tethering may sometimes result in a multidomain protein behaving as "less than the sum of its parts". We survey these cases for which structure additivity does not guarantee thermodynamic additivity. Protein destabilization due to fusion to other domains may be linked in some cases to biological function and should be taken into account when designing large assemblies.
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Affiliation(s)
- Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science , Rehovot 76100, Israel
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18
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Abstract
Szent-Győrgi called water the "matrix of life" and claimed that there was no life without it. This statement is true, as far as we know, on our planet, but it is not clear whether it must hold throughout the cosmos. To evaluate that question requires a close consideration of the many varied and subtle roles that water plays in living cells-a consideration that must be free of both an assumed essentialism that gives water an almost mystical life-giving agency and a traditional tendency to see it as a merely passive solvent. Water is a participant in the "life of the cell," and here I describe some of the features of that active agency. Water's value for molecular biology comes from both the structural and dynamic characteristics of its status as a complex, structured liquid as well as its nature as a polar, protic, and amphoteric reagent. Any discussion of water as life's matrix must, however, begin with an acknowledgment that our understanding of it as both a liquid and a solvent is still incomplete.
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19
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Schnupf U, Brady JW. Water structuring above solutes with planar hydrophobic surfaces. Phys Chem Chem Phys 2017; 19:11851-11863. [PMID: 28435966 DOI: 10.1039/c7cp00179g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Many important biological solutes possess not only polar and hydrogen bonding functionalities, but also weakly-hydrating, or hydrophobic, surfaces. Theories of the hydration of such surfaces predict that their solvent interactions will change from a wetting type interaction to a dewetting regime as a function of the solute size, with a gradual transition in behavior taking place around characteristic lengths of ∼1 nm. Aggregations of non-polar species over this size range will undergo a transition from being dominated by entropy to being dominated by enthalpy. These transitions can be understood in part in terms of the geometries required of the solvating water molecules. We report here a series of simulations in aqueous solution of organic molecules with planar faces of increasing size, ranging from cyclopropane to circumcircumcoronene, in order to explore the transition in behavior for such solutes as their size increases. For this series, the dewetting transition occurred gradually, converging asymptotically to a limiting separation value for first layer water molecules of around 3.3 Å, while the transition in hydrogen bonding orientational structure occurred between cyclopropane and cyclopentadene. Water immediately adjacent to the largest planar hydrophobic surfaces oriented in ways that resembled on average the structural organization of the basal planes of ice.
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Affiliation(s)
- Udo Schnupf
- Department of Chemistry and Biochemistry, Bradley University, Peoria, IL 61625, USA
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20
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Custer GS, Das P, Matysiak S. Interplay between Conformational Heterogeneity and Hydration in the Folding Landscape of a Designed Three-Helix Bundle. J Phys Chem B 2017; 121:2731-2738. [PMID: 28282142 DOI: 10.1021/acs.jpcb.6b12286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Water is known to play a critical role in protein folding and stability. Here we develop and employ a coarse-grained (CG) model to directly explore the role of water in shaping the conformational landscape explored during protein folding. For this purpose, we simulate a designed sequence with binary patterning of neutral and hydrophobic residues, which is capable of folding to a three-helix bundle in explicit water. We find two folded states of this sequence, with rotation of the helices occurring to trade between hydrophobic packing and water expulsion from the core. This work provides insight into the role of water and hydrophobicity in generating competing folded states for a protein.
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Affiliation(s)
- Gregory S Custer
- Fischell Department of Bioengineering, University of Maryland , College Park, Maryland 20742, United States
| | - Payel Das
- IBM Thomas J. Watson Research Center , Yorktown Heights, New York 10598, United States
| | - Silvina Matysiak
- Fischell Department of Bioengineering, University of Maryland , College Park, Maryland 20742, United States
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21
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Robust Denaturation of Villin Headpiece by MoS2 Nanosheet: Potential Molecular Origin of the Nanotoxicity. Sci Rep 2016; 6:28252. [PMID: 27312409 PMCID: PMC4911589 DOI: 10.1038/srep28252] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 06/02/2016] [Indexed: 12/13/2022] Open
Abstract
MoS2 nanosheet, a new two-dimensional transition metal dichalcogenides nanomaterial, has attracted significant attentions lately due to many potential promising biomedical applications. Meanwhile, there is also a growing concern on its biocompatibility, with little known on its interactions with various biomolecules such as proteins. In this study, we use all-atom molecular dynamics simulations to investigate the interaction of a MoS2 nanosheet with Villin Headpiece (HP35), a model protein widely used in protein folding studies. We find that MoS2 exhibits robust denaturing capability to HP35, with its secondary structures severely destroyed within hundreds of nanosecond simulations. Both aromatic and basic residues are critical for the protein anchoring onto MoS2 surface, which then triggers the successive protein unfolding process. The main driving force behind the adsorption process is the dispersion interaction between protein and MoS2 monolayer. Moreover, water molecules at the interface between some key hydrophobic residues (e.g. Trp-64) and MoS2 surface also help to accelerate the process driven by nanoscale drying, which provides a strong hydrophobic force. These findings might have shed new light on the potential nanotoxicity of MoS2 to proteins with atomic details, which should be helpful in guiding future biomedical applications of MoS2 with its nanotoxicity mitigated.
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22
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Meng XY, Li B, Liu S, Kang H, Zhao L, Zhou R. EGCG in Green Tea Induces Aggregation of HMGB1 Protein through Large Conformational Changes with Polarized Charge Redistribution. Sci Rep 2016; 6:22128. [PMID: 26899177 PMCID: PMC4762017 DOI: 10.1038/srep22128] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 02/08/2016] [Indexed: 12/13/2022] Open
Abstract
As a major effective component in green tea, (-)-epigallocatechin-3-gallate (EGCG)'s potential benefits to human health have been widely investigated. Recent experimental evidences indicate that EGCG can induce the aggregation of HMGB1 protein, a late mediator of inflammation, which subsequently stimulates the autophagic degradation and thus provides protection from lethal endotoxemia and sepsis. In this study, we use molecular dynamics (MD) simulations to explore the underlying molecular mechanism of this aggregation of HMGB1 facilitated by EGCG. Our simulation results reveal that EGCG firmly binds to HMGB1 near Cys106, which supports previous preliminary experimental evidence. A large HMGB1 conformational change is observed, where Box A and Box B, two homogenous domains of HMGB1, are repositioned and packed together by EGCG. This new HMGB1 conformation has large molecular polarity and distinctive electrostatic potential surface. We suggest that the highly polarized charge distribution leads to the aggregation of HMGB1, which differs from the previous hypothesis that two HMGB1 monomers are linked by the dimer of EGCG. Possible aggregating modes have also been investigated with potential of mean force (PMF) calculations. Finally, we conclude that the conformation induced by EGCG is more aggregation-prone with higher binding free energies as compared to those without EGCG.
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Affiliation(s)
- Xuan-Yu Meng
- Institute of Quantitative Biology and Medicine, SRMP and RAD-X, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
- Department of Physiology and Biophysics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, VA, USA
| | - Baoyu Li
- Institute of Quantitative Biology and Medicine, SRMP and RAD-X, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Shengtang Liu
- Institute of Quantitative Biology and Medicine, SRMP and RAD-X, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Hongsuk Kang
- IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA
| | - Lin Zhao
- Institute of Quantitative Biology and Medicine, SRMP and RAD-X, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Ruhong Zhou
- Institute of Quantitative Biology and Medicine, SRMP and RAD-X, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
- IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA
- Department of Chemistry, Columbia University, New York, NY 10027, USA
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23
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Kathuria SV, Chan YH, Nobrega RP, Özen A, Matthews CR. Clusters of isoleucine, leucine, and valine side chains define cores of stability in high-energy states of globular proteins: Sequence determinants of structure and stability. Protein Sci 2015; 25:662-75. [PMID: 26660714 DOI: 10.1002/pro.2860] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 12/03/2015] [Accepted: 12/03/2015] [Indexed: 01/05/2023]
Abstract
Measurements of protection against exchange of main chain amide hydrogens (NH) with solvent hydrogens in globular proteins have provided remarkable insights into the structures of rare high-energy states that populate their folding free-energy surfaces. Lacking, however, has been a unifying theory that rationalizes these high-energy states in terms of the structures and sequences of their resident proteins. The Branched Aliphatic Side Chain (BASiC) hypothesis has been developed to explain the observed patterns of protection in a pair of TIM barrel proteins. This hypothesis supposes that the side chains of isoleucine, leucine, and valine (ILV) residues often form large hydrophobic clusters that very effectively impede the penetration of water to their underlying hydrogen bond networks and, thereby, enhance the protection against solvent exchange. The linkage between the secondary and tertiary structures enables these ILV clusters to serve as cores of stability in high-energy partially folded states. Statistically significant correlations between the locations of large ILV clusters in native conformations and strong protection against exchange for a variety of motifs reported in the literature support the generality of the BASiC hypothesis. The results also illustrate the necessity to elaborate this simple hypothesis to account for the roles of adjacent hydrocarbon moieties in defining stability cores of partially folded states along folding reaction coordinates.
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Affiliation(s)
- Sagar V Kathuria
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St., Worcester, Massachusetts, 01605
| | - Yvonne H Chan
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St., Worcester, Massachusetts, 01605
| | - R Paul Nobrega
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St., Worcester, Massachusetts, 01605
| | - Ayşegül Özen
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St., Worcester, Massachusetts, 01605
| | - C Robert Matthews
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St., Worcester, Massachusetts, 01605
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24
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Characterization of a novel water pocket inside the human Cx26 hemichannel structure. Biophys J 2015; 107:599-612. [PMID: 25099799 DOI: 10.1016/j.bpj.2014.05.037] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 05/12/2014] [Accepted: 05/14/2014] [Indexed: 01/09/2023] Open
Abstract
Connexins (Cxs) are a family of vertebrate proteins constituents of gap junction channels (GJCs) that connect the cytoplasm of adjacent cells by the end-to-end docking of two Cx hemichannels. The intercellular transfer through GJCs occurs by passive diffusion allowing the exchange of water, ions, and small molecules. Despite the broad interest to understand, at the molecular level, the functional state of Cx-based channels, there are still many unanswered questions regarding structure-function relationships, perm-selectivity, and gating mechanisms. In particular, the ordering, structure, and dynamics of water inside Cx GJCs and hemichannels remains largely unexplored. In this work, we describe the identification and characterization of a believed novel water pocket-termed the IC pocket-located in-between the four transmembrane helices of each human Cx26 (hCx26) monomer at the intracellular (IC) side. Using molecular dynamics (MD) simulations to characterize hCx26 internal water structure and dynamics, six IC pockets were identified per hemichannel. A detailed characterization of the dynamics and ordering of water including conformational variability of residues forming the IC pockets, together with multiple sequence alignments, allowed us to propose a functional role for this cavity. An in vitro assessment of tracer uptake suggests that the IC pocket residue Arg-143 plays an essential role on the modulation of the hCx26 hemichannel permeability.
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25
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Liu J, Yang Z, Li H, Gu Z, Garate JA, Zhou R. Dewetting transition assisted clearance of (NFGAILS) amyloid fibrils from cell membranes by graphene. J Chem Phys 2015; 141:22D520. [PMID: 25494791 DOI: 10.1063/1.4901113] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Clearance of partially ordered oligomers and monomers deposited on cell membrane surfaces is believed to be an effective route to alleviate many potential protein conformational diseases (PCDs). With large-scale all-atom molecular dynamics simulations, here we show that graphene nanosheets can easily and quickly win a competitive adsorption of human islet amyloid polypeptides (hIAPP22-28) NFGAILS and associated fibrils against cell membrane, due to graphene's unique two-dimensional, highly hydrophobic surface with its all-sp(2) hybrid structure. A nanoscale dewetting transition was observed at the interfacial region between the fibril (originally deposited on the membrane) and the graphene nanosheet, which significantly assisted the adsorption of fibrils onto graphene from the membrane. The π-π stacking interaction between Phe23 and graphene played a crucial role, providing the driving force for the adsorption at the graphene surface. This study renders new insight towards the importance of water during the interactions between amyloid peptides, the phospholipidic membrane, and graphene, which might shed some light on future developments of graphene-based nanomedicine for preventing/curing PCDs like type II diabetes mellitus.
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Affiliation(s)
- Jiajia Liu
- Institute of Quantitative Biology and Medicine, SRMP and RAD-X, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, and Jiangsu Provincial Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou 215123, China
| | - Zaixing Yang
- Institute of Quantitative Biology and Medicine, SRMP and RAD-X, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, and Jiangsu Provincial Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou 215123, China
| | - Haotian Li
- Bio-X Lab, Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Zonglin Gu
- Institute of Quantitative Biology and Medicine, SRMP and RAD-X, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, and Jiangsu Provincial Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou 215123, China
| | | | - Ruhong Zhou
- Institute of Quantitative Biology and Medicine, SRMP and RAD-X, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, and Jiangsu Provincial Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou 215123, China
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26
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Chong Y, Ge C, Yang Z, Garate JA, Gu Z, Weber JK, Liu J, Zhou R. Reduced Cytotoxicity of Graphene Nanosheets Mediated by Blood-Protein Coating. ACS NANO 2015; 9:5713-24. [PMID: 26040772 DOI: 10.1021/nn5066606] [Citation(s) in RCA: 198] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The advent and pending wide use of nanoscale materials urges a biosafety assessment and safe design of nanomaterials that demonstrate applicability to human medicine. In biological microenvironment, biomolecules will bind onto nanoparticles forming corona and endow nanoparticles new biological identity. Since blood-circulatory system will most likely be the first interaction organ exposed to these nanomaterials, a deep understanding of the basic interaction mechanisms between serum proteins and foreign nanoparticles may help to better clarify the potential risks of nanomaterials and provide guidance on safe design of nanomaterials. In this study, the adsorption of four high-abundance blood proteins onto the carbon-based nanomaterial graphene oxide (GO) and reduced GO (rGO) were investigated via experimental (AFM, florescence spectroscopy, SPR) and simulation-based (molecular dynamics) approaches. Among the proteins in question, we observe competitive binding to the GO surface that features a mélange of distinct packing modes. Our MD simulations reveal that the protein adsorption is mainly enthalpically driven through strong π-π stacking interactions between GO and aromatic protein residues, in addition to hydrophobic interactions. Overall, these results were in line with previous findings related to adsorption of serum proteins onto single-walled carbon nanotubes (SWCNTs), but GO exhibits a dramatic enhancement of adsorption capacity compared to this one-dimensional carbon form. Encouragingly, protein-coated GO resulted in a markedly less cytotoxicity than pristine and protein-coated SWCNTs, suggesting a useful role for this planar nanomaterial in biomedical applications.
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Affiliation(s)
- Yu Chong
- †Institute of Quantitative Biology and Medicine, SRMP and RAD-X, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Cuicui Ge
- †Institute of Quantitative Biology and Medicine, SRMP and RAD-X, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Zaixing Yang
- †Institute of Quantitative Biology and Medicine, SRMP and RAD-X, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Jose Antonio Garate
- ‡IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Zonglin Gu
- †Institute of Quantitative Biology and Medicine, SRMP and RAD-X, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Jeffrey K Weber
- ‡IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Jiajia Liu
- †Institute of Quantitative Biology and Medicine, SRMP and RAD-X, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Ruhong Zhou
- †Institute of Quantitative Biology and Medicine, SRMP and RAD-X, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
- ‡IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
- §Department of Chemistry, Columbia University, New York, New York 10027, United States
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27
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Luan B, Huynh T, Zhao L, Zhou R. Potential toxicity of graphene to cell functions via disrupting protein-protein interactions. ACS NANO 2015; 9:663-9. [PMID: 25494677 DOI: 10.1021/nn506011j] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
While carbon-based nanomaterials such as graphene and carbon nanotubes (CNTs) have become popular in state-of-the-art nanotechnology, their biological safety and underlying molecular mechanism is still largely unknown. Experimental studies have been focused at the cellular level and revealed good correlations between cell's death and the application of CNTs or graphene. Using large-scale all-atom molecular dynamics simulations, we theoretically investigate the potential toxicity of graphene to a biological cell at molecular level. Simulation results show that the hydrophobic protein-protein interaction (or recognition) that is essential to biological functions can be interrupted by a graphene nanosheet. Due to the hydrophobic nature of graphene, it is energetically favorable for a graphene nanosheet to enter the hydrophobic interface of two contacting proteins, such as a dimer. The forced separation of two functional proteins can disrupt the cell's metabolism and even lead to the cell's mortality.
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Affiliation(s)
- Binquan Luan
- Computational Biological Center, IBM Thomas J. Watson Research , Yorktown Heights, New York 10598, United States
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28
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Remsing RC, Weeks JD. Hydrophobicity Scaling of Aqueous Interfaces by an Electrostatic Mapping. J Phys Chem B 2014; 119:9268-77. [DOI: 10.1021/jp509903n] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Richard C. Remsing
- Institute
for Physical Science and Technology, Department of Chemistry and Biochemistry,
and Chemical Physics Program, University of Maryland, College Park, Maryland 20742, United States
- Department
of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - John D. Weeks
- Institute
for Physical Science and Technology, Department of Chemistry and Biochemistry,
and Chemical Physics Program, University of Maryland, College Park, Maryland 20742, United States
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29
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Zhou R, Gao H. Cytotoxicity of graphene: recent advances and future perspective. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2014; 6:452-74. [PMID: 24957946 DOI: 10.1002/wnan.1277] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Revised: 04/16/2014] [Accepted: 04/18/2014] [Indexed: 01/22/2023]
Abstract
Graphene, a unique two-dimensional single-atom-thin nanomaterial with exceptional structural, mechanical, and electronic properties, has spurred an enormous interest in many fields, including biomedical applications, which at the same time ignites a growing concern on its biosafety and potential cytotoxicity to human and animal cells. In this review, we present a summary of some very recent studies on this important subject with both experimental and theoretical approaches. The molecular interactions of graphene with proteins, DNAs, and cell membranes (both bacteria and mammalian cells) are discussed in detail. Severe distortions in structures and functions of these biomacromolecules by graphene are identified and characterized. For example, the graphene is shown to disrupt bacteria cell membranes by insertion/cutting as well as destructive extraction of lipid molecules directly. More interestingly, this cytotoxicity has been shown to have implications in de novo design of nanomedicine, such as graphene-based band-aid, a potential 'green' antibiotics due to its strong physical-based (instead of chemical-based) antibacterial capability. These studies have provided a better understanding of graphene nanotoxicity at both cellular and molecular levels, and also suggested therapeutic potential by using graphene's cytotoxicity against bacteria cells.
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Affiliation(s)
- Ruhong Zhou
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, NY, USA; Department of Chemistry, Columbia University, New York, NY, USA
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30
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Yang Z, Xia Z, Huynh T, King JA, Zhou R. Dissecting the contributions of β-hairpin tyrosine pairs to the folding and stability of long-lived human γD-crystallins. NANOSCALE 2014; 6:1797-807. [PMID: 24352614 PMCID: PMC3976203 DOI: 10.1039/c3nr03782g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Ultraviolet-radiation-induced damage to and aggregation of human lens crystallin proteins are thought to be a significant pathway to age-related cataract. The aromatic residues within the duplicated Greek key domains of γ- and β-crystallins are the main ultraviolet absorbers and are susceptible to direct and indirect ultraviolet damage. The previous site-directed mutagenesis studies have revealed a striking difference for two highly conserved homologous β-hairpin Tyr pairs, at the N-terminal domain (N-td) and C-terminal domain (C-td), respectively, in their contribution to the overall stability of HγD-Crys, but why they behave so differently still remains a mystery. In this paper, we systematically investigated the underlying molecular mechanism and detailed contributions of these two Tyr pairs with large scale molecular dynamics simulations. A series of different tyrosine-to-alanine pair(s) substitutions were performed in either the N-td, the C-td, or both. Our results suggest that the Y45A/Y50A pair substitution in the N-td mainly affects the stability of the N-td itself, while the Y133A/Y138A pair substitution in the C-td leads to a more cooperative unfolding of both N-td and C-td. The stability of motif 2 in the N-td is mainly determined by the interdomain interface, while motif 1 in the N-td or motifs 3 and 4 in the C-td are mainly stabilized by the intradomain hydrophobic core. The damage to any tyrosine pair(s) can directly introduce some apparent water leakage to the hydrophobic core at the interface, which in turn causes a serious loss in the stability of the N-td. However, for the C-td substitutions, it may further impair the stable "sandwich-like" Y133-R167-Y138 cluster (through cation-π interactions) in the wild-type, thus causing the loop regions near the residue A138 to undergo large fluctuations, which in turn results in the intrusion of water into the hydrophobic core of the C-td and induces the C-td to lose its stability. These findings help resolve the "mystery" on why these two Tyr pairs display such a striking difference in their contributions to the overall protein stability despite their highly homologous nature.
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Affiliation(s)
- Zaixing Yang
- Institute of Quantitative Biology and Medicine, SRMP and RAD-X & Collaborative Innovation Center of Suzhou Nano Science and Technology, Jiangsu Provincial Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou 215123, China.
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31
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Kapcha LH, Rossky PJ. A simple atomic-level hydrophobicity scale reveals protein interfacial structure. J Mol Biol 2013; 426:484-98. [PMID: 24120937 DOI: 10.1016/j.jmb.2013.09.039] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 09/27/2013] [Indexed: 10/26/2022]
Abstract
Many amino acid residue hydrophobicity scales have been created in an effort to better understand and rapidly characterize water-protein interactions based only on protein structure and sequence. There is surprisingly low consistency in the ranking of residue hydrophobicity between scales, and their ability to provide insightful characterization varies substantially across subject proteins. All current scales characterize hydrophobicity based on entire amino acid residue units. We introduce a simple binary but atomic-level hydrophobicity scale that allows for the classification of polar and non-polar moieties within single residues, including backbone atoms. This simple scale is first shown to capture the anticipated hydrophobic character for those whole residues that align in classification among most scales. Examination of a set of protein binding interfaces establishes good agreement between residue-based and atomic-level descriptions of hydrophobicity for five residues, while the remaining residues produce discrepancies. We then show that the atomistic scale properly classifies the hydrophobicity of functionally important regions where residue-based scales fail. To illustrate the utility of the new approach, we show that the atomic-level scale rationalizes the hydration of two hydrophobic pockets and the presence of a void in a third pocket within a single protein and that it appropriately classifies all of the functionally important hydrophilic sites within two otherwise hydrophobic pores. We suggest that an atomic level of detail is, in general, necessary for the reliable depiction of hydrophobicity for all protein surfaces. The present formulation can be implemented simply in a manner no more complex than current residue-based approaches.
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Affiliation(s)
- Lauren H Kapcha
- Department of Chemistry and Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, TX 78712-1167, USA
| | - Peter J Rossky
- Department of Chemistry and Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, TX 78712-1167, USA.
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32
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UV-radiation induced disruption of dry-cavities in human γD-crystallin results in decreased stability and faster unfolding. Sci Rep 2013; 3:1560. [PMID: 23532089 PMCID: PMC3609025 DOI: 10.1038/srep01560] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 03/11/2013] [Indexed: 11/28/2022] Open
Abstract
Age-onset cataracts are believed to be expedited by the accumulation of UV-damaged human γD-crystallins in the eye lens. Here we show with molecular dynamics simulations that the stability of γD-crystallin is greatly reduced by the conversion of tryptophan to kynurenine due to UV-radiation, consistent with previous experimental evidences. Furthermore, our atomic-detailed results reveal that kynurenine attracts more waters and other polar sidechains due to its additional amino and carbonyl groups on the damaged tryptophan sidechain, thus breaching the integrity of nearby dry center regions formed by the two Greek key motifs in each domain. The damaged tryptophan residues cause large fluctuations in the Tyr-Trp-Tyr sandwich-like hydrophobic clusters, which in turn break crucial hydrogen-bonds bridging two β-strands in the Greek key motifs at the “tyrosine corner”. Our findings may provide new insights for understanding of the molecular mechanism of the initial stages of UV-induced cataractogenesis.
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33
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Abstract
Hofmeister effects are part of a larger story--one in which the devil is perhaps in the details, but which promises to give us a much deeper understanding of how the solvent is a part of cell and molecular biology.
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34
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Lv W, Wu R. The interfacial-organized monolayer water film (MWF) induced "two-step" aggregation of nanographene: both in stacking and sliding assembly pathways. NANOSCALE 2013; 5:2765-2775. [PMID: 23429907 DOI: 10.1039/c3nr33447c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
A computational investigation was carried out to understand the aggregation of nanoscale graphene with two typical pathways of stacking assembly and sliding assembly in water. The interfacial-organized monolayer water film (MWF) induced "two-step" aggregation of nanographene in both stacking and sliding assembly pathways was reported for the first time. By means of potential mean forces (PMFs) calculation, no energy barrier was observed during the sliding assembly of two graphene nanosheets, while the PMF profiles could be impacted by the contact forms of nanographene and the MWF within the interplate of two graphene nanosheets. To explore the potential physical basis of the "hindering role" of self-organized interfacial water, the dynamical and structural properties as well as the status of hydrogen bonds (H-bonds) for interfacial water were investigated. We found that the compact, ordered structure and abundant H-bonds of the MWF could be taken as the fundamental aspects of the "hindering role" of interfacial water for the hydrophobic assembly of nanographene. These findings are displaying a potential to further understand the hydrophobic assembly which mostly dominate the behaviors of nanomaterials, proteins etc. in aqueous solutions.
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Affiliation(s)
- Wenping Lv
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
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35
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Das P, Kapoor D, Halloran KT, Zhou R, Matthews CR. Interplay between drying and stability of a TIM barrel protein: a combined simulation-experimental study. J Am Chem Soc 2013; 135:1882-90. [PMID: 23293932 PMCID: PMC3637939 DOI: 10.1021/ja310544t] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Recent molecular dynamics simulations have suggested important roles for nanoscale dewetting in the stability, function, and folding dynamics of proteins. Using a synergistic simulation-experimental approach on the αTS TIM barrel protein, we validated this hypothesis by revealing the occurrence of drying inside hydrophobic amino acid clusters and its manifestation in experimental measures of protein stability and structure. Cavities created within three clusters of branched aliphatic amino acids [isoleucine, leucine, and valine (ILV) clusters] were found to experience strong water density fluctuations or intermittent dewetting transitions in simulations. Individually substituting 10 residues in the large ILV cluster at the N-terminus with less hydrophobic alanines showed a weakening or diminishing effect on dewetting that depended on the site of the mutation. Our simulations also demonstrated that replacement of buried leucines with isosteric, polar asparagines enhanced the wetting of the N- and C-terminal clusters. The experimental results on the stability, secondary structure, and compactness of the native and intermediate states for the asparagine variants are consistent with the preferential drying of the large N-terminal cluster in the intermediate. By contrast, the region encompassing the small C-terminal cluster experiences only partial drying in the intermediate, and its structure and stability are unaffected by the asparagine substitution. Surprisingly, the structural distortions required to accommodate the replacement of leucine by asparagine in the N-terminal cluster revealed the existence of alternative stable folds in the native basin. This combined simulation-experimental study demonstrates the critical role of drying within hydrophobic ILV clusters in the folding and stability of the αTS TIM barrel.
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Affiliation(s)
- Payel Das
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598
| | - Divya Kapoor
- Department of Biochemistry & Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Kevin T. Halloran
- Department of Biochemistry & Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Ruhong Zhou
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598
- Department of Chemistry, Columbia University, New York, NY 10027
| | - C. Robert Matthews
- Department of Biochemistry & Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
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36
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Wang S, Tu Y, Wan R, Fang H. Evaporation of Tiny Water Aggregation on Solid Surfaces with Different Wetting Properties. J Phys Chem B 2012; 116:13863-7. [DOI: 10.1021/jp302142s] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Shen Wang
- Shanghai Institute of Applied
Physics, Chinese Academy of Sciences, P.O.
Box 800-204, Shanghai, 201800, China
- Graduate School of the Chinese Academy of Sciences, Beijing 100080,
China
| | - Yusong Tu
- Institute of Systems
Biology, Shanghai University, Shanghai,
200444, China
| | - Rongzheng Wan
- Shanghai Institute of Applied
Physics, Chinese Academy of Sciences, P.O.
Box 800-204, Shanghai, 201800, China
| | - Haiping Fang
- Shanghai Institute of Applied
Physics, Chinese Academy of Sciences, P.O.
Box 800-204, Shanghai, 201800, China
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37
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Arviv O, Levy Y. Folding of multidomain proteins: Biophysical consequences of tethering even in apparently independent folding. Proteins 2012; 80:2780-98. [DOI: 10.1002/prot.24161] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2012] [Revised: 07/11/2012] [Accepted: 07/16/2012] [Indexed: 01/09/2023]
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38
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Bandyopadhyay D, Choudhury N. Characterizing hydrophobicity at the nanoscale: A molecular dynamics simulation study. J Chem Phys 2012; 136:224505. [DOI: 10.1063/1.4725185] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
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39
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40
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Giovambattista N, Rossky P, Debenedetti P. Computational Studies of Pressure, Temperature, and Surface Effects on the Structure and Thermodynamics of Confined Water. Annu Rev Phys Chem 2012; 63:179-200. [DOI: 10.1146/annurev-physchem-032811-112007] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- N. Giovambattista
- Department of Physics, Brooklyn College of the City University of New York, Brooklyn, New York 11210;
| | - P.J. Rossky
- Institute for Computational Engineering and Sciences, Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712;
| | - P.G. Debenedetti
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544-5263;
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41
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Wang C, Zhou B, Tu Y, Duan M, Xiu P, Li J, Fang H. Critical Dipole Length for the Wetting Transition Due to Collective Water-dipoles Interactions. Sci Rep 2012; 2:358. [PMID: 22496954 PMCID: PMC3323886 DOI: 10.1038/srep00358] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 03/19/2012] [Indexed: 11/09/2022] Open
Abstract
The wetting behavior of water on the solid surfaces is fundamental to various physical, chemical and biological processes. Conventionally, the surface with charges or charge dipoles is hydrophilic, whereas the non-polar surface is hydrophobic though some exceptions were recently reported. Using molecular dynamics simulations, we show that there is a critical length of the charge dipoles on the solid surface. The solid surface still exhibited hydrophobic behavior when the dipole length was less than the critical value, indicating that the water molecules on the solid surface seemed not "feel" attractive interactions from the charge dipoles on the solid surface. Those unexpected observations result from the collective interactions between the water molecules and charge dipoles on the solid surface, where the steric exclusion effect between water molecules greatly reduces the water-dipole interactions. Remarkably, the steric exclusion effect is also important for surfaces with charge dipole lengths greater than this critical length.
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42
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Xia Z, Huynh T, Kang SG, Zhou R. Free-energy simulations reveal that both hydrophobic and polar interactions are important for influenza hemagglutinin antibody binding. Biophys J 2012; 102:1453-61. [PMID: 22455929 PMCID: PMC3309282 DOI: 10.1016/j.bpj.2012.01.043] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 01/25/2012] [Accepted: 01/27/2012] [Indexed: 11/24/2022] Open
Abstract
Antibodies binding to conserved epitopes can provide a broad range of neutralization to existing influenza subtypes and may also prevent the propagation of potential pandemic viruses by fighting against emerging strands. Here we propose a computational framework to study structural binding patterns and detailed molecular mechanisms of viral surface glycoprotein hemagglutinin (HA) binding with a broad spectrum of neutralizing monoclonal antibody fragments (Fab). We used rigorous free-energy perturbation (FEP) methods to calculate the antigen-antibody binding affinities, with an aggregate underlying molecular-dynamics simulation time of several microseconds (∼2 μs) using all-atom, explicit-solvent models. We achieved a high accuracy in the validation of our FEP protocol against a series of known binding affinities for this complex system, with <0.5 kcal/mol errors on average. We then introduced what to our knowledge are novel mutations into the interfacial region to further study the binding mechanism. We found that the stacking interaction between Trp-21 in HA2 and Phe-55 in the CDR-H2 of Fab is crucial to the antibody-antigen association. A single mutation of either W21A or F55A can cause a binding affinity decrease of ΔΔG > 4.0 kcal/mol (equivalent to an ∼1000-fold increase in the dissociation constant K(d)). Moreover, for group 1 HA subtypes (which include both the H1N1 swine flu and the H5N1 bird flu), the relative binding affinities change only slightly (< ±1 kcal/mol) when nonpolar residues at the αA helix of HA mutate to conservative amino acids of similar size, which explains the broad neutralization capability of antibodies such as F10 and CR6261. Finally, we found that the hydrogen-bonding network between His-38 (in HA1) and Ser-30/Gln-64 (in Fab) is important for preserving the strong binding of Fab against group 1 HAs, whereas the lack of such hydrogen bonds with Asn-38 in most group 2 HAs may be responsible for the escape of antibody neutralization. These large-scale simulations may provide new insight into the antigen-antibody binding mechanism at the atomic level, which could be essential for designing more-effective vaccines for influenza.
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Affiliation(s)
- Zhen Xia
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas
| | - Tien Huynh
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York
| | - Seung-gu Kang
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York
| | - Ruhong Zhou
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York
- Department of Chemistry, Columbia University, New York, New York
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43
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Yang Z, Shi B, Lu H, Xiu P, Zhou R. Dewetting Transitions in the Self-Assembly of Two Amyloidogenic β-Sheets and the Importance of Matching Surfaces. J Phys Chem B 2011; 115:11137-44. [DOI: 10.1021/jp2046454] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Zaixing Yang
- Bio-X Lab, Department of Physics, and Soft Matter Research Center, Zhejiang University, Hangzhou 310027, China
| | - Biyun Shi
- Bio-X Lab, Department of Physics, and Soft Matter Research Center, Zhejiang University, Hangzhou 310027, China
| | - Hangjun Lu
- Department of Physics, Zhejiang Normal University, 321004, Jinhua, China
| | - Peng Xiu
- Bio-X Lab, Department of Physics, and Soft Matter Research Center, Zhejiang University, Hangzhou 310027, China
| | - Ruhong Zhou
- Computational Biology Center, IBM Thomas J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, New York 10598, United States
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44
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Mason PE, Lerbret A, Saboungi ML, Neilson GW, Dempsey CE, Brady JW. Glucose interactions with a model peptide. Proteins 2011; 79:2224-32. [PMID: 21574187 DOI: 10.1002/prot.23047] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2010] [Revised: 02/12/2011] [Accepted: 03/03/2011] [Indexed: 11/07/2022]
Abstract
Molecular dynamics simulations have been conducted of the helical polypeptide melittin, in concentrated aqueous solutions of the alpha and beta anomers of D-glucopyranose. Glucose is an osmolyte, and it is expected to be preferentially excluded from the surfaces of proteins. This was indeed found to be the case in the simulations. The results indicate that the observed exclusion may have a contribution from an under-representation of hydrogen bonding interactions between glucose groups and exposed side chains, compared to water. However, glucose was found to bind quite specifically to melittin by stacking its hydrophobic face, consisting of aliphatic protons, against the flat hydrophobic face of the indole group of the tryptophan-19 side chain. Although the binding site for this interaction is localized, the binding is weak for both anomers, with a binding free energy estimated as only ∼0.5 kcal/mol (i.e. near k(B)T). The face of the sugar stacked against the Trp indole ring is different for the two anomers of glucose, due to the disruption of the H1-H3-H5 hydrophobic triad of the beta anomer by the axial C1 hydroxyl group in the alpha anomer. The measurable affinity of the sugar for the Trp side chain is consistent with the very frequent occurrence of this group in the binding sites of proteins that complex with sugars.
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Affiliation(s)
- Phillip E Mason
- Department of Food Science, Stocking Hall, Cornell University, Ithaca, New York 14853, USA
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45
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Adhesive water networks facilitate binding of protein interfaces. Nat Commun 2011; 2:261. [DOI: 10.1038/ncomms1258] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Accepted: 03/02/2011] [Indexed: 12/23/2022] Open
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46
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Wang J, Kudesia S, Bratko D, Luzar A. Computational probe of cavitation events in protein systems. Phys Chem Chem Phys 2011; 13:19902-10. [PMID: 21922115 DOI: 10.1039/c1cp22082a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Jihang Wang
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284-2006, USA
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47
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Gnanasekaran R, Xu Y, Leitner DM. Dynamics of water clusters confined in proteins: a molecular dynamics simulation study of interfacial waters in a dimeric hemoglobin. J Phys Chem B 2010; 114:16989-96. [PMID: 21126033 DOI: 10.1021/jp109173t] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Water confined in proteins exhibits dynamics distinct from the dynamics of water in the bulk or near the surface of a biomolecule. We examine the water dynamics at the interface of the two globules of the homodimeric hemoglobin from Scapharca inaequivalvis (HbI) by molecular dynamics (MD) simulations, with focus on water-protein hydrogen bond lifetimes and rotational anisotropy of the interfacial waters. We find that relaxation of the waters at the interface of both deoxy- and oxy-HbI, which contain a cluster of 17 and 11 interfacial waters, respectively, is well described by stretched exponentials with exponents from 0.1 to 0.6 and relaxation times of tens to thousands of picoseconds. The interfacial water molecules of oxy-HbI exhibit slower rotational relaxation and hydrogen bond rearrangement than those of deoxy-HbI, consistent with an allosteric transition from unliganded to liganded conformers involving the expulsion of several water molecules from the interface. Though the interfacial waters are translationally and rotationally static on the picosecond time scale, they contribute to fast communication between the globules via vibrations. We find that the interfacial waters enhance vibrational energy transport across the interface by ≈10%.
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48
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Setny P, Baron R, McCammon JA. How Can Hydrophobic Association Be Enthalpy Driven? J Chem Theory Comput 2010; 6:2866-2871. [PMID: 20844599 PMCID: PMC2938831 DOI: 10.1021/ct1003077] [Citation(s) in RCA: 176] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2010] [Indexed: 01/19/2023]
Abstract
Hydrophobic association is often recognized as being driven by favorable entropic contributions. Here, using explicit solvent molecular dynamics simulations we investigate binding in a model hydrophobic receptor-ligand system which appears, instead, to be driven by enthalpy and opposed by entropy. We use the temperature dependence of the potential of mean force to analyze the thermodynamic contributions along the association coordinate. Relating such contributions to the ongoing changes in system hydration allows us to demonstrate that the overall binding thermodynamics is determined by the expulsion of disorganized water from the receptor cavity. Our model study sheds light on the solvent-induced driving forces for receptor-ligand association of general, transferable relevance for biological systems with poorly hydrated binding sites.
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Affiliation(s)
- Piotr Setny
- Corresponding authors. E-mail: (P.S.), (R.B.)
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49
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Young T, Hua L, Huang X, Abel R, Friesner R, Berne BJ. Dewetting transitions in protein cavities. Proteins 2010; 78:1856-69. [PMID: 20225258 DOI: 10.1002/prot.22699] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
In a previous analysis of the solvation of protein active sites, a drying transition was observed in the narrow hydrophobic binding cavity of Cox-2. With the use of a crude metric that often seems able to discriminate those protein cavities that dry from those that do not, we made an extensive search of the PDB, and identified five other proteins that, in molecular dynamics simulations, undergo drying transitions in their active sites. Because such cavities need not desolvate before binding hydrophobic ligands they often exhibit very large binding affinities. This article gives evidence that drying in protein cavities is not unique to Cox-2.
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Affiliation(s)
- Tom Young
- Department of Chemistry, Columbia University, New York, NY 10027, USA.
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50
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Xu L, Molinero V. Liquid−Vapor Oscillations of Water Nanoconfined between Hydrophobic Disks: Thermodynamics and Kinetics. J Phys Chem B 2010; 114:7320-8. [DOI: 10.1021/jp102443m] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Limei Xu
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, and WPI-Advanced Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Sendai 980-8577, Japan
| | - Valeria Molinero
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, and WPI-Advanced Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Sendai 980-8577, Japan
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