1
|
Nordquist EB, Schultz SA, Chen J. Using Metadynamics To Explore the Free Energy of Dewetting in Biologically Relevant Nanopores. J Phys Chem B 2022; 126:6428-6437. [PMID: 35998613 PMCID: PMC9932947 DOI: 10.1021/acs.jpcb.2c04157] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Water confined within hydrophobic spaces can undergo cooperative dewetting transitions due to slight changes in water density and pressure that push water toward the vapor phase. Many transmembrane protein ion channels contain nanoscale hydrophobic pores that could undergo dewetting transitions, sometimes blocking the flow of ions without physical blockages. Standard molecular dynamics simulations have been extensively applied to study the behavior of water in nanoscale pores, but the large free energy barriers of dewetting often prevent direct sampling of both wet and dry states and quantitative studies of the hydration thermodynamics of biologically relevant pores. Here, we describe a metadynamics protocol that uses the number of waters within the pore as the collective variable to drive many reversible transitions between relevant hydration states and calculate well-converged free energy profiles of pore hydration. By creating model nanopore systems and changing their radius and morphology and including various cosolvents, we quantify how these pore properties and cosolvents affect the dewetting transition. The results reveal that the dewetting free energy of nanoscale pores is determined by two key thermodynamic parameters, namely, the effective surface tension coefficients of water-air and water-pore interfaces. Importantly, while the effect of salt can be fully captured in the water activity dependence, amphipathic cosolvents such as alcohols modify both dry and wet states of the pore and dramatically shift the wet-dry equilibrium. The metadynamics approach could be applied to studies of dewetting transitions within nanoscale pores of proteins and provide new insights into why different pore properties evolved in biological systems.
Collapse
Affiliation(s)
- Erik B. Nordquist
- Department of Chemistry, University of Massachusetts, Amherst Massachusetts, USA 01003
| | - Samantha A. Schultz
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst Massachusetts, USA 01003
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst Massachusetts, USA 01003
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst Massachusetts, USA 01003
| |
Collapse
|
2
|
Li C, Lin D, Zhao W. Electric Field Induced Dewetting of Hydrophobic Nanocavities at Ambient Temperature. NANOMATERIALS (BASEL, SWITZERLAND) 2020; 10:E736. [PMID: 32290614 PMCID: PMC7221969 DOI: 10.3390/nano10040736] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/09/2020] [Accepted: 04/09/2020] [Indexed: 11/26/2022]
Abstract
The understanding of water dewetting in nanoporous materials is of great importance in various fields of science and technology. Herein, we report molecular dynamics simulation results of dewetting of water droplet in hydrophobic nanocavities between graphene walls under the influence of electric field. At ambient temperature, the rate of dewetting induced by electric field is significantly large. Whereas, it is a very low rate of dewetting induced by high temperature (423 K) due to the strong interaction of the hydrogen-bonding networks of water droplets in nanocavities. In addition, the electric filed induced formation of a water column has been found in a vacuum chamber. When the electric field is turned off, the water column will transform into a water droplet. Importantly, the results demonstrate that the rate of electric field-induced dewetting increases with growth of the electric field. Overall, our results suggest that electric field may have a great potential application for nanomaterial dewetting.
Collapse
Affiliation(s)
| | - Dongdong Lin
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China;
| | - Wenhui Zhao
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China;
| |
Collapse
|
3
|
Ebrahim-Habibi MB, Ghobeh M, Mahyari FA, Rafii-Tabar H, Sasanpour P. An investigation into non-covalent functionalization of a single-walled carbon nanotube and a graphene sheet with protein G:A combined experimental and molecular dynamics study. Sci Rep 2019; 9:1273. [PMID: 30718580 PMCID: PMC6362288 DOI: 10.1038/s41598-018-37311-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 12/06/2018] [Indexed: 12/15/2022] Open
Abstract
Investigation of non-covalent interaction of hydrophobic surfaces with the protein G (PrG) is necessary due to their frequent utilization in immunosensors and ELISA. It has been confirmed that surfaces, including carbonous-nanostructures (CNS) could orient proteins for a better activation. Herein, PrG interaction with single-walled carbon nanotube (SWCNT) and graphene (Gra) nanostructures was studied by employing experimental and MD simulation techniques. It is confirmed that the PrG could adequately interact with both SWCNT and Gra and therefore fine dispersion for them was achieved in the media. Results indicated that even though SWCNT was loaded with more content of PrG in comparison with the Gra, the adsorption of the PrG on Gra did not induce significant changes in the IgG tendency. Several orientations of the PrG were adopted in the presence of SWCNT or Gra; however, SWCNT could block the PrG-FcR. Moreover, it was confirmed that SWCNT reduced the α-helical structure content in the PrG. Reduction of α-helical structure of the PrG and improper orientation of the PrG-SWCNT could remarkably decrease the PrG tendency to the Fc of the IgG. Importantly, the Gra could appropriately orient the PrG by both exposing the PrG-FcR and also by blocking the fragment of the PrG that had tendency to interact with Fab in IgG.
Collapse
Affiliation(s)
- Mohammad-Bagher Ebrahim-Habibi
- Department of Medical Physics and Biomedical Engineering, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Ghobeh
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | | | - Hashem Rafii-Tabar
- Department of Medical Physics and Biomedical Engineering, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Pezhman Sasanpour
- Department of Medical Physics and Biomedical Engineering, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
4
|
Zhang L, Bell DR, Luan B, Zhou R. Exploring the binding mechanism between human profilin (PFN1) and polyproline-10 through binding mode screening. J Chem Phys 2019; 150:015102. [PMID: 30621420 DOI: 10.1063/1.5053922] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The large magnitude of protein-protein interaction (PPI) pairs within the human interactome necessitates the development of predictive models and screening tools to better understand this fundamental molecular communication. However, despite enormous efforts from various groups to develop predictive techniques in the last decade, PPI complex structures are in general still very challenging to predict due to the large number of degrees of freedom. In this study, we use the binding complex of human profilin (PFN1) and polyproline-10 (P10) as a model system to examine various approaches, with the aim of going beyond normal protein docking for PPI prediction and evaluation. The potential of mean force (PMF) was first obtained from the time-consuming umbrella sampling, which confirmed that the most stable binding structure identified by the maximal PMF difference is indeed the crystallographic binding structure. Moreover, crucial residues previously identified in experimental studies, W3, H133, and S137 of PFN1, were found to form favorable hydrogen bonds with P10, suggesting a zipping process during the binding between PFN1 and P10. We then explored both regular molecular dynamics (MD) and steered molecular dynamics (SMD) simulations, seeking for better criteria of ranking the PPI prediction. Despite valuable information obtained from conventional MD simulations, neither the commonly used interaction energy between the two binding parties nor the long-term root mean square displacement correlates well with the PMF results. On the other hand, with a sizable collection of trajectories, we demonstrated that the average and minimal rupture works calculated from SMD simulations correlate fairly well with the PMFs (R 2 = 0.67), making this a promising PPI screening method.
Collapse
Affiliation(s)
- Leili Zhang
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, USA
| | - David R Bell
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, USA
| | - Binquan Luan
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, USA
| | - Ruhong Zhou
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, USA
| |
Collapse
|
5
|
Biswas B, Muttathukattil AN, Reddy G, Singh PC. Contrasting Effects of Guanidinium Chloride and Urea on the Activity and Unfolding of Lysozyme. ACS OMEGA 2018; 3:14119-14126. [PMID: 31458105 PMCID: PMC6644995 DOI: 10.1021/acsomega.8b01911] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 10/12/2018] [Indexed: 05/03/2023]
Abstract
Cosolvents play an important role in regulating the stability and function of proteins present in the cell. We studied the role of cosolvents, urea and guanidinium chloride (GdmCl), which act as protein denaturants, in the catalytic activity and structural stability of the protein lysozyme using activity measurements, spectroscopy, and molecular dynamics simulations. We find that the activity of lysozyme increases on the addition of urea, whereas it decreases sharply on the addition of GdmCl. At low GdmCl concentrations ([GdmCl] < 4 M), the activity of lysozyme decreases, even though there is no significant perturbation in the structure of the lysozyme folded state. We find that this is due to the strong interaction of the Gdm+ ion with the residues Asp52 and Glu35, which are present in the lysozyme catalytic site. In contrast, urea interacts with Trp63 present in the loop region present near the active site of lysozyme, inducing minor conformational changes in lysozyme, which can increase the activity of lysozyme. At higher denaturant concentrations, experiments show that GdmCl completely denatures the protein, whereas the folded state is stable in the presence of urea. We further show that GdmCl denatures lysozyme with the disulfide bonds intact in the protein, whereas urea denatures the protein only when the disulfide bonds are broken using reducing agents.
Collapse
Affiliation(s)
- Biswajit Biswas
- Department
of Spectroscopy, Indian Association for
the Cultivation of Science, 2A & 2B Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Aswathy N. Muttathukattil
- Solid
State and Structural Chemistry Unit, Indian
Institute of Science, Bengaluru 560012, Karnataka, India
| | - Govardhan Reddy
- Solid
State and Structural Chemistry Unit, Indian
Institute of Science, Bengaluru 560012, Karnataka, India
- E-mail: (G.R.)
| | - Prashant Chandra Singh
- Department
of Spectroscopy, Indian Association for
the Cultivation of Science, 2A & 2B Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
- E-mail: (P.C.S.)
| |
Collapse
|
6
|
The opposing effect of urea and high pressure on the conformation of the protein β-hairpin: A molecular dynamics simulation study. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2017.12.054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
7
|
Anand A, Patey GN. Mechanism of Urea Crystal Dissolution in Water from Molecular Dynamics Simulation. J Phys Chem B 2018; 122:1213-1222. [PMID: 29260571 DOI: 10.1021/acs.jpcb.7b07096] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Molecular dynamics simulations are used to determine the mechanism of urea crystal dissolution in water under sink conditions. Crystals of cubic and tablet shapes are considered, and results are reported for four commonly used water models. The dissolution rates for different water models can differ considerably, but the overall dissolution mechanism remains the same. Urea dissolution occurs in three stages: a relatively fast initial stage, a slower intermediate stage, and a final stage. We show that the long intermediate stage is well described by classical rate laws, which assume that the dissolution rate is proportional to the active surface area. By carrying out simulations at different temperatures, we show that urea dissolution is an activated process, with an activation energy of ∼32 kJ mol-1. Our simulations give no indication of a significant diffusion layer, and we conclude that the detachment of molecules from the crystal is the rate-determining step for dissolution. The results we report for urea are consistent with earlier observations for the dissolution of NaCl crystals. This suggests that the three-stage mechanism and classical rate laws might apply to the dissolution of other ionic and molecular crystals.
Collapse
Affiliation(s)
- Abhinav Anand
- Department of Chemistry, University of British Columbia , Vancouver, British Columbia, Canada V6T 1Z1
| | - G N Patey
- Department of Chemistry, University of British Columbia , Vancouver, British Columbia, Canada V6T 1Z1
| |
Collapse
|
8
|
Zheng T, Yang Z, Gui D, Liu Z, Wang X, Dai X, Liu S, Zhang L, Gao Y, Chen L, Sheng D, Wang Y, Diwu J, Wang J, Zhou R, Chai Z, Albrecht-Schmitt TE, Wang S. Overcoming the crystallization and designability issues in the ultrastable zirconium phosphonate framework system. Nat Commun 2017; 8:15369. [PMID: 28555656 PMCID: PMC5459948 DOI: 10.1038/ncomms15369] [Citation(s) in RCA: 236] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 03/23/2017] [Indexed: 12/22/2022] Open
Abstract
Metal-organic frameworks (MOFs) based on zirconium phosphonates exhibit superior chemical stability suitable for applications under harsh conditions. These compounds mostly exist as poorly crystallized precipitates, and precise structural information has therefore remained elusive. Furthermore, a zero-dimensional zirconium phosphonate cluster acting as secondary building unit has been lacking, leading to poor designability in this system. Herein, we overcome these challenges and obtain single crystals of three zirconium phosphonates that are suitable for structural analysis. These compounds are built by previously unknown isolated zirconium phosphonate clusters and exhibit combined high porosity and ultrastability even in fuming acids. SZ-2 possesses the largest void volume recorded in zirconium phosphonates and SZ-3 represents the most porous crystalline zirconium phosphonate and the only porous MOF material reported to survive in aqua regia. SZ-2 and SZ-3 can effectively remove uranyl ions from aqueous solutions over a wide pH range, and we have elucidated the removal mechanism. Zirconium phosphonate based metal-organic frameworks often exhibit superior chemical stabilities, but typically exist as poorly crystalline or amorphous materials. Here the authors exploit an ionothermal method to obtain highly porous and remarkably stable single crystalline zirconium phosphonate frameworks that can efficiently remove uranyl ions from aqueous solutions.
Collapse
Affiliation(s)
- Tao Zheng
- School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China.,School of Environment and Biological Engineering, Nanjing University of Science &Technology, Nanjing 210094, China
| | - Zaixing Yang
- School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China
| | - Daxiang Gui
- School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China
| | - Zhiyong Liu
- School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China
| | - Xiangxiang Wang
- School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China
| | - Xing Dai
- School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China
| | - Shengtang Liu
- School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China
| | - Linjuan Zhang
- Shanghai Institute of Applied Physics and Key Laboratory of Nuclear Radiation and Nuclear Energy Technology, Chinese Academy of Sciences, Shanghai 201800, China
| | - Yang Gao
- School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China
| | - Lanhua Chen
- School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China
| | - Daopeng Sheng
- School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China
| | - Yanlong Wang
- School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China
| | - Juan Diwu
- School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China
| | - Jianqiang Wang
- Shanghai Institute of Applied Physics and Key Laboratory of Nuclear Radiation and Nuclear Energy Technology, Chinese Academy of Sciences, Shanghai 201800, China
| | - Ruhong Zhou
- School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China.,Computational Biology Center, IBM Thomas J Watson Research Center, Yorktown Heights, New York 10598, USA.,Department of Chemistry, Columbia University, New York, New York 10027, USA
| | - Zhifang Chai
- School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China
| | - Thomas E Albrecht-Schmitt
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, Florida 32306, USA
| | - Shuao Wang
- School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China
| |
Collapse
|
9
|
Chen P, Nishiyama Y, Wohlert J, Lu A, Mazeau K, Ismail AE. Translational Entropy and Dispersion Energy Jointly Drive the Adsorption of Urea to Cellulose. J Phys Chem B 2017; 121:2244-2251. [PMID: 28221796 DOI: 10.1021/acs.jpcb.6b11914] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Pan Chen
- Aachener
Verfahrenstechnik, RWTH Aachen University, Turmstrasse 46, D-52064 Aachen, Germany
- Wallenberg
Wood Science Center, and the Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, SE-10044 Stockholm, Sweden
| | - Yoshiharu Nishiyama
- CERMAV, Univ. Grenoble Alpes, F-38000 Grenoble, France
- CERMAV, CNRS, F-38000 Grenoble, France
| | - Jakob Wohlert
- Wallenberg
Wood Science Center, and the Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, SE-10044 Stockholm, Sweden
| | - Ang Lu
- College
of Chemistry and Molecular Science, Wuhan University, Wuhan 430072, China
| | - Karim Mazeau
- CERMAV, Univ. Grenoble Alpes, F-38000 Grenoble, France
- CERMAV, CNRS, F-38000 Grenoble, France
| | - Ahmed E. Ismail
- Department
of Chemical and Biomedical Engineering, West Virginia University, Morgantown, West Virginia 26505, United States
| |
Collapse
|
10
|
Duan G, Zhang Y, Luan B, Weber JK, Zhou RW, Yang Z, Zhao L, Xu J, Luo J, Zhou R. Graphene-Induced Pore Formation on Cell Membranes. Sci Rep 2017; 7:42767. [PMID: 28218295 PMCID: PMC5317030 DOI: 10.1038/srep42767] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 01/13/2017] [Indexed: 01/21/2023] Open
Abstract
Examining interactions between nanomaterials and cell membranes can expose underlying mechanisms of nanomaterial cytotoxicity and guide the design of safer nanomedical technologies. Recently, graphene has been shown to exhibit potential toxicity to cells; however, the molecular processes driving its lethal properties have yet to be fully characterized. We here demonstrate that graphene nanosheets (both pristine and oxidized) can produce holes (pores) in the membranes of A549 and Raw264.7 cells, substantially reducing cell viability. Electron micrographs offer clear evidence of pores created on cell membranes. Our molecular dynamics simulations reveal that multiple graphene nanosheets can cooperate to extract large numbers of phospholipids from the membrane bilayer. Strong dispersion interactions between graphene and lipid-tail carbons result in greatly depleted lipid density within confined regions of the membrane, ultimately leading to the formation of water-permeable pores. This cooperative lipid extraction mechanism for membrane perforation represents another distinct process that contributes to the molecular basis of graphene cytotoxicity.
Collapse
Affiliation(s)
- Guangxin Duan
- 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
| | - Yuanzhao Zhang
- IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA
| | - Binquan Luan
- IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA
| | - Jeffrey K Weber
- IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA
| | - Royce W Zhou
- Department of Oncology, The Affiliated Hospital of Nanjing Medical University, Changzhou No.2 People's Hospital, Changzhou, 213003, 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
| | - 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
| | - Jiaying Xu
- 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
| | - Judong Luo
- 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 Oncology, The Affiliated Hospital of Nanjing Medical University, Changzhou No.2 People's Hospital, Changzhou, 213003, 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
| |
Collapse
|
11
|
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.
Collapse
|
12
|
Gu Z, Zhang Y, Luan B, Zhou R. DNA translocation through single-layer boron nitride nanopores. SOFT MATTER 2016; 12:817-23. [PMID: 26537824 DOI: 10.1039/c5sm02197a] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Ultra-thin nanopores have become promising biological sensors because of their outstanding signal-to-noise ratio and spatial resolution. Here, we show that boron nitride (BN), which is a new two-dimensional (2D) material similar to graphene, could be utilized for making a nanopore with an atomic thickness. Using an all-atom molecular dynamics simulation, we investigated the dynamics of DNA translocation through the BN nanopore. The results of our simulations demonstrated that it is possible to detect different double-stranded DNA (dsDNA) sequences from the recording of ionic currents through the pore during the DNA translocation. Surprisingly, opposite to results for a graphene nanopore, we found the calculated blockage current for poly(A-T)40 in a BN nanopore to be less than that for poly(G-C)40. Also in contrast with the case of graphene nanopores, dsDNA models moved smoothly and in an unimpeded manner through the BN nanopores in the simulations, suggesting a potential advantage for using BN nanopores to design stall-free sequencing devices. BN nanopores, which display several properties (such as being hydrophilic and non-metallic) that are superior to those of graphene, are thus expected to find applications in the next generation of high-speed and low-cost biological sensors.
Collapse
Affiliation(s)
- Zonglin Gu
- School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, 215123, China
| | | | | | | |
Collapse
|
13
|
Duan G, Kang SG, Tian X, Garate JA, Zhao L, Ge C, Zhou R. Protein corona mitigates the cytotoxicity of graphene oxide by reducing its physical interaction with cell membrane. NANOSCALE 2015; 7:15214-24. [PMID: 26315610 DOI: 10.1039/c5nr01839k] [Citation(s) in RCA: 163] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Many recent studies have shown that the way nanoparticles interact with cells and biological molecules can vary greatly in the serum-containing or serum-free culture medium. However, the underlying molecular mechanisms of how the so-called "protein corona" formed in serum medium affects nanoparticles' biological responses are still largely unresolved. Thus, it is critical to understand how absorbed proteins on the surfaces of nanoparticles alter their biological effects. In this work, we have demonstrated with both experimental and theoretical approaches that protein BSA coating can mitigate the cytotoxicity of graphene oxide (GO) by reducing its cell membrane penetration. Our cell viability and cellular uptake experiments showed that protein corona decreased cellular uptake of GO, thus significantly mitigating the potential cytotoxicity of GO. The electron microscopy images also confirmed that protein corona reduced the cellular morphological damage by limiting GO penetration into the cell membrane. Further molecular dynamics (MD) simulations validated the experimental results and revealed that the adsorbed BSA in effect weakened the interaction between the phospholipids and graphene surface due to a reduction of the available surface area plus an unfavorable steric effect, thus significantly reducing the graphene penetration and lipid bilayer damaging. These findings provide new insights into the underlying molecular mechanism of this important graphene protein corona interaction with cell membranes, and should have implications in future development of graphene-based biomedical applications.
Collapse
Affiliation(s)
- Guangxin Duan
- 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.
| | | | | | | | | | | | | |
Collapse
|
14
|
Anitha K, Namsani S, Singh JK. Removal of Heavy Metal Ions Using a Functionalized Single-Walled Carbon Nanotube: A Molecular Dynamics Study. J Phys Chem A 2015; 119:8349-58. [DOI: 10.1021/acs.jpca.5b03352] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Affiliation(s)
- K. Anitha
- Department
of Chemical Engineering, Indian Institute of Technology Kanpur, Kanpur, UP-208016, India
| | - Sadanandam Namsani
- Department
of Chemical Engineering, Indian Institute of Technology Kanpur, Kanpur, UP-208016, India
| | - Jayant K Singh
- Department
of Chemical Engineering, Indian Institute of Technology Kanpur, Kanpur, UP-208016, India
| |
Collapse
|
15
|
The role of basic residues in the adsorption of blood proteins onto the graphene surface. Sci Rep 2015; 5:10873. [PMID: 26034971 PMCID: PMC4451687 DOI: 10.1038/srep10873] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 05/05/2015] [Indexed: 12/12/2022] Open
Abstract
With its many unique properties, graphene has shown great potential in various biomedical applications, while its biocompatibility has also attracted growing concerns. Previous studies have shown that the formation of protein-graphene corona could effectively reduce its cytotoxicity; however, the underlying molecular mechanism remains not well-understood. Herein, we use extensive molecular dynamics simulations to demonstrate that blood proteins such as bovine fibrinogen (BFG) can absorb onto the graphene surface quickly and tightly to form a corona complex. Aromatic residues contributed significantly during this adsorption process due to the strong π−π stacking interactions between their aromatic rings and the graphene sp2-carbons. Somewhat surprisingly, basic residues like arginine, also played an equally or even stronger role during this process. The strong dispersion interactions between the sidechains of these solvent-exposed basic residues and the graphene surface provide the driving force for a tight binding of these basic residues. To the best of our knowledge, this is the first study with blood proteins to show that, in addition to the aromatic residues, the basic residues also play an important role in the formation of protein-graphene corona complexes.
Collapse
|
16
|
Abstract
Construction of nano-devices that can generate controllable unidirectional rotation is an important part of nanotechnology. Here, we design a nano-turbine composed of carbon nanotube and graphene nanoblades, which can be driven by fluid flow. Rotation motion of nano-turbine is quantitatively studied by molecular dynamics simulations on this model system. A robust linear relationship is achieved with this nano-turbine between its rotation rate and the fluid flow velocity spanning two orders of magnitude, and this linear relationship remains intact at various temperatures. More interestingly, a striking difference from its macroscopic counterpart is identified: the rotation rate is much smaller (by a factor of ~15) than that of the macroscopic turbine with the same driving flow. This discrepancy is shown to be related to the disruption of water flow at nanoscale, together with the water slippage at graphene surface and the so-called “dragging effect”. Moreover, counterintuitively, the ratio of “effective” driving flow velocity increases as the flow velocity increases, suggesting that the linear dependence on the flow velocity can be more complicated in nature. These findings may serve as a foundation for the further development of rotary nano-devices and should also be helpful for a better understanding of the biological molecular motors.
Collapse
|
17
|
Lv M, He B, Liu Z, Xiu P, Tu Y. Charge-signal multiplication mediated by urea wires inside Y-shaped carbon nanotubes. J Chem Phys 2014; 141:044707. [DOI: 10.1063/1.4890725] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- Mei Lv
- Department of Mathematics, and Institute of Systems Biology, Shanghai University, Shanghai 200444, China
| | - Bing He
- School of Computer Engineering and Science, Shanghai University, Shanghai 200444, China
| | - Zengrong Liu
- Department of Mathematics, and Institute of Systems Biology, Shanghai University, Shanghai 200444, China
| | - Peng Xiu
- Department of Engineering Mechanics, and Soft Matter Research Center, Zhejiang University, Hangzhou 310027, China
| | - Yusong Tu
- Department of Mathematics, and Institute of Systems Biology, Shanghai University, Shanghai 200444, China
- College of Physics Science and Technology, Yangzhou University, Yangzhou 225009, China
| |
Collapse
|
18
|
Zhu Z, Sheng N, Wan R, Fang H. Intrinsic Autocorrelation Time of Picoseconds for Thermal Noise in Water. J Phys Chem A 2014; 118:8936-41. [DOI: 10.1021/jp5009785] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Zhi Zhu
- Division of Interfacial
Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China
- University of Chinese Academy of Sciences, Beijing 100080, China
| | - Nan Sheng
- Division of Interfacial
Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China
- University of Chinese Academy of Sciences, Beijing 100080, China
| | - Rongzheng Wan
- Division of Interfacial
Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China
| | - Haiping Fang
- Division of Interfacial
Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China
| |
Collapse
|
19
|
Dasgupta A, Udgaonkar JB, Das P. Multistage Unfolding of an SH3 Domain: An Initial Urea-Filled Dry Molten Globule Precedes a Wet Molten Globule with Non-Native Structure. J Phys Chem B 2014; 118:6380-92. [DOI: 10.1021/jp410019f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Amrita Dasgupta
- National
Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Jayant B. Udgaonkar
- National
Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Payel Das
- Computational
Biology Center, IBM Thomas J. Watson Research Center, 1101 Kitchawan
Road, Yorktown Heights, New
York 10598, United States
| |
Collapse
|
20
|
Cai Z, Li J, Yin C, Yang Z, Wu J, Zhou R. Effect of urea concentration on aggregation of amyloidogenic hexapeptides (NFGAIL). J Phys Chem B 2013; 118:48-57. [PMID: 24328094 DOI: 10.1021/jp407776e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We have performed large-scale all-atom molecular dynamics (MD) simulations to study the aggregation behavior of four NFGAIL hexapeptides in the aqueous urea solution, with a urea concentration ranging from 0 to 5 M. We find that urea in general suppresses the peptide aggregation, but suppression slows down in the intermediation concentration regime around 3 M. Two competing mechanisms of urea are determined: urea molecules accumulated near the first solvation shell (FSS) tend to unfold the hexapeptide, which favors aggregation; on the other hand, the tight hydrogen bonds formed between urea and peptide mainchains hinder the association of peptides which disfavors the formation of the β-sheet. Furthermore, the different nonlinear urea concentration dependences of the urea-peptide and peptide-peptide hydrogen bonds lead to a nonmonotonic behavior, with a weak enhancement in the peptide aggregation around 3 M.
Collapse
Affiliation(s)
- Zhuowei Cai
- Department of Physics, Zhejiang University , Hangzhou, 310027, China
| | | | | | | | | | | |
Collapse
|
21
|
Carr JK, Buchanan LE, Schmidt JR, Zanni MT, Skinner JL. Structure and dynamics of urea/water mixtures investigated by vibrational spectroscopy and molecular dynamics simulation. J Phys Chem B 2013; 117:13291-300. [PMID: 23841646 DOI: 10.1021/jp4037217] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Urea/water is an archetypical "biological" mixture and is especially well-known for its relevance to protein thermodynamics as urea acts as a protein denaturant at high concentration. This behavior has given rise to an extended debate concerning urea's influence on water structure. On the basis of a variety of methods and of definitions of the water structure, urea has been variously described as a structure-breaker, a structure-maker, or as remarkably neutral toward water. Because of its sensitivity to microscopic structure and dynamics, vibrational spectroscopy can help resolve these debates. We report experimental and theoretical spectroscopic results for the OD stretch of HOD/H2O/urea mixtures (linear IR, 2DIR, and pump-probe anisotropy decay) and for the CO stretch of urea-D4/D2O mixtures (linear IR only). Theoretical results are obtained using existing approaches for water and a modification of a frequency map developed for acetamide. All absorption spectra are remarkably insensitive to urea concentration, consistent with the idea that urea only very weakly perturbs the water structure. Both this work and experiments by Rezus and Bakker, however, show that water's rotational dynamics are slowed down by urea. Analysis of the simulations casts doubt on the suggestion that urea immobilizes particular doubly hydrogen bonded water molecules.
Collapse
Affiliation(s)
- J K Carr
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
| | | | | | | | | |
Collapse
|
22
|
Zhou X, Wang C, Wu F, Feng M, Li J, Lu H, Zhou R. The ice-like water monolayer near the wall makes inner water shells diffuse faster inside a charged nanotube. J Chem Phys 2013; 138:204710. [DOI: 10.1063/1.4807383] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
23
|
Tian X, Yang Z, Zhou B, Xiu P, Tu Y. Alcohol-induced drying of carbon nanotubes and its implications for alcohol/water separation: A molecular dynamics study. J Chem Phys 2013; 138:204711. [DOI: 10.1063/1.4807484] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
24
|
Toward an atomistic description of the urea-denatured state of proteins. Proc Natl Acad Sci U S A 2013; 110:5933-8. [PMID: 23536295 DOI: 10.1073/pnas.1216589110] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present here the characterization of the structural, dynamics, and energetics of properties of the urea-denatured state of ubiquitin, a small prototypical soluble protein. By combining state-of-the-art molecular dynamics simulations with NMR and small-angle X-ray scattering data, we were able to: (i) define the unfolded state ensemble, (ii) understand the energetics stabilizing unfolded structures in urea, (iii) describe the dedifferential nature of the interactions of the fully unfolded proteins with urea and water, and (iv) characterize the early stages of protein refolding when chemically denatured proteins are transferred to native conditions. The results presented herein are unique in providing a complete picture of the chemically unfolded state of proteins and contribute to deciphering the mechanisms that stabilize the native state of proteins, as well as those that maintain them unfolded in the presence of urea.
Collapse
|
25
|
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
| |
Collapse
|
26
|
Xia Z, Das P, Shakhnovich EI, Zhou R. Collapse of unfolded proteins in a mixture of denaturants. J Am Chem Soc 2012; 134:18266-74. [PMID: 23057830 DOI: 10.1021/ja3031505] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Both urea and guanidinium chloride (GdmCl) are frequently used as protein denaturants. Given that proteins generally adopt extended or unfolded conformations in either aqueous urea or GdmCl, one might expect that the unfolded protein chains will remain or become further extended due to the addition of another denaturant. However, a collapse of denatured proteins is revealed using atomistic molecular dynamics simulations when a mixture of denaturants is used. Both hen egg-white lysozyme and protein L are found to undergo collapse in the denaturant mixture. The collapse of the protein conformational ensembles is accompanied by a decreased solubility and increased non-native self-interactions of hydrophobic residues in the urea/GdmCl mixture. The increase of non-native interactions rather than the native contacts indicates that the proteins experience a simple collapse transition from the fully denatured states. During the protein collapse, the relatively stronger denaturant GdmCl displays a higher tendency to be absorbed onto the protein surface due to their stronger electrostatic interactions with proteins. At the same time, urea molecules also accumulate near the protein surface, resulting in an enhanced "local crowding" for the protein near its first solvation shell. This rearrangement of denaturants near the protein surface and crowded local environment induce the protein collapse, mainly by burying their hydrophobic residues. These findings from molecular simulations are then further explained by a simple analytical model based on statistical mechanics.
Collapse
Affiliation(s)
- Zhen Xia
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, USA
| | | | | | | |
Collapse
|
27
|
Salvalaglio M, Vetter T, Giberti F, Mazzotti M, Parrinello M. Uncovering Molecular Details of Urea Crystal Growth in the Presence of Additives. J Am Chem Soc 2012; 134:17221-33. [DOI: 10.1021/ja307408x] [Citation(s) in RCA: 149] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matteo Salvalaglio
- Institute of Process Engineering, ETH Zurich, CH-8092 Zurich, Switzerland
- Department of Chemistry and
Applied Biosciences, ETH Zurich, Zurich,
Switzerland
| | - Thomas Vetter
- Institute of Process Engineering, ETH Zurich, CH-8092 Zurich, Switzerland
| | - Federico Giberti
- Department of Chemistry and
Applied Biosciences, ETH Zurich, Zurich,
Switzerland
| | - Marco Mazzotti
- Institute of Process Engineering, ETH Zurich, CH-8092 Zurich, Switzerland
| | - Michele Parrinello
- Department of Chemistry and
Applied Biosciences, ETH Zurich, Zurich,
Switzerland
- Facoltà
di Informatica,
Istituto di Scienze Computazionali, Università della Svizzera Italiana Via G. Buffi 13, 6900 Lugano
Switzerland
| |
Collapse
|
28
|
Yang Z, Xiu P, Shi B, Hua L, Zhou R. Coherent microscopic picture for urea-induced denaturation of proteins. J Phys Chem B 2012; 116:8856-62. [PMID: 22780326 DOI: 10.1021/jp304114h] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In a previous study, we explored the mechanism of urea-induced denaturation of proteins by performing molecular dynamics (MD) simulations of hen lysozyme in 8 M urea and supported the "direct interaction mechanism" whereby urea denatures protein via dispersion interaction (Hua, L.; Zhou, R. H.; Thirumalai, D.; Berne, B. J. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 16928). Here we perform large scale MD simulations of five representative protein/peptide systems in aqueous urea to investigate if the above mechanism is common to other proteins. In all cases, accumulations of urea around proteins/peptide are observed, suggesting that urea denatures proteins by directly attacking protein backbones and side chains rather than indirectly disrupting water structure as a "water breaker". Consistent with our previous case study of lysozyme, the current energetic analyses with five protein/peptide systems reveal that urea's preferential binding to proteins mainly comes from urea's stronger dispersion interactions with proteins than with bulk solution, whereas the electrostatic (hydrogen-bonded) interactions only play a relatively minor (even negative) role during this denaturation process. Furthermore, the simulations of the peptide system at different urea concentrations (8 and 4.5 M), and with different force fields (CHARMM and OPLSAA) suggest that the above mechanism is robust, independent of the urea concentration and force field used. Last, we emphasize the importance of periodic boundary conditions in pairwise energetic analyses. This article provides a comprehensive study on the physical mechanism of urea-induced protein denaturation and suggests that the "dispersion-interaction-driven" mechanism should be general.
Collapse
Affiliation(s)
- Zaixing Yang
- Department of Engineering Mechanics, and Soft Matter Research Center, Zhejiang University, Hangzhou 310027, China
| | | | | | | | | |
Collapse
|
29
|
Abstract
The dewetting transitions of two hydrophobic plates immersed in pure water, aqueous ethanol solutions with concentrations from 25% to 90%, and pure ethanol were investigated by molecular dynamics simulations, where the dewetting transition was analogous to a first-order phase transition from liquid to vapor. It was found that the dewetting transitions occurred except that in the pure ethanol system. Although the ethanol molecules prefer to locate in the vicinity of the two plates, the inter-plate region is unfavorable for water molecules, due to losing more than one hydrogen bond. Moreover, each inter-plate water molecule forms hydrogen bonds on average with about two ethanol molecules. These intermolecular hydrogen bonds cause water and ethanol to cooperatively fill or exit the inter-plate region. Thus, water molecules play a more important role in the inter-plate filling/empty process, and induce the ethanol dewetting transition. Our results provide insight into the effect of water on the ethanol dewetting phenomena.
Collapse
Affiliation(s)
- Xiuping Ren
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai, 201800, China
| | | | | |
Collapse
|
30
|
Das P. Effect of cosolvents on nano-confined water: a molecular dynamics study. NANOSCALE 2012; 4:2931-2936. [PMID: 22441726 DOI: 10.1039/c2nr30070b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We present results from atomistic molecular dynamics simulations to characterize the effects of cosolvents, such as urea and guanidinium (Gdm) salts, on the water confined in hydrophobic carbon nanotubes. We observed complete drying of the nanotube interiors of diameter ranging from 8 to 17 Å in urea. In contrast, the water population within nanotube cores smaller than 12 Å remains unaffected in GdmCl solution, whereas larger nanotube interiors become partially dehydrated with prevailing presence of stable Gdm(+)-Gdm(+) dimers. The molecular arrangement and the lifetime inside the nanotube were found to be characteristics of a particular cosolvent. In both urea and GdmCl solutions, preferential cosolvent intrusion resulting in nanotube dehydration is driven by the stronger dispersion interaction of cosolvent than water with the nanotube. The partial drying of the hydrophobic core is attributed to guanidinium's better hydration and weaker self-association propensity compared to urea, as well as to its moderate ion-pairing with strongly hydrated chloride ions. The Gdm(+) induced dehydration varies with the charge density of counter-ions, as the presence of high charge-density sulfate ions impedes penetration of guanidinium, and consequent dehydration of the nanotube. These findings provide important insights into the effect of cosolvents on the nano-confined water in a hydrophobic environment.
Collapse
Affiliation(s)
- Payel Das
- IBM T.J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, NY 10598, USA.
| |
Collapse
|
31
|
Xiu P, Tu Y, Tian X, Fang H, Zhou R. Molecular wire of urea in carbon nanotube: a molecular dynamics study. NANOSCALE 2012; 4:652-658. [PMID: 22159294 DOI: 10.1039/c1nr10793c] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We perform molecular dynamics simulations of narrow single-walled carbon nanotubes (SWNTs) in aqueous urea to investigate the structure and dynamical behavior of urea molecules inside the SWNT. Even at low urea concentrations (e.g., 0.5 M), we have observed spontaneous and continuous filling of SWNT with a one-dimensional urea wire (leaving very few water molecules inside the SWNT). The urea wire is structurally ordered, both translationally and orientationally, with a contiguous hydrogen-bonded network and concerted urea's dipole orientations. Interestingly, despite the symmetric nature of the whole system, the potential energy profile of urea along the SWNT is asymmetric, arising from the ordering of asymmetric urea partial charge distribution (or dipole moment) in confined environment. Furthermore, we study the kinetics of confined urea and find that the permeation of urea molecules through the SWNT decreases significantly (by a factor of ∼20) compared to that of water molecules, due to the stronger dispersion interaction of urea with SWNT than water, and a maximum in urea permeation happens around a concentration of 5 M. These findings might shed some light on the better understanding of unique properties of molecular wires (particularly the wires formed by polar organic small molecules) confined within both artificial and biological nanochannels, and are expected to have practical applications such as the electronic devices for signal transduction and multiplication at the nanoscale.
Collapse
Affiliation(s)
- Peng Xiu
- Bio-X Lab, Department of Physics, and Soft Matter Research Center, Zhejiang University, Hangzhou, 310027, China
| | | | | | | | | |
Collapse
|
32
|
Li W, Zhou R, Mu Y. Salting Effects on Protein Components in Aqueous NaCl and Urea Solutions: Toward Understanding of Urea-Induced Protein Denaturation. J Phys Chem B 2012; 116:1446-51. [DOI: 10.1021/jp210769q] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Weifeng Li
- School of Physical and Mathematical
Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore
| | - Ruhong Zhou
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights,
New York 10598, United States
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive,
Singapore
| |
Collapse
|
33
|
Yang Z, Wang Z, Tian X, Xiu P, Zhou R. Amino acid analogues bind to carbon nanotube via π-π interactions: Comparison of molecular mechanical and quantum mechanical calculations. J Chem Phys 2012; 136:025103. [DOI: 10.1063/1.3675486] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
|