1
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Sauciuc A, Whittaker J, Tadema M, Tych K, Guskov A, Maglia G. Blobs form during the single-file transport of proteins across nanopores. Proc Natl Acad Sci U S A 2024; 121:e2405018121. [PMID: 39264741 PMCID: PMC11420176 DOI: 10.1073/pnas.2405018121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 08/05/2024] [Indexed: 09/14/2024] Open
Abstract
The transport of biopolymers across nanopores is an important biological process currently under investigation for the rapid analysis of DNA and proteins. While the transport of DNA is generally understood, methods to induce unfolded protein translocation have only recently been discovered (Yu et al., 2023, Sauciuc et al., 2023). Here, we found that during electroosmotically driven translocation of polypeptides, blob-like structures typically form inside nanopores, often obstructing their transport and preventing addressing individual amino acids. This is in contrast with the electrophoretic transport of DNA, where the formation of such structures has not been reported. Comparisons between different nanopore sizes and shapes and modifications by different surface chemistries allowed formulating a mechanism for blob formation. We also show that single-file transport can be achieved by using 1) nanopores that have an entry and an internal diameter smaller than the persistence length of the polymer, 2) nanopores with a nonsticky (i.e., nonaromatic) inner surface, and 3) moderate translocation velocities. These experiments provide a basis for understanding polypeptide transport under confinement and for improving the design and engineering of nanopores for protein analysis.
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Affiliation(s)
- Adina Sauciuc
- Chemical Biology I, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Jacob Whittaker
- Chemical Biology I, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Matthijs Tadema
- Chemical Biology I, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Katarzyna Tych
- Chemical Biology I, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Albert Guskov
- Chemical Biology I, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Giovanni Maglia
- Chemical Biology I, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
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2
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Sauciuc A, Whittaker J, Tadema M, Tych K, Guskov A, Maglia G. Unravelled proteins form blobs during translocation across nanopores. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.23.576815. [PMID: 38328101 PMCID: PMC10849628 DOI: 10.1101/2024.01.23.576815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
The electroosmotic-driven transport of unravelled proteins across nanopores is an important biological process that is now under investigation for the rapid analysis and sequencing of proteins. For this approach to work, however, it is crucial that the polymer is threaded in single file. Here we found that, contrary to the electrophoretic transport of charged polymers such as DNA, during polypeptide translocation blob-like structures typically form inside nanopores. Comparisons between different nanopore sizes, shapes and surface chemistries showed that under electroosmotic-dominated regimes single-file transport of polypeptides can be achieved using nanopores that simultaneously have an entry and an internal diameter that is smaller than the persistence length of the polymer, have a uniform non-sticky ( i . e . non-aromatic) nanopore inner surface, and using moderate translocation velocities.
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3
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Stuber A, Schlotter T, Hengsteler J, Nakatsuka N. Solid-State Nanopores for Biomolecular Analysis and Detection. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2024; 187:283-316. [PMID: 38273209 DOI: 10.1007/10_2023_240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
Advances in nanopore technology and data processing have rendered DNA sequencing highly accessible, unlocking a new realm of biotechnological opportunities. Commercially available nanopores for DNA sequencing are of biological origin and have certain disadvantages such as having specific environmental requirements to retain functionality. Solid-state nanopores have received increased attention as modular systems with controllable characteristics that enable deployment in non-physiological milieu. Thus, we focus our review on summarizing recent innovations in the field of solid-state nanopores to envision the future of this technology for biomolecular analysis and detection. We begin by introducing the physical aspects of nanopore measurements ranging from interfacial interactions at pore and electrode surfaces to mass transport of analytes and data analysis of recorded signals. Then, developments in nanopore fabrication and post-processing techniques with the pros and cons of different methodologies are examined. Subsequently, progress to facilitate DNA sequencing using solid-state nanopores is described to assess how this platform is evolving to tackle the more complex challenge of protein sequencing. Beyond sequencing, we highlight the recent developments in biosensing of nucleic acids, proteins, and sugars and conclude with an outlook on the frontiers of nanopore technologies.
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Affiliation(s)
- Annina Stuber
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland
| | - Tilman Schlotter
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland
| | - Julian Hengsteler
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland
| | - Nako Nakatsuka
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland.
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4
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Ghanta KP, Mondal S, Hajari T, Bandyopadhyay S. Impact of an Ionic Liquid on Amino Acid Side Chains: A Perspective from Molecular Simulation Studies. J Chem Inf Model 2023; 63:959-972. [PMID: 36721873 DOI: 10.1021/acs.jcim.2c01310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Ionic liquids (ILs) are known to modify the structural stability of proteins. The modification of the protein conformation is associated with the accumulation of ILs around the amino acid (AA) side chains and the nature of interactions between them. To understand the microscopic picture of the structural arrangements of ILs around the AA side chains, room temperature molecular dynamics (MD) simulations have been carried out in this work with a series of hydrophobic, polar and charged AAs in aqueous solutions containing the IL 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF4]) at 2 M concentration. The calculations revealed distinctly nonuniform distribution of the IL components around different AAs. In particular, it is demonstrated that the BMIM+ cations preferentially interact with the aromatic AAs through favorable stacking interactions between the cation imidazolium head groups and the aromatic AA side chains. This results in preferential parallel alignments and enhanced population of the cations around the aromatic AAs. The potential of mean force (PMF) calculations revealed that such favorable stacking interactions provide greater stability to the contact pairs (CPs) formed between the aromatic AAs and the IL cations as compared to the other AAs. It is further quantified that for most of the AAs (except the cationic ones), a favorable enthalpy contribution more than compensates for the entropy cost to form stable CPs with the IL cations. These findings are likely to provide valuable fundamental information toward understanding the effects of ILs on protein conformational stability.
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Affiliation(s)
- Krishna Prasad Ghanta
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur721302, India
| | - Souvik Mondal
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur721302, India
| | - Timir Hajari
- Department of Chemistry, City College, Kolkata700009, India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur721302, India
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5
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El Harrar T, Gohlke H. Cumulative Millisecond-Long Sampling for a Comprehensive Energetic Evaluation of Aqueous Ionic Liquid Effects on Amino Acid Interactions. J Chem Inf Model 2023; 63:281-298. [PMID: 36520535 DOI: 10.1021/acs.jcim.2c01123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The interactions of amino acid side-chains confer diverse energetic contributions and physical properties to a protein's stability and function. Various computational tools estimate the effect of changing a given amino acid on the protein's stability based on parametrized (free) energy functions. When parametrized for the prediction of protein stability in water, such energy functions can lead to suboptimal results for other solvents, such as ionic liquids (IL), aqueous ionic liquids (aIL), or salt solutions. However, to our knowledge, no comprehensive data are available describing the energetic effects of aIL on intramolecular protein interactions. Here, we present the most comprehensive set of potential of mean force (PMF) profiles of pairwise protein-residue interactions to date, covering 50 relevant interactions in water, the two biotechnologically relevant aIL [BMIM/Cl] and [BMIM/TfO], and [Na/Cl]. These results are based on a cumulated simulation time of >1 ms. aIL and salt ions can weaken, but also strengthen, specific residue interactions by more than 3 kcal mol-1, depending on the residue pair, residue-residue configuration, participating ions, and concentration, necessitating considering such interactions specifically. These changes originate from a complex interplay of competitive or cooperative noncovalent ion-residue interactions, changes in solvent structural dynamics, or unspecific charge screening effects and occur at the contact distance but also at larger, solvent-separated distances. This data provide explanations at the atomistic and energetic levels for complex IL effects on protein stability and should help improve the prediction accuracies of computational tools that estimate protein stability based on (free) energy functions.
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Affiliation(s)
- Till El Harrar
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Holger Gohlke
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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6
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Vu QV, Jiang Y, Li MS, O'Brien EP. The driving force for co-translational protein folding is weaker in the ribosome vestibule due to greater water ordering. Chem Sci 2021; 12:11851-11857. [PMID: 34659725 PMCID: PMC8442680 DOI: 10.1039/d1sc01008e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 08/02/2021] [Indexed: 01/12/2023] Open
Abstract
Interactions between the ribosome and nascent chain can destabilize folded domains in the ribosome exit tunnel's vestibule, the last 3 nm of the exit tunnel where tertiary folding can occur. Here, we test if a contribution to this destabilization is a weakening of hydrophobic association, the driving force for protein folding. Using all-atom molecular dynamics simulations, we calculate the potential-of-mean force between two methane molecules along the center line of the ribosome exit tunnel and in bulk solution. Associated methanes, we find, are half as stable in the ribosome's vestibule as compared to bulk solution, demonstrating that the hydrophobic effect is weakened by the presence of the ribosome. This decreased stability arises from a decrease in the amount of water entropy gained upon the association of the methanes. And this decreased entropy gain originates from water molecules being more ordered in the vestibule as compared to bulk solution. Therefore, the hydrophobic effect is weaker in the vestibule because waters released from the first solvation shell of methanes upon association do not gain as much entropy in the vestibule as they do upon release in bulk solution. These findings mean that nascent proteins pass through a ribosome vestibule environment that can destabilize folded structures, which has the potential to influence co-translational protein folding pathways, energetics, and kinetics.
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Affiliation(s)
- Quyen V. Vu
- Institute of Physics, Polish Academy of SciencesAl. Lotnikow 32/4602-668 WarsawPoland
| | - Yang Jiang
- Department of Chemistry, Penn State UniversityUniversity ParkPennsylvaniaUSA
| | - Mai Suan Li
- Institute of Physics, Polish Academy of SciencesAl. Lotnikow 32/4602-668 WarsawPoland,Institute for Computational Sciences and TechnologyQuang Trung Software City, Tan Chanh Hiep Ward, District 12Ho Chi Minh CityVietnam
| | - Edward P. O'Brien
- Department of Chemistry, Penn State UniversityUniversity ParkPennsylvaniaUSA,Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Penn State UniversityUniversity ParkPennsylvaniaUSA,Institute for Computational and Data Sciences, Penn State UniversityUniversity ParkPennsylvaniaUSA
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7
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Suvlu D, Thirumalai D, Rasaiah JC. Water-Mediated Interactions Determine Helix Formation of Peptides in Open Nanotubes. J Phys Chem B 2021; 125:817-824. [PMID: 33464101 DOI: 10.1021/acs.jpcb.0c10178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Water-mediated interactions (WMIs) play diverse roles in molecular biology. They are particularly relevant in geometrically confined spaces such as the interior of the chaperonin, at the interface between ligands and their binding partners, and in the ribosome tunnel. Inspired in part by the geometry of the ribosome tunnel, we consider confinement effects on the stability of peptides. We describe results from replica exchange molecular dynamics simulations of a system containing a 23-alanine or 23-serine polypeptide confined to nonpolar and polar nanotubes in the gas phase and when open to a water reservoir. We quantify the effect of water in determining the preferred conformational states of these polypeptides by calculating the difference in the solvation free energy for the helix and coil states in the open nanotube in the two phases. Our simulations reveal several possibilities. We find that nanoscopic confinement preferentially stabilizes the helical state of polypeptides with hydrophobic side chains, which is explained by the entropic stabilization mechanism proposed on the basis of polymer physics. Polypeptide chains with hydrophilic side chains can adopt helical structures within nanotubes, but helix formation is sensitive to the nature of the nanotube due to WMIs. We elaborate on the potential implications of our findings to the stability of peptides in the ribosome tunnel.
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Affiliation(s)
- Dylan Suvlu
- University of Maine, Orono, Maine 04469, United States
| | - D Thirumalai
- The University of Texas at Austin, Austin, Texas 78712, United States
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8
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Koculi E, Thirumalai D. Retardation of Folding Rates of Substrate Proteins in the Nanocage of GroEL. Biochemistry 2021; 60:460-464. [PMID: 33464880 DOI: 10.1021/acs.biochem.0c00903] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Escherichia coli ATP-consuming chaperonin machinery, a complex between GroEL and GroES, has evolved to facilitate folding of substrate proteins (SPs) that cannot do so spontaneously. A series of kinetic experiments show that the SPs are encapsulated in the GroEL/ES nanocage for a short duration. If confinement of the SPs is the mechanism by which GroEL/ES facilitates folding, it follows that the assisted folding rate, relative to the bulk value, should always be enhanced. Here, we show that this is not the case for the folding of rhodanese in the presence of the full machinery of GroEL/ES and ATP. The assisted folding rate of rhodanese decreases. On the basis of our finding and those reported in other studies, we suggest that the ATP-consuming chaperonin machinery has evolved to optimize the product of the folding rate and the yield of the folded SPs on the biological time scale. Neither the rate nor the yield is separately maximized.
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Affiliation(s)
- Eda Koculi
- Department of Biology, Johns Hopkins University, 144 Mudd Hall, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - D Thirumalai
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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9
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The effect of synergistic amino acids-ionic liquids in methane hydrate inhibition by COSMO-RS application. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114837] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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10
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Korobko I, Mazal H, Haran G, Horovitz A. Measuring protein stability in the GroEL chaperonin cage reveals massive destabilization. eLife 2020; 9:56511. [PMID: 32716842 PMCID: PMC7440923 DOI: 10.7554/elife.56511] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 07/25/2020] [Indexed: 01/29/2023] Open
Abstract
The thermodynamics of protein folding in bulk solution have been thoroughly investigated for decades. By contrast, measurements of protein substrate stability inside the GroEL/ES chaperonin cage have not been reported. Such measurements require stable encapsulation, that is no escape of the substrate into bulk solution during experiments, and a way to perturb protein stability without affecting the chaperonin system itself. Here, by establishing such conditions, we show that protein stability in the chaperonin cage is reduced dramatically by more than 5 kcal mol-1 compared to that in bulk solution. Given that steric confinement alone is stabilizing, our results indicate that hydrophobic and/or electrostatic effects in the cavity are strongly destabilizing. Our findings are consistent with the iterative annealing mechanism of action proposed for the chaperonin GroEL.
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Affiliation(s)
- Ilia Korobko
- Departments of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Hisham Mazal
- Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Gilad Haran
- Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Amnon Horovitz
- Departments of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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11
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Eggenberger OM, Ying C, Mayer M. Surface coatings for solid-state nanopores. NANOSCALE 2019; 11:19636-19657. [PMID: 31603455 DOI: 10.1039/c9nr05367k] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Since their introduction in 2001, solid-state nanopores have been increasingly exploited for the detection and characterization of biomolecules ranging from single DNA strands to protein complexes. A major factor that enables the application of nanopores to the analysis and characterization of a broad range of macromolecules is the preparation of coatings on the pore wall to either prevent non-specific adhesion of molecules or to facilitate specific interactions of molecules of interest within the pore. Surface coatings can therefore be useful to minimize clogging of nanopores or to increase the residence time of target analytes in the pore. This review article describes various coatings and their utility for changing pore diameters, increasing the stability of nanopores, reducing non-specific interactions, manipulating surface charges, enabling interactions with specific target molecules, and reducing the noise of current recordings through nanopores. We compare the coating methods with respect to the ease of preparing the coating, the stability of the coating and the requirement for specialized equipment to prepare the coating.
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Affiliation(s)
- Olivia M Eggenberger
- Adolphe Merkle Institute, Chemin des Verdiers 4, University of Fribourg, Fribourg, Switzerland.
| | - Cuifeng Ying
- Adolphe Merkle Institute, Chemin des Verdiers 4, University of Fribourg, Fribourg, Switzerland.
| | - Michael Mayer
- Adolphe Merkle Institute, Chemin des Verdiers 4, University of Fribourg, Fribourg, Switzerland.
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12
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Wei C, Zhao W, Shi X, Pei C, Wei P, Zhang J, Li H. Thick Two-Dimensional Water Film Confined between the Atomically Thin Mica Nanosheet and Hydrophilic Substrate. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:5130-5139. [PMID: 30907594 DOI: 10.1021/acs.langmuir.8b04232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The interesting properties of water molecules confined in a two-dimensional (2D) environment have aroused great attention. However, the study of 2D-confined water at the hydrophilic-hydrophilic interface is largely unexplored due to the lack of appropriate system. In this work, the behavior of water molecules confined between an atomically thin mica nanosheet and a hydrophilic SiO2/Si substrate was investigated using an atomic force microscope in detail at ambient conditions. The confined water molecules aggregated as droplets when the relative humidity (RH) of the environment was 11%. A large-area 2D water film with a uniform thickness of ∼2 nm was observed when the mica flake was incubated at 33% RH for 1 h before being mechanically exfoliated on a SiO2/Si substrate. Interestingly, the water film showed ordered edges with a predominant angle of 120°, which was the same with the lattice orientation of the mica nanosheet on top of it. The water film showed a fluidic behavior at the early stage and reached a stable state after 48 h under ambient conditions. The surface properties of the upper mica nanosheet and the underlying substrate played a crucial role in manipulating the behavior of confined water molecules. When the surface of the upper mica nanosheet was modified by Na+, Ni2+, and aminopropyltriethoxysilane (APS), only some small water droplets were observed instead of a water film. The surface of the underlying SiO2/Si substrate was functionalized by hydrophilic APS and hydrophobic octadecyltrimethoxysiliane (OTS). The small water droplets were imaged on a hydrophobic OTS-SiO2/Si substrate, while the water film with regular edges was maintained on a hydrophilic APS-SiO2/Si substrate. Our results might provide an alternative molecular view for investigating structures and properties of confined water molecules in 2D environments.
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Affiliation(s)
- Cong Wei
- Key Laboratory of Flexible Electronics (KLOFE) and Institute of Advanced Materials (IAM) , Nanjing Tech University (NanjingTech) , 30 South Puzhu Road , Nanjing 211816 , P.R. China
| | - Weihao Zhao
- Key Laboratory of Flexible Electronics (KLOFE) and Institute of Advanced Materials (IAM) , Nanjing Tech University (NanjingTech) , 30 South Puzhu Road , Nanjing 211816 , P.R. China
| | - Xiaotong Shi
- Key Laboratory of Flexible Electronics (KLOFE) and Institute of Advanced Materials (IAM) , Nanjing Tech University (NanjingTech) , 30 South Puzhu Road , Nanjing 211816 , P.R. China
| | - Chengjie Pei
- Key Laboratory of Flexible Electronics (KLOFE) and Institute of Advanced Materials (IAM) , Nanjing Tech University (NanjingTech) , 30 South Puzhu Road , Nanjing 211816 , P.R. China
| | - Pei Wei
- Key Laboratory of Flexible Electronics (KLOFE) and Institute of Advanced Materials (IAM) , Nanjing Tech University (NanjingTech) , 30 South Puzhu Road , Nanjing 211816 , P.R. China
| | - Jindong Zhang
- Key Laboratory of Flexible Electronics (KLOFE) and Institute of Advanced Materials (IAM) , Nanjing Tech University (NanjingTech) , 30 South Puzhu Road , Nanjing 211816 , P.R. China
| | - Hai Li
- Key Laboratory of Flexible Electronics (KLOFE) and Institute of Advanced Materials (IAM) , Nanjing Tech University (NanjingTech) , 30 South Puzhu Road , Nanjing 211816 , P.R. China
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13
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Puri S, Chaudhuri TK. Inter and intra-subunit interactions at the subunit interface of chaperonin GroEL are essential for its stability and assembly. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:331-343. [PMID: 30661519 DOI: 10.1016/j.bbapap.2018.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 10/13/2018] [Accepted: 10/18/2018] [Indexed: 10/28/2022]
Abstract
Chaperonin GroEL helps in the folding of substrate proteins under normal and stress conditions. Although it remains stable and functional during stress conditions, the quantitative estimation of stability parameters and the specific amino-acid residues playing a role in its stability are not known in sufficient detail. The reason for poor understanding is its large size, multimeric nature, and irreversible unfolding process. The X-ray crystal structure reveals that equatorial domain forms almost all intra and inter-subunit interactions for assembly of GroEL. Considering all these facts, we adopted alternate strategies to use monomeric GroEL, native GroEL and equatorial domain mutants (GroELK4E/GroELD523K/GroELD473C) to study the assembly and stability of GroEL. Loss of inter-subunit interaction involving K4 residue of one subunit and E59, I60, E61, I62 residues of adjacent subunit due to K4E mutation affect the oligomerization efficiency of GroEL subunits while the equilibrium unfolding studies on wild-type monomeric GroEL, native GroEL, and the selected mutants together demonstrate that intra-subunit interactions involving K4 and D523 of the same subunit play a critical role in the thermodynamic stability of both native and monomeric GroEL without affecting the oligomerization of subunits. The stability order between the GroELwild-type(M) and its variants is GroELwild-type(M) ≥ GroELD473C(M)˃GroELD523K(M)˃GroELK4E.
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Affiliation(s)
- Sarita Puri
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Tapan K Chaudhuri
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
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14
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Van Meervelt V, Soskine M, Singh S, Schuurman-Wolters GK, Wijma HJ, Poolman B, Maglia G. Real-Time Conformational Changes and Controlled Orientation of Native Proteins Inside a Protein Nanoreactor. J Am Chem Soc 2017; 139:18640-18646. [PMID: 29206456 PMCID: PMC6150693 DOI: 10.1021/jacs.7b10106] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
Protein conformations play crucial
roles in most, if not all, biological
processes. Here we show that the current carried through a nanopore
by ions allows monitoring conformational changes of single and native
substrate-binding domains (SBD) of an ATP-Binding Cassette importer
in real-time. Comparison with single-molecule Förster Resonance
Energy Transfer and ensemble measurements revealed that proteins trapped
inside the nanopore have bulk-like properties. Two ligand-free and
two ligand-bound conformations of SBD proteins were inferred and their
kinetic constants were determined. Remarkably, internalized proteins
aligned with the applied voltage bias, and their orientation could
be controlled by the addition of a single charge to the protein surface.
Nanopores can thus be used to immobilize proteins on a surface with
a specific orientation, and will be employed as nanoreactors for single-molecule
studies of native proteins. Moreover, nanopores with internal protein
adaptors might find further practical applications in multianalyte
sensing devices.
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Affiliation(s)
- Veerle Van Meervelt
- Department of Chemistry, University of Leuven , Leuven B-3001, Belgium.,Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Groningen 9747 AG, The Netherlands
| | - Misha Soskine
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Groningen 9747 AG, The Netherlands
| | - Shubham Singh
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Groningen 9747 AG, The Netherlands
| | - Gea K Schuurman-Wolters
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Groningen 9747 AG, The Netherlands
| | - Hein J Wijma
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Groningen 9747 AG, The Netherlands
| | - Bert Poolman
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Groningen 9747 AG, The Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Groningen 9747 AG, The Netherlands
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15
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Chavis AE, Brady KT, Hatmaker GA, Angevine CE, Kothalawala N, Dass A, Robertson JWF, Reiner JE. Single Molecule Nanopore Spectrometry for Peptide Detection. ACS Sens 2017; 2:1319-1328. [PMID: 28812356 PMCID: PMC11274829 DOI: 10.1021/acssensors.7b00362] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Sensing and characterization of water-soluble peptides is of critical importance in a wide variety of bioapplications. Single molecule nanopore spectrometry (SMNS) is based on the idea that one can use biological protein nanopores to resolve different sized molecules down to limits set by the blockade duration and noise. Previous work has shown that this enables discrimination between polyethylene glycol (PEG) molecules that differ by a single monomer unit. This paper describes efforts to extend SMNS to a variety of biologically relevant, water-soluble peptides. We describe the use of Au25(SG)18 clusters, previously shown to improve PEG detection, to increase the on- and off-rate of peptides to the pore. In addition, we study the role that fluctuations play in the single molecule nanopore spectrometry (SMNS) methodology and show that modifying solution conditions to increase peptide flexibility (via pH or chaotropic salt) leads to a nearly 2-fold reduction in the current blockade fluctuations and a corresponding narrowing of the peaks in the blockade distributions. Finally, a model is presented that connects the current blockade depths to the mass of the peptides, which shows that our enhanced SMNS detection improves the mass resolution of the nanopore sensor more than 2-fold for the largest cationic peptides studied.
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Affiliation(s)
- Amy E. Chavis
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Kyle T. Brady
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Grace A. Hatmaker
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Christopher E. Angevine
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Nuwan Kothalawala
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Amala Dass
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Joseph W. F. Robertson
- Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8120, United States
| | - Joseph E. Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
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16
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Suvlu D, Samaratunga S, Thirumalai D, Rasaiah JC. Thermodynamics of Helix-Coil Transitions of Polyalanine in Open Carbon Nanotubes. J Phys Chem Lett 2017; 8:494-499. [PMID: 28060517 DOI: 10.1021/acs.jpclett.6b02620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Understanding structure formation in polypeptide chains and synthetic polymers encapsulated in pores is important in biology and nanotechnology. We present replica exchange molecular dynamics studies of the phase diagram for α-helix formation of capped polyalanine in nanotubes (NT) open to a water reservoir as a function of the NT diameter and hydrophobicity. A helix forms only in a narrow range of diameters, which surprisingly is comparable to the width of the ribosome tunnel. Increasing the hydrophobicity enhances helicity in the NT. Helix formation in polyalanine is driven by a small negative enthalpy and a positive entropy change at ≈300 K, in contrast to the large negative entropy change that destabilizes the helix and favors the coiled state in bulk water. There is an anticorrelation between water density inside the nanotube and structure formation. Confinement-induced helix formation depends on amino acid sequence. There is complete absence of helix in polyglutamine and polyserine confined to a open carbon nanotube.
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Affiliation(s)
- Dylan Suvlu
- Department of Chemistry, University of Maine , Orono, Maine 04469, United States
| | | | - D Thirumalai
- Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Jayendran C Rasaiah
- Department of Chemistry, University of Maine , Orono, Maine 04469, United States
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17
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Shi G, Dang Y, Pan T, Liu X, Liu H, Li S, Zhang L, Zhao H, Li S, Han J, Tai R, Zhu Y, Li J, Ji Q, Mole RA, Yu D, Fang H. Unexpectedly Enhanced Solubility of Aromatic Amino Acids and Peptides in an Aqueous Solution of Divalent Transition-Metal Cations. PHYSICAL REVIEW LETTERS 2016; 117:238102. [PMID: 27982649 DOI: 10.1103/physrevlett.117.238102] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Indexed: 06/06/2023]
Abstract
We experimentally observed considerable solubility of tryptophan (Trp) in a CuCl_{2} aqueous solution, which could reach 2-5 times the solubility of Trp in pure water. Theoretical studies show that the strong cation-π interaction between Cu^{2+} and the aromatic ring in Trp modifies the electronic distribution of the aromatic ring to enhance significantly the water affinity of Trp. Similar solubility enhancement has also been observed for other divalent transition-metal cations (e.g., Zn^{2+} and Ni^{2+}), another aromatic amino acid (phenylalanine), and three aromatic peptides (Trp-Phe, Phe-Phe, and Trp-Ala-Phe).
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Affiliation(s)
- Guosheng Shi
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Yaru Dang
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- School of Chemical Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Tingting Pan
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- School of Chemical Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xing Liu
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Hui Liu
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- School of Chemical Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Shaoxian Li
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- Center for Terahertz Waves and College of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin 300072, China
| | - Lijuan Zhang
- Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201204, China
| | - Hongwei Zhao
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Shaoping Li
- School of Chemical Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Jiaguang Han
- Center for Terahertz Waves and College of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin 300072, China
| | - Renzhong Tai
- Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201204, China
| | - Yiming Zhu
- Shanghai Key Lab of Modern Optical System, University of Shanghai for Science and Technology, No. 516, Jungong Road, 200093, Shanghai, China
| | - Jichen Li
- School of Physics and Astronomy, the University of Manchester, Manchester M13 9PL, United Kingdom
| | - Qing Ji
- Institute of Biophysics, Hebei University of Technology, Tianjin 300401, China
| | - R A Mole
- Australian Nuclear Science and Technology Organisation, Lucas Heights, New South Wales 2234, Australia
| | - Dehong Yu
- Australian Nuclear Science and Technology Organisation, Lucas Heights, New South Wales 2234, Australia
| | - Haiping Fang
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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18
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Jamali AA, Ferdousi R, Razzaghi S, Li J, Safdari R, Ebrahimie E. DrugMiner: comparative analysis of machine learning algorithms for prediction of potential druggable proteins. Drug Discov Today 2016; 21:718-24. [PMID: 26821132 DOI: 10.1016/j.drudis.2016.01.007] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 12/05/2015] [Accepted: 01/19/2016] [Indexed: 12/14/2022]
Abstract
Application of computational methods in drug discovery has received increased attention in recent years as a way to accelerate drug target prediction. Based on 443 sequence-derived protein features, we applied the most commonly used machine learning methods to predict whether a protein is druggable as well as to opt for superior algorithm in this task. In addition, feature selection procedures were used to provide the best performance of each classifier according to the optimum number of features. When run on all features, Neural Network was the best classifier, with 89.98% accuracy, based on a k-fold cross-validation test. Among all the algorithms applied, the optimum number of most-relevant features was 130, according to the Support Vector Machine-Feature Selection (SVM-FS) algorithm. This study resulted in the discovery of new drug target which potentially can be employed in cell signaling pathways, gene expression, and signal transduction. The DrugMiner web tool was developed based on the findings of this study to provide researchers with the ability to predict druggable proteins. DrugMiner is freely available at www.DrugMiner.org.
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Affiliation(s)
- Ali Akbar Jamali
- Research Center for Pharmaceutical Nanotechnology (RCPN), Tabriz University of Medical Sciences, Tabriz, Iran
| | - Reza Ferdousi
- Department of Health Information Management, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran
| | - Saeed Razzaghi
- Information Technology Center, The University of Zanjan, Zanjan, Iran
| | - Jiuyong Li
- School of Information Technology and Mathematical Sciences, Division of Information Technology, Engineering and the Environment, The University of South Australia, Adelaide, SA, Australia
| | - Reza Safdari
- Department of Health Information Management, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran.
| | - Esmaeil Ebrahimie
- School of Information Technology and Mathematical Sciences, Division of Information Technology, Engineering and the Environment, The University of South Australia, Adelaide, SA, Australia; Department of Genetics & Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia; School of Biological Sciences, Faculty of Science and Engineering, Flinders University, Adelaide, SA, Australia.
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19
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Vaitheeswaran S, Thirumalai D. Entropy and enthalpy of interaction between amino acid side chains in nanopores. J Chem Phys 2014; 141:22D523. [PMID: 25494794 DOI: 10.1063/1.4901204] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Understanding the stabilities of proteins in nanopores requires a quantitative description of confinement induced interactions between amino acid side chains. We use molecular dynamics simulations to study the nature of interactions between the side chain pairs ALA-PHE, SER-ASN, and LYS-GLU in bulk water and in water-filled nanopores. The temperature dependence of the bulk solvent potentials of mean force and the interaction free energies in cylindrical and spherical nanopores is used to identify the corresponding entropic and enthalpic components. The entropically stabilized hydrophobic interaction between ALA and PHE in bulk water is enthalpically dominated upon confinement depending on the relative orientations between the side chains. In the case of SER-ASN, hydrogen bonded configurations that are similar in bulk water are thermodynamically distinct in a cylindrical pore, thus making rotamer distributions different from those in the bulk. Remarkably, salt bridge formation between LYS-GLU is stabilized by entropy in contrast to the bulk. Implications of our findings for confinement-induced alterations in protein stability are briefly outlined.
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Affiliation(s)
- S Vaitheeswaran
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, USA
| | - D Thirumalai
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, USA
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20
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Bhattacharya A, Best RB, Mittal J. Smoothing of the GB1 hairpin folding landscape by interfacial confinement. Biophys J 2013; 103:596-600. [PMID: 22947876 DOI: 10.1016/j.bpj.2012.07.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Revised: 06/26/2012] [Accepted: 07/02/2012] [Indexed: 11/30/2022] Open
Abstract
We study the effects of confinement between planar walls on the folding thermodynamics of a β-hairpin, using large-scale replica-exchange molecular-dynamics simulations with an all-atom model and explicit solvent. We find that the folding free-energy landscape of this peptide observed in bulk is significantly modified when the peptide is confined between the walls. Most notably, the propensity of the peptide to form a misfolded state observed in the bulk solution becomes negligible under confinement. The absence of the misfolded state under confinement can be explained by an increased tendency of hydrophobic aromatic side chains to stay near the walls, because the misfolded state is characterized by a nonnative arrangement of aromatic side chains. These results from a simple confinement model may provide clues about the role of chaperonin confinement in smoothing folding landscapes by avoiding trapped intermediates.
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Affiliation(s)
| | - Robert B Best
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Jeetain Mittal
- Department of Chemical Engineering, Lehigh University, Bethlehem, Pennsylvania.
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21
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Marino KA, Bolhuis PG. Confinement-induced states in the folding landscape of the Trp-cage miniprotein. J Phys Chem B 2012; 116:11872-80. [PMID: 22954175 DOI: 10.1021/jp306727r] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Although protein folding is typically studied in dilute solution, folding in a cell will be affected by interactions with other biomolecules and excluded volume effects. Here, we examine the effect of hydrophobic confinement on folding of the Trp-cage miniprotein. We used replica exchange molecular dynamics simulations to probe the differences between folding in the bulk, on a hydrophobic surface, and confined between two hydrophobic walls. In addition to promotion of helix formation due to reduced conformational entropy of the unfolded state upon confinement, adsorption of Trp-cage to a hydrophobic surface stabilizes intermediate structures not present in the bulk. These new intermediate structures may alter the folding mechanism and kinetics and show the importance of including environmental effects when studying protein folding.
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Affiliation(s)
- Kristen A Marino
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, PO Box 94157, 1090 GD Amsterdam, The Netherlands
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22
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Chen WW, Sing Tay DK, Leong SSJ, Kwak SK. Three-dimensional structure of human β-defensin 28 via homology modelling and molecular dynamics. MOLECULAR SIMULATION 2012. [DOI: 10.1080/08927022.2011.604854] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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23
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Abstract
A variety of neurodegenerative diseases are associated with amyloid plaques, which begin as soluble protein oligomers but develop into amyloid fibrils. Our incomplete understanding of this process underscores the need to decipher the principles governing protein aggregation. Mechanisms of in vivo amyloid formation involve a number of coconspirators and complex interactions with membranes. Nevertheless, understanding the biophysical basis of simpler in vitro amyloid formation is considered important for discovering ligands that preferentially bind regions harboring amyloidogenic tendencies. The determination of the fibril structure of many peptides has set the stage for probing the dynamics of oligomer formation and amyloid growth through computer simulations. Most experimental and simulation studies, however, have been interpreted largely from the perspective of proteins: the role of solvent has been relatively overlooked in oligomer formation and assembly to protofilaments and amyloid fibrils. In this Account, we provide a perspective on how interactions with water affect folding landscapes of amyloid beta (Aβ) monomers, oligomer formation in the Aβ16-22 fragment, and protofilament formation in a peptide from yeast prion Sup35. Explicit molecular dynamics simulations illustrate how water controls the self-assembly of higher order structures, providing a structural basis for understanding the kinetics of oligomer and fibril growth. Simulations show that monomers of Aβ peptides sample a number of compact conformations. The formation of aggregation-prone structures (N*) with a salt bridge, strikingly similar to the structure in the fibril, requires overcoming a high desolvation barrier. In general, sequences for which N* structures are not significantly populated are unlikely to aggregate. Oligomers and fibrils generally form in two steps. First, water is expelled from the region between peptides rich in hydrophobic residues (for example, Aβ16-22), resulting in disordered oligomers. Then the peptides align along a preferred axis to form ordered structures with anti-parallel β-strand arrangement. The rate-limiting step in the ordered assembly is the rearrangement of the peptides within a confining volume. The mechanism of protofilament formation in a polar peptide fragment from the yeast prion, in which the two sheets are packed against each other and create a dry interface, illustrates that water dramatically slows self-assembly. As the sheets approach each other, two perfectly ordered one-dimensional water wires form. They are stabilized by hydrogen bonds to the amide groups of the polar side chains, resulting in the formation of long-lived metastable structures. Release of trapped water from the pore creates a helically twisted protofilament with a dry interface. Similarly, the driving force for addition of a solvated monomer to a preformed fibril is water release; the entropy gain and favorable interpeptide hydrogen bond formation compensate for entropy loss in the peptides. We conclude by offering evidence that a two-step model, similar to that postulated for protein crystallization, must also hold for higher order amyloid structure formation starting from N*. Distinct water-laden polymorphic structures result from multiple N* structures. Water plays multifarious roles in all of these protein aggregations. In predominantly hydrophobic sequences, water accelerates fibril formation. In contrast, water-stabilized metastable intermediates dramatically slow fibril growth rates in hydrophilic sequences.
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Affiliation(s)
- D Thirumalai
- Biophysics Program, Institute for Physical Science and Technology, Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States.
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24
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Yuzlenko O, Lazaridis T. Interactions between ionizable amino acid side chains at a lipid bilayer-water interface. J Phys Chem B 2011; 115:13674-84. [PMID: 21985663 DOI: 10.1021/jp2052213] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Potentials of mean force (PMF) between ionizable amino acid side chains (Arg, Lys, His, Glu) in the headgroup area of a palmitoyl oleoyl phosphatidylcholine lipid bilayer were obtained from all-atom molecular dynamics simulations and the adaptive biasing force method. Simulations in bulk water were also performed for comparison. Side chains were constrained in collinear, stacking, and orthogonal (T-shaped) orientations. The most structured and attractive PMFs were observed for hydrogen-bonded side chains. Contact minima occurred at a distance of 2.6-3.1 Å between selected atoms or centers of mass with the most attractive interaction (-9.6 kcal/mol) observed between Arg(+) and Glu(-). Hydrogen bonds play a significant role in stabilizing these interactions. Interactions between like charged side chains can also be very attractive if the charges are screened by surrounding molecules or groups (e.g., the PMF value at the contact minimum for Arg(+)···Arg(+) is -7.6 kcal/mol). Like charged side chains can have contact minima as close as 3.6 Å. The PMFs depend strongly on the relative orientation of the side chains. In agreement with experimental studies and other simulations, we found the stacking arrangement of like charged side chains to be the most favorable orientation. Interaction energies and Lennard-Jones energies between side chains, headgroups, and water molecules were analyzed in order to rationalize the observed PMFs and their dependence on orientation. In general, the results cannot be explained by simple dielectric arguments.
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Affiliation(s)
- Olga Yuzlenko
- Department of Chemistry, City College of the City University of New York, 160 Convent Avenue, New York, New York 10031, USA
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25
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Yoo S, Xantheas SS. The role of hydrophobic surfaces in altering water-mediated peptide-peptide interactions in an aqueous environment. J Phys Chem A 2011; 115:6088-92. [PMID: 21247205 DOI: 10.1021/jp1107137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using Born-Oppenheimer molecular dynamics within the density functional framework, we calculated the effective force acting on water-mediated peptide-peptide interaction between antiparallel β-sheets in an aqueous environment and also in the vicinity of a hydrophobic surface. From the magnitude of the effective force (corresponding to the slope of the free energy as a function of the interpeptide distance) and its sign (a negative value indicates an effective attraction, whereas a positive value indicates an effective repulsion) we can elucidate the fundamental differences of the water-mediated peptide-peptide interactions in those two environments. The computed effective forces indicate that the water-mediated interaction between peptides in an aqueous environment is attractive in the range of interpeptide distance d = 7-8 Å when hydrophobic surfaces are not nearby. Due to the stabilization of the water molecules bridging between the two β-sheets, a free energy barrier exists between the direct and indirect (water-mediated) interpeptide interactions. However, when the peptides are in the proximity of hydrophobic surfaces, this free energy barrier decreases because the hydrophobic surfaces enhance the interpeptide attraction by the destabilization and ease-to-libration of the bridging water molecules between them.
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Affiliation(s)
- Soohaeng Yoo
- Chemical and Materials Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K1-83, Richland, Washington 99352, USA
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26
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Zhao J, Culligan PJ, Qiao Y, Zhou Q, Li Y, Tak M, Park T, Chen X. Electrolyte solution transport in electropolar nanotubes. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2010; 22:315301. [PMID: 21399357 DOI: 10.1088/0953-8984/22/31/315301] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Electrolyte transport in nanochannels plays an important role in a number of emerging areas. Using non-equilibrium molecular dynamics (NEMD) simulations, the fundamental transport behavior of an electrolyte/water solution in a confined model nanoenvironment is systematically investigated by varying the nanochannel dimension, solid phase, electrolyte phase, ion concentration and transport rate. It is found that the shear resistance encountered by the nanofluid strongly depends on these material/system parameters; furthermore, several effects are coupled. The mechanisms of the nanofluidic transport characteristics are explained by considering the unique molecular/ion structure formed inside the nanochannel. The lower shear resistance observed in some of the systems studies could be beneficial for nanoconductors, while the higher shear resistance (or higher effective viscosity) observed in other systems might enhance the performance of energy dissipation devices.
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Affiliation(s)
- Jianbing Zhao
- Department of Earth and Environmental Engineering, School of Engineering and Applied Sciences, Columbia University, New York, NY 10027, USA
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27
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Bouamrani A, Hu Y, Tasciotti E, Li L, Chiappini C, Liu X, Ferrari M. Mesoporous silica chips for selective enrichment and stabilization of low molecular weight proteome. Proteomics 2010; 10:496-505. [PMID: 20013801 DOI: 10.1002/pmic.200900346] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The advanced properties of mesoporous silica have been demonstrated in applications, which include chemical sensing, filtration, catalysis, drug delivery and selective biomolecular uptake. These properties depend on the architectural, physical and chemical properties of the material, which in turn are determined by the processing parameters in evaporation-induced self-assembly. In this study, we introduce a combinatorial approach for the removal of the high molecular weight proteins and for the specific isolation and enrichment of low molecular weight species. This approach is based on mesoporous silica chips able to fractionate, selectively harvest and protect from enzymatic degradation, peptides and proteins present in complex human biological fluids. We present the characterization of the harvesting properties of a wide range of mesoporous chips using a library of peptides and proteins standard and their selectivity on the recovery of serum peptidome. Using MALDI-TOF-MS, we established the correlation between the harvesting specificity and the physicochemical properties of mesoporous silica surfaces. The introduction of this mesoporous material with fine controlled properties will provide a powerful platform for proteomics application offering a rapid and efficient methodology for low molecular weight biomarker discovery.
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Affiliation(s)
- Ali Bouamrani
- Department of Nanomedicine and BioMedical Engineering, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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28
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Zuo G, Wang J, Qin M, Xue B, Wang W. Effect of solvation-related interaction on the low-temperature dynamics of proteins. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 81:031917. [PMID: 20365780 DOI: 10.1103/physreve.81.031917] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2009] [Revised: 12/06/2009] [Indexed: 05/29/2023]
Abstract
The effect of solvation-related interaction on the low-temperature dynamics of proteins is studied by taking into account the desolvation barriers in the interactions of native contacts. It is found out that about the folding transition temperature, the protein folds in a cooperative manner, and the water molecules are expelled from the hydrophobic core at the final stage in the folding process. At low temperature, however, the protein would generally be trapped in many metastable conformations with some water molecules frozen inside the protein. The desolvation takes an important role in these processes. The number of frozen water molecules and that of frozen states of proteins are further analyzed with the methods based on principal component analysis (PCA) and the clustering of conformations. It is found out that both the numbers of frozen water molecules and the frozen states of the protein increase quickly below a certain temperature. Especially, the number of frozen states of the protein increases exponentially following the decrease in the temperature, which resembles the basic features of glassy dynamics. Interestingly, it is observed that the freezing of water molecules and that of protein conformations happen at almost the same temperature. This suggests that the solvation-related interaction performs an important role for the low-temperature dynamics of the model protein.
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Affiliation(s)
- Guanghong Zuo
- Nanjing National Laboratory of Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
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29
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Elcock AH. Models of macromolecular crowding effects and the need for quantitative comparisons with experiment. Curr Opin Struct Biol 2010; 20:196-206. [PMID: 20167475 DOI: 10.1016/j.sbi.2010.01.008] [Citation(s) in RCA: 232] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Revised: 01/17/2010] [Accepted: 01/21/2010] [Indexed: 01/19/2023]
Abstract
In recent years significant effort has been devoted to exploring the potential effects of macromolecular crowding on protein folding and association phenomena. Theoretical calculations and molecular simulations have, in particular, been exploited to describe aspects of protein behavior in crowded and confined conditions and many aspects of the simulated behavior have reflected, at least at a qualitative level, the behavior observed in experiments. One major and immediate challenge for the theorists is to now produce models capable of making quantitatively accurate predictions of in vitro behavior. A second challenge is to derive models that explain results obtained from experiments performed in vivo, the results of which appear to call into question the assumed dominance of excluded-volume effects in vivo.
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Affiliation(s)
- Adrian H Elcock
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA.
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30
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Zhang L, Zhao G, Sun Y. Effects of Ligand Density on Hydrophobic Charge Induction Chromatography: Molecular Dynamics Simulation. J Phys Chem B 2010; 114:2203-11. [DOI: 10.1021/jp903852c] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lin Zhang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Guofeng Zhao
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yan Sun
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
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31
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Jewett AI, Shea JE. Reconciling theories of chaperonin accelerated folding with experimental evidence. Cell Mol Life Sci 2010; 67:255-76. [PMID: 19851829 PMCID: PMC11115962 DOI: 10.1007/s00018-009-0164-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Revised: 09/14/2009] [Accepted: 09/25/2009] [Indexed: 10/20/2022]
Abstract
For the last 20 years, a large volume of experimental and theoretical work has been undertaken to understand how chaperones like GroEL can assist protein folding in the cell. The most accepted explanation appears to be the simplest: GroEL, like most other chaperones, helps proteins fold by preventing aggregation. However, evidence suggests that, under some conditions, GroEL can play a more active role by accelerating protein folding. A large number of models have been proposed to explain how this could occur. Focused experiments have been designed and carried out using different protein substrates with conclusions that support many different mechanisms. In the current article, we attempt to see the forest through the trees. We review all suggested mechanisms for chaperonin-mediated folding and weigh the plausibility of each in light of what we now know about the most stringent, essential, GroEL-dependent protein substrates.
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Affiliation(s)
- Andrew I. Jewett
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106 USA
- Department of Physics, University of California, Santa Barbara, CA 93106 USA
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106 USA
- Department of Physics, University of California, Santa Barbara, CA 93106 USA
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Hénin J, Fiorin G, Chipot C, Klein ML. Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables. J Chem Theory Comput 2009; 6:35-47. [PMID: 26614317 DOI: 10.1021/ct9004432] [Citation(s) in RCA: 300] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A new implementation of the adaptive biasing force (ABF) method is described. This implementation supports a wide range of collective variables and can be applied to the computation of multidimensional energy profiles. It is provided to the community as part of a code that implements several analogous methods, including metadynamics. ABF and metadynamics have not previously been tested side by side on identical systems. Here, numerical tests are carried out on processes including conformational changes in model peptides and translocation of a halide ion across a lipid membrane through a peptide nanotube. On the basis of these examples, we discuss similarities and differences between the ABF and metadynamics schemes. Both approaches provide enhanced sampling and free energy profiles in quantitative agreement with each other in different applications. The method of choice depends on the dimension of the reaction coordinate space, the height of the barriers, and the relaxation times of degrees of freedom in the orthogonal space, which are not explicitly described by the chosen collective variables.
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Affiliation(s)
- Jérome Hénin
- Center for Molecular Modeling, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, Institute for Computational Molecular Science and Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, and Department of Physics and Beckman Institute for Advanced Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61820
| | - Giacomo Fiorin
- Center for Molecular Modeling, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, Institute for Computational Molecular Science and Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, and Department of Physics and Beckman Institute for Advanced Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61820
| | - Christophe Chipot
- Center for Molecular Modeling, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, Institute for Computational Molecular Science and Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, and Department of Physics and Beckman Institute for Advanced Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61820
| | - Michael L Klein
- Center for Molecular Modeling, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, Institute for Computational Molecular Science and Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, and Department of Physics and Beckman Institute for Advanced Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61820
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Ligand migration through the internal hydrophobic cavities in human neuroglobin. Proc Natl Acad Sci U S A 2009; 106:18984-9. [PMID: 19850865 DOI: 10.1073/pnas.0905433106] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Neuroglobin (Ngb), a member of the globin superfamily, was found in the brain of vertebrates and is suggested to play a neuroprotective function under hypoxic conditions by scavenging nitrogen monoxide (NO) through a dioxygenase activity. In order for such a reaction to efficiently take place and to minimize the release of reactive intermediates in the cytosol, the cosubstrates O(2) and NO and other unstable reaction intermediates should bind sequentially to docking sites in the protein matrix. We have characterized the accessibility of these sites by analyzing the geminate CO rebinding kinetics to the heme moiety observed upon nanosecond flash photolysis of the Ngb-CO complex encapsulated in silica gels. The geminate rebinding phase showed a remarkable complexity, revealing the presence of a system of secondary docking sites where ligands are stored for hundreds of microseconds. Most kinetics steps display little temperature dependence, demonstrating that ligands can easily migrate through the cavities, except for the slowest reaction intermediate, possibly reflecting a structural conformational change reshaping the system of cavities. This conformational change is unrelated with distal His E7 binding to the heme, as it persists for the HE7L mutant. Overall, data are consistent with the presence of a discrete system of docking sites, possibly acting as reservoirs for the putative cosubstrates and for other reactive species involved in the physiologically relevant reaction.
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Homouz D, Hoffman B, Cheung MS. Hydrophobic interactions of hexane in nanosized water droplets. J Phys Chem B 2009; 113:12337-42. [PMID: 19725588 DOI: 10.1021/jp907318d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We use all-atomistic molecular dynamics simulations to study hydrophobic interactions of hexane in nanosized water droplets where the hydrogen bonding network of water molecules is disrupted at the surface. As a result of the competition between the energetics of a hexane molecule and the distribution of water molecules that lost the ability to form hydrogen bonds at the boundary, all-trans-hexane molecules are statistically favored at the surface of a nanosized water droplet and such a statistical trend increases as the size of a nano water droplet decreases. Changes in the radial distribution and the orientation of water molecules surrounding hexane in nanosized water droplets over bulk water are indicative of the finite-size effects on the structural distribution of a short, topologically complex hydrocarbon chain.
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Affiliation(s)
- Dirar Homouz
- Department of Physics, University of Houston, 4800 Calhoun Road, Houston, Texas 77204, USA
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Tian J, Garcia AE. An alpha-helical peptide in AOT micelles prefers to be localized at the water/headgroup interface. Biophys J 2009; 96:L57-9. [PMID: 19450460 DOI: 10.1016/j.bpj.2009.03.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2009] [Revised: 03/10/2009] [Accepted: 03/12/2009] [Indexed: 11/19/2022] Open
Abstract
A model alpha-helical peptide encapsulated in a reverse micelle is used to study the structure and dynamics of proteins under constrained environments that mimic the membrane-water environment in cells. Molecular dynamics simulations of the self assembly of systems composed of a peptide, sodium bis(2-ethylhexyl) sulfosuccinate (AOT), water, and isooctane show that the peptide prefers to be located at the water/AOT headgroups interface. We explore the effect of the AOT headgroup charge and the peptide charge and find that the peptides migrate to the interface in all cases. These results show that the peptides prefer the constrained hydration environment of the AOT headgroups. The driving force for this configuration is the gain in entropy by released water molecules that otherwise would solvate the protein and surfactant headgroups.
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Sobolewski E, Makowski M, Oldziej S, Czaplewski C, Liwo A, Scheraga HA. Towards temperature-dependent coarse-grained potentials of side-chain interactions for protein folding simulations. I: molecular dynamics study of a pair of methane molecules in water at various temperatures. Protein Eng Des Sel 2009; 22:547-52. [PMID: 19556395 DOI: 10.1093/protein/gzp028] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
By means of molecular dynamics simulations of a pair of methane molecules in a TIP3P periodic water box with the NVT scheme at six temperatures and, additionally, the NPT scheme at three temperatures ranging from T = 283 to 373 K, we determined the potential of mean force (PMF) of pairs of interacting methane molecules in water as functions of distance between the methane molecules. The PMFs converge to a single baseline only for r> 11 A at all temperatures. The curves of the dimensionless PMF obtained at different temperatures with the NVT scheme overlap almost perfectly in the region of the contact minimum and still very well in the regions of the desolvation maximum and the solvent-separated minimum, which suggests that the temperature-dependent hydrophobic interaction potentials at constant volume in united-residue force fields can be obtained by scaling the respective dimensionless potentials by RT, R being the universal gas constant. For the dimensionless potentials of mean force obtained with the NPT scheme, the depth of the contact minimum increases, whereas the height of the desolvation maximum and the depth of the solvent-separated minimum decrease with temperature, in agreement with results reported in the literature.
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Affiliation(s)
- Emil Sobolewski
- Laboratory of Biopolymer Structure, Intercollegiate Faculty of Biotechnology, University of Gdańsk, Medical University of Gdańsk, Kładki 24, 80-822 Gdańsk
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Vaitheeswaran S, Reddy G, Thirumalai D. Water-mediated interactions between hydrophobic and ionic species in cylindrical nanopores. J Chem Phys 2009; 130:094502. [PMID: 19275404 DOI: 10.1063/1.3080720] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We use Metropolis Monte Carlo and umbrella sampling to calculate the free energies of interaction of two methane molecules and their charged derivatives in cylindrical water-filled pores. Confinement strongly alters the interactions between the nonpolar solutes and completely eliminates the solvent separated minimum (SSM) that is seen in bulk water. The free energy profiles show that the methane molecules are either in contact or at separations corresponding to the diameter and the length of the cylindrical pore. Analytic calculations that estimate the entropy of the solutes, which are solvated at the pore surface, qualitatively explain the shape of the free energy profiles. Adding charges of opposite sign and magnitude 0.4e or e (where e is the electronic charge) to the methane molecules decreases their tendency for surface solvation and restores the SSM. We show that confinement induced ion-pair formation occurs whenever l(B)/D approximately O(1), where l(B) is the Bjerrum length and D is the pore diameter. The extent of stabilization of the SSM increases with ion charge density as long as l(B)/D<1. In pores with D<or=1.2 nm, in which the water is strongly layered, increasing the charge magnitude from 0.4e to e reduces the stability of the SSM. As a result, ion-pair formation that occurs with negligible probability in the bulk is promoted. In larger diameter pores that can accommodate a complete hydration layer around the solutes, the stability of the SSM is enhanced.
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Affiliation(s)
- S Vaitheeswaran
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, USA
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