1
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Dhingra K, Sinha I, Snyder M, Roush D, Cramer SM. Exploring preferred binding domains of IgG1 mAbs to multimodal adsorbents using a combined biophysics and simulation approach. Biotechnol Prog 2024; 40:e3415. [PMID: 38043031 DOI: 10.1002/btpr.3415] [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: 08/28/2023] [Revised: 10/19/2023] [Accepted: 11/13/2023] [Indexed: 12/04/2023]
Abstract
In this work, we employ a recently developed biophysical technique that uses diethylpyrocarbonate (DEPC) covalent labeling and mass spectrometry for the identification of mAb binding patches to two multimodal cation exchange resins at different pH. This approach compares the labeling results obtained in the bound and unbound states to identify residues that are sterically shielded and thus located in the mAb binding domains. The results at pH 6 for one mAb (mAb B) indicated that while the complementarity determining region (CDR) had minimal interactions with both resins, the FC domain was actively involved in binding. In contrast, DEPC/MS data with another mAb (mAb C) indicated that both the CDR and FC domains were actively involved in binding. These results corroborated chromatographic retention data with these two mAbs and their fragments and helped to explain the significantly stronger retention of both the intact mAb C and its Fab fragment. In contrast, labeling results with mAb C at pH 7, indicated that only the CDR played a significant role in resin binding, again corroborating chromatographic data. The binding domains identified from the DEPC/MS experiments were also examined using protein surface hydrophobicity maps obtained using a recently developed sparse sampling molecular dynamics (MD) approach in concert with electrostatic potential maps. These results demonstrate that the DEPC covalent labeling/mass spectrometry technique can provide important information about the domain contributions of multidomain proteins such as monoclonal antibodies when interacting with multimodal resins over a range of pH conditions.
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Affiliation(s)
- Kabir Dhingra
- Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York, USA
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Imee Sinha
- Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York, USA
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Mark Snyder
- Process Chemistry Division, Bio-Rad Laboratories, Hercules, California, USA
| | - David Roush
- Process R&D, Merck &Co., Inc., Rahway, New Jersey, USA
| | - Steven M Cramer
- Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York, USA
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
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2
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Kariev AM, Green ME. Water, Protons, and the Gating of Voltage-Gated Potassium Channels. MEMBRANES 2024; 14:37. [PMID: 38392664 PMCID: PMC10890431 DOI: 10.3390/membranes14020037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/17/2024] [Accepted: 01/23/2024] [Indexed: 02/24/2024]
Abstract
Ion channels are ubiquitous throughout all forms of life. Potassium channels are even found in viruses. Every cell must communicate with its surroundings, so all cells have them, and excitable cells, in particular, especially nerve cells, depend on the behavior of these channels. Every channel must be open at the appropriate time, and only then, so that each channel opens in response to the stimulus that tells that channel to open. One set of channels, including those in nerve cells, responds to voltage. There is a standard model for the gating of these channels that has a section of the protein moving in response to the voltage. However, there is evidence that protons are moving, rather than protein. Water is critical as part of the gating process, although it is hard to see how this works in the standard model. Here, we review the extensive evidence of the importance of the role of water and protons in gating these channels. Our principal example, but by no means the only example, will be the Kv1.2 channel. Evidence comes from the effects of D2O, from mutations in the voltage sensing domain, as well as in the linker between that domain and the gate, and at the gate itself. There is additional evidence from computations, especially quantum calculations. Structural evidence comes from X-ray studies. The hydration of ions is critical in the transfer of ions in constricted spaces, such as the gate region and the pore of a channel; we will see how the structure of the hydrated ion fits with the structure of the channel. In addition, there is macroscopic evidence from osmotic experiments and streaming current measurements. The combined evidence is discussed in the context of a model that emphasizes the role of protons and water in gating these channels.
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Affiliation(s)
- Alisher M Kariev
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031, USA
| | - Michael E Green
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031, USA
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3
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Sinha I, Garde S, Cramer SM. Comparative Analysis of Protein Surface Hydrophobicity Maps Determined by Sparse Sampling INDUS and Spatial Aggregation Propensity. J Phys Chem B 2023; 127:10304-10314. [PMID: 37993107 DOI: 10.1021/acs.jpcb.3c04902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
Protein surface hydrophobicity plays a central role in various biological processes such as protein folding and aggregation, as well as in the design and manufacturing of biotherapeutics. While the hydrophobicity of protein surface patches has been linked to their constituent residue hydropathies, recent research has shown that protein surface hydrophobicity is more complex and characterized by the response of water to these surfaces. In this work, we employ water density perturbations to map the surface hydrophobicity of a set of model proteins using sparse indirect umbrella sampling simulations (SSI). This technique is used to identify hydrophobic surface patches for the set of model proteins, and the results are compared to those obtained from the widely adopted spatial aggregation propensity (SAP) technique. While SAP-based calculations show agreement with SSI in some cases, there are several examples of disagreement. We identify four general classes of difference in behavior and study factors that contribute to these differences. We find that the SAP method can sometimes mask the effect of weakly nonpolar or isolated nonpolar residues that can lead to strong hydrophobic patches on the protein surface. In addition, hydrophobic patches identified by SAP can exhibit shifts in both position and strength on the SSI map. Our results demonstrate that the combination of topography and chemical context controls the hydrophobicity of a given patch above and beyond the intrinsic polarity of the residues present on the patch surface. The availability of more accurate protein hydrophobicity maps in concert with new classes of hydrophobic molecular descriptors may create significant opportunities for in silico prediction of protein behavior for a range of applications, such as protein design, biomanufacturability, and downstream bioprocessing.
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Affiliation(s)
- Imee Sinha
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States of America
| | - Shekhar Garde
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States of America
| | - Steven M Cramer
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States of America
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4
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Azizi K, Laio A, Hassanali A. Solvation thermodynamics from cavity shapes of amino acids. PNAS NEXUS 2023; 2:pgad239. [PMID: 37545648 PMCID: PMC10400782 DOI: 10.1093/pnasnexus/pgad239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 07/07/2023] [Accepted: 07/17/2023] [Indexed: 08/08/2023]
Abstract
According to common physical chemistry wisdom, the solvent cavities hosting a solute are tightly sewn around it, practically coinciding with its van der Waals surface. Solvation entropy is primarily determined by the surface and the volume of the cavity while enthalpy is determined by the solute-solvent interaction. In this work, we challenge this picture, demonstrating by molecular dynamics simulations that the cavities surrounding the 20 amino acids deviate significantly from the molecular surface. Strikingly, the shape of the cavity alone can be used to predict the solvation free energy, entropy, enthalpy, and hydrophobicity. Solute-solvent interactions involving the different chemical moieties of the amino acid, determine indirectly the cavity shape, and the properties of the branches but do not have to be taken explicitly into account in the prediction model.
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Affiliation(s)
- Khatereh Azizi
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
| | - Alessandro Laio
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
- SISSA, Via Bonomea 265, I-34136 Trieste, Italy
| | - Ali Hassanali
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
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5
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Zhang H, Sundaresan S, Webb MA. Molecular Dynamics Investigation of Nanoscale Hydrophobicity of Polymer Surfaces: What Makes Water Wet? J Phys Chem B 2023. [PMID: 37043668 DOI: 10.1021/acs.jpcb.3c00616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
The wettability of a polymer surface─related to its hydrophobicity or tendency to repel water─can be crucial for determining its utility, such as for a coating or a purification membrane. While wettability is commonly associated with the macroscopic measurement of a contact angle between surface, water, and air, the molecular physics that underlie these macroscopic observations are not fully known, and anticipating the relative behavior of different polymers is challenging. To address this gap in molecular-level understanding, we use molecular dynamics simulations to investigate and contrast interactions of water with six chemically distinct polymers: polytetrafluoroethylene, polyethylene, polyvinyl chloride, poly(methyl methacrylate), Nylon-66, and poly(vinyl alcohol). We show that several prospective quantitative metrics for hydrophobicity agree well with experimental contact angles. Moreover, the behavior of water in proximity to these polymer surfaces can be distinguished with analysis of interfacial water dynamics, extent of hydrogen bonding, and molecular orientation─even when macroscopic measures of hydrophobicity are similar. The predominant factor dictating wettability is found to be the extent of hydrogen bonding between polymer and water, but the precise manifestation of hydrogen bonding and its impact on surface water structure varies. In the absence of hydrogen bonding, other molecular interactions and polymer mechanics control hydrophobic ordering. These results provide new insights into how polymer chemistry specifically impacts water-polymer interactions and translates to surface hydrophobicity. Such factors may facilitate the design or processing of polymer surfaces to achieve targeted wetting behavior, and presented analyses can be useful in studying the interfacial physics of other systems.
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Affiliation(s)
- Hang Zhang
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Sankaran Sundaresan
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Michael A Webb
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
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6
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Sinha I, Cramer SM, Ashbaugh HS, Garde S. Connecting Non-Gaussian Water Density Fluctuations to the Lengthscale Dependent Crossover in Hydrophobic Hydration. J Phys Chem B 2022; 126:7604-7614. [PMID: 36154059 DOI: 10.1021/acs.jpcb.2c04990] [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
We connect density fluctuations in liquid water to lengthscale dependent crossover in hydrophobic hydration. Specifically, we employ indirect umbrella sampling (INDUS) simulations to characterize density fluctuations in observation volumes of various sizes and shapes in water and as a function of temperature and salt concentration. Consistent with previous observations, density fluctuations are Gaussian in small molecular scale volumes, but they display non-Gaussian "low-density fat tails" in larger volumes. These non-Gaussian tails are indicative of the proximity of water to its liquid to vapor phase transition and have implications on biomolecular interactions and function. We show that the onset of non-Gaussian fluctuations in large volumes is accompanied by the formation of a cavity in the observation volume. We develop a model that uses the physics of cavity-water interface formation as a key ingredient and show that it captures the nature of non-Gaussian density fluctuations over a broad region in water and in salt solutions. We discuss the limitations of this model in the very low density region of the distribution. Our calculations provide new insights into the origins of non-Gaussian density fluctuations in water and their connections to lengthscale dependent crossover in hydrophobic hydration.
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Affiliation(s)
- Imee Sinha
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States
| | - Steven M Cramer
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States
| | - Henry S Ashbaugh
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70123, United States
| | - Shekhar Garde
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States
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7
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Superhydrophilicity of α-Alumina Surfaces Results from Tight Binding of Interfacial Waters to Specific Aluminols. J Colloid Interface Sci 2022; 628:943-954. [DOI: 10.1016/j.jcis.2022.07.164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 11/21/2022]
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8
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Thakur AC, Remsing RC. Distributed charge models of liquid methane and ethane for dielectric effects and solvation. Mol Phys 2021. [DOI: 10.1080/00268976.2021.1933228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Atul C. Thakur
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
| | - Richard C. Remsing
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
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9
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Ashbaugh HS, Vats M, Garde S. Bridging Gaussian Density Fluctuations from Microscopic to Macroscopic Volumes: Applications to Non-Polar Solute Hydration Thermodynamics. J Phys Chem B 2021; 125:8152-8164. [PMID: 34283590 PMCID: PMC8389927 DOI: 10.1021/acs.jpcb.1c04087] [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] [Indexed: 11/28/2022]
Abstract
![]()
The hydration of
hydrophobic solutes is intimately related to the
spontaneous formation of cavities in water through ambient density
fluctuations. Information theory-based modeling and simulations have
shown that water density fluctuations in small volumes are approximately
Gaussian. For limiting cases of microscopic and macroscopic volumes,
water density fluctuations are known exactly and are rigorously related
to the density and isothermal compressibility of water. Here, we develop
a theory—interpolated gaussian fluctuation theory (IGFT)—that
builds an analytical bridge to describe water density fluctuations
from microscopic to molecular scales. This theory requires no detailed
information about the water structure beyond the effective size of
a water molecule and quantities that are readily obtained from water’s
equation-of-state—namely, the density and compressibility.
Using simulations, we show that IGFT provides a good description of
density fluctuations near the mean, that is, it characterizes the
variance of occupancy fluctuations over all solute sizes. Moreover,
when combined with the information theory, IGFT reproduces the well-known
signatures of hydrophobic hydration, such as entropy convergence and
solubility minima, for atomic-scale solutes smaller than the crossover
length scale beyond which the Gaussian assumption breaks down. We
further show that near hydrophobic and hydrophilic self-assembled
monolayer surfaces in contact with water, the normalized solvent density
fluctuations within observation volumes depend similarly on size as
observed in the bulk, suggesting the feasibility of a modified version
of IGFT for interfacial systems. Our work highlights the utility of
a density fluctuation-based approach toward understanding and quantifying
the solvation of non-polar solutes in water and the forces that drive
them toward surfaces with different hydrophobicities.
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Affiliation(s)
- Henry S Ashbaugh
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Mayank Vats
- Center for Biotechnology and Interdisciplinary Studies and the Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Shekhar Garde
- Center for Biotechnology and Interdisciplinary Studies and the Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
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10
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Identifying hydrophobic protein patches to inform protein interaction interfaces. Proc Natl Acad Sci U S A 2021; 118:2018234118. [PMID: 33526682 DOI: 10.1073/pnas.2018234118] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Interactions between proteins lie at the heart of numerous biological processes and are essential for the proper functioning of the cell. Although the importance of hydrophobic residues in driving protein interactions is universally accepted, a characterization of protein hydrophobicity, which informs its interactions, has remained elusive. The challenge lies in capturing the collective response of the protein hydration waters to the nanoscale chemical and topographical protein patterns, which determine protein hydrophobicity. To address this challenge, here, we employ specialized molecular simulations wherein water molecules are systematically displaced from the protein hydration shell; by identifying protein regions that relinquish their waters more readily than others, we are then able to uncover the most hydrophobic protein patches. Surprisingly, such patches contain a large fraction of polar/charged atoms and have chemical compositions that are similar to the more hydrophilic protein patches. Importantly, we also find a striking correspondence between the most hydrophobic protein patches and regions that mediate protein interactions. Our work thus establishes a computational framework for characterizing the emergent hydrophobicity of amphiphilic solutes, such as proteins, which display nanoscale heterogeneity, and for uncovering their interaction interfaces.
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11
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Dhabal D, Jiang Z, Pallath A, Patel AJ. Characterizing the Interplay between Polymer Solvation and Conformation. J Phys Chem B 2021; 125:5434-5442. [PMID: 33978411 DOI: 10.1021/acs.jpcb.1c02191] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Conformational transitions of flexible molecules, especially those driven by hydrophobic effects, tend to be hindered by desolvation barriers. For such transitions, it is thus important to characterize and understand the interplay between solvation and conformation. Using specialized molecular simulations, here we perform such a characterization for a hydrophobic polymer solvated in water. We find that an external potential, which unfavorably perturbs the polymer hydration waters, can trigger a coil-to-globule or collapse transition, and that the relative stabilities of the collapsed and extended states can be quantified by the strength of the requisite potential. Our results also provide mechanistic insights into the collapse transition, highlighting that the bottleneck to polymer collapse is the formation of a sufficiently large cluster, and the collective dewetting of such a cluster. We also study the collapse of the hydrophobic polymer in octane, a nonpolar solvent, and interestingly, we find that the mechanistic details of the transition are qualitatively similar to that in water.
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Affiliation(s)
- Debdas Dhabal
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Zhitong Jiang
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Akash Pallath
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Amish J Patel
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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12
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Monroe J, Barry M, DeStefano A, Aydogan Gokturk P, Jiao S, Robinson-Brown D, Webber T, Crumlin EJ, Han S, Shell MS. Water Structure and Properties at Hydrophilic and Hydrophobic Surfaces. Annu Rev Chem Biomol Eng 2020; 11:523-557. [PMID: 32169001 DOI: 10.1146/annurev-chembioeng-120919-114657] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The properties of water on both molecular and macroscopic surfaces critically influence a wide range of physical behaviors, with applications spanning from membrane science to catalysis to protein engineering. Yet, our current understanding of water interfacing molecular and material surfaces is incomplete, in part because measurement of water structure and molecular-scale properties challenges even the most advanced experimental characterization techniques and computational approaches. This review highlights progress in the ongoing development of tools working to answer fundamental questions on the principles that govern the interactions between water and surfaces. One outstanding and critical question is what universal molecular signatures capture the hydrophobicity of different surfaces in an operationally meaningful way, since traditional macroscopic hydrophobicity measures like contact angles fail to capture even basic properties of molecular or extended surfaces with any heterogeneity at the nanometer length scale. Resolving this grand challenge will require close interactions between state-of-the-art experiments, simulations, and theory, spanning research groups and using agreed-upon model systems, to synthesize an integrated knowledge of solvation water structure, dynamics, and thermodynamics.
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Affiliation(s)
- Jacob Monroe
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
| | - Mikayla Barry
- Department of Materials, University of California, Santa Barbara, California 93106, USA
| | - Audra DeStefano
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
| | - Pinar Aydogan Gokturk
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Sally Jiao
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
| | - Dennis Robinson-Brown
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
| | - Thomas Webber
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
| | - Ethan J Crumlin
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Songi Han
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA; .,Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
| | - M Scott Shell
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
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13
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Yadav HOS, Kuo AT, Urata S, Shinoda W. Effects of Packing Density and Chain Length on the Surface Hydrophobicity of Thin Films Composed of Perfluoroalkyl Acrylate Chains: A Molecular Dynamics Study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:14316-14323. [PMID: 31596100 DOI: 10.1021/acs.langmuir.9b02656] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A good understanding of the surface hydrophobicity of fluorinated materials is useful for their application as coating materials. The present study investigates the surface hydrophobicity of perfluoroalkyl acrylate (PFA) thin films using molecular dynamics simulations. Surface hydrophobicity is characterized by examining the contact angle of a water droplet on PFA surfaces and the cavity formation free energy in the vicinity of the surface. It is found that the calculated microscopic contact angles are in good agreement with the experimental results and partially capture the difference in the hydrophobicity of the surface arising from the variation of packing density and side chain length of PFA. The variations of cavity formation free energy in the vicinity of the surface elucidate that the surface hydrophobicity is mainly governed by the packing density rather than the chain length of PFA. The hydrophobicity generally increases with decreasing the packing density to some extent and then turns to decrease as further reducing the packing density. At higher packing density, the surface hydrophobicity slightly decreases with increasing the chain length, while at the lower packing density, the surface hydrophobicity is increased when chain length of PFA is longer than six carbons. Furthermore, we found that the influence of packing density on the surface hydrophobicity is directly related to the variation of the surface roughness and chain flexibility, that is, the surface hydrophobicity increases with increase in the surface roughness, while the chain flexibility plays a secondary role in the enhancement by affecting the stability of water staying near the interface. The study provides a significant insight into the local hydrophobicity and microscopic structure of the PFA surfaces, which would be useful for the application of surface modification.
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Affiliation(s)
- Hari O S Yadav
- Department of Materials Chemistry , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8603 , Japan
| | - An-Tsung Kuo
- Innovative Technology Laboratories , AGC Inc. , Yokohama , Kanagawa 230-0045 , Japan
| | - Shingo Urata
- Innovative Technology Laboratories , AGC Inc. , Yokohama , Kanagawa 230-0045 , Japan
| | - Wataru Shinoda
- Department of Materials Chemistry , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8603 , Japan
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14
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Heyden M. Heterogeneity of water structure and dynamics at the protein-water interface. J Chem Phys 2019; 150:094701. [PMID: 30849897 DOI: 10.1063/1.5081739] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
In this molecular dynamics simulation study, we analyze the local structural and dynamic properties of water hydrating the protein ubiquitin on a spatial grid with 1 Å resolution. This allows for insights into the spatial distribution of water number densities, molecular orientations, translations, and rotations as a function of distance from the protein surface. Water molecule orientations follow a heterogeneous distribution with preferred local orientations of water dipoles and O-H bond vectors up to 10-15 Å distances from the protein, while local variations of the water number density converge to homogeneous bulk-like values within less than 8 Å. Interestingly, we find that the long-ranged orientational structure of water does not impact either the translational or rotational dynamics of water. Instead, heterogeneous distributions of local dynamical parameters and averaged dynamical retardation factors are only found close to the protein surface and follow a distance dependence comparable to heterogeneities in the local water number density. This study shows that the formation of nanodomains of preferred water orientations far from the protein does not significantly impact dynamical processes probed as a non-local average in most experiments.
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Affiliation(s)
- Matthias Heyden
- School of Molecular Sciences and Center for Biological Physics, Arizona State University, Tempe, Arizona 85287-1604, USA
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15
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Jiang Z, Remsing RC, Rego NB, Patel AJ. Characterizing Solvent Density Fluctuations in Dynamical Observation Volumes. J Phys Chem B 2019; 123:1650-1661. [PMID: 30682885 DOI: 10.1021/acs.jpcb.8b11423] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Hydrophobic effects drive diverse aqueous assemblies, such as micelle formation or protein folding, wherein the solvent plays an important role. Consequently, characterizing the free energetics of solvent density fluctuations can lead to important insights into these processes. Although techniques such as the indirect umbrella sampling (INDUS) method can be used to characterize solvent fluctuations in static observation volumes of various sizes and shapes, characterizing how the solvent mediates inherently dynamic processes, such as self-assembly or conformational change, remains a challenge. In this work, we generalize the INDUS method to facilitate the enhanced sampling of solvent fluctuations in dynamical observation volumes, whose positions and shapes can evolve. We illustrate the usefulness of this generalization by characterizing water density fluctuations in dynamical volumes pertaining to the hydration of flexible solutes, the assembly of small hydrophobes, and conformational transitions in a model peptide. We also use the method to probe the dynamics of hard spheres.
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Affiliation(s)
| | - Richard C Remsing
- Institute for Computational Molecular Science , Temple University , Philadelphia , Pennsylvania 19122 , United States
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16
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Rego NB, Xi E, Patel AJ. Protein Hydration Waters Are Susceptible to Unfavorable Perturbations. J Am Chem Soc 2019; 141:2080-2086. [DOI: 10.1021/jacs.8b11448] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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17
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Heyden M. Disassembling solvation free energies into local contributions—Toward a microscopic understanding of solvation processes. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1390] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Matthias Heyden
- School of Molecular Sciences Arizona State University Tempe Arizona
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18
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Xi E, Marks SM, Fialoke S, Patel AJ. Sparse sampling of water density fluctuations near liquid-vapor coexistence. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1457218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Erte Xi
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania , Philadelphia, PA, USA
| | - Sean M. Marks
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania , Philadelphia, PA, USA
| | - Suruchi Fialoke
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania , Philadelphia, PA, USA
| | - Amish J. Patel
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania , Philadelphia, PA, USA
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19
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Alvarado YJ, Ferrebuz A, Paz JL, Rodríguez-Lugo P, Restrepo J, Romero F, Fernández-Acuña J, Williams YO, Toro-Mendoza J. Surface Behavior of BSA/Water/Carbohydrate Systems from Molecular Polarizability Measurements. J Phys Chem B 2018; 122:4231-4238. [PMID: 29582658 DOI: 10.1021/acs.jpcb.7b11998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The effect of the presence of glucose and sucrose on the nonintrinsic contribution to partial molar volume ⟨Θ⟩ni of bovine serum albumin (BSA) is determined by means of static and dynamic electronic polarizability measurements. For that aim, a combined strategy based on high-resolution refractometry, high exactitude densitometry, and synchronous fluorescence spectroscopy is applied. Both static and dynamic mean electronic molecular polarizability values are found to be sensitive to the presence of glucose. In the case of sucrose, the polarizability of BSA is not appreciably affected. In fact, our results revealed that the electronic changes observed occurred without a modification of the native conformation of BSA. On the contrary, a nonmonotonous behavior with the concentration is observed in presence of glucose. These results advocate the influence of the electronic polarization on the repulsive and attractive protein-carbohydrate interactions. An analysis using the scaled particle theory indicates that the accumulation of glucose on the protein surface promotes dehydration. Inversely, hydration and preferential exclusion occur in the vicinity of the protein surface for sucrose-enriched systems.
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Affiliation(s)
| | | | - Jose Luis Paz
- Departamento de Física , Escuela Politécnica Nacional , Ladron de Guevara , Quito 170517 , Ecuador
| | - Patricia Rodríguez-Lugo
- Laboratorio de Electrónica Molecular, Facultad Experimental de Ciencias, Departamento de Química , Universidad del Zulia , Maracaibo 4001 , Venezuela
| | | | - Freddy Romero
- Center for Translational Medicine and Korman Lung Center , Thomas Jefferson University , Philadelphia , Pennsylvania 19107 , United States
| | - Jaqueline Fernández-Acuña
- Centro de Estudios Interdisciplinarios de la Física , Instituto Venezolano de Investigaciones Científicas (IVIC) , Caracas 1020A , Venezuela
| | - Yhan O'Neil Williams
- Centro de Estudios Interdisciplinarios de la Física , Instituto Venezolano de Investigaciones Científicas (IVIC) , Caracas 1020A , Venezuela
| | - Jhoan Toro-Mendoza
- Centro de Estudios Interdisciplinarios de la Física , Instituto Venezolano de Investigaciones Científicas (IVIC) , Caracas 1020A , Venezuela
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20
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Wei Q, Zhao W, Yang Y, Cui B, Xu Z, Yang X. Method Evaluations for Adsorption Free Energy Calculations at the Solid/Water Interface through Metadynamics, Umbrella Sampling, and Jarzynski's Equality. Chemphyschem 2018; 19:690-702. [DOI: 10.1002/cphc.201701241] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 12/18/2017] [Indexed: 12/18/2022]
Affiliation(s)
- Qichao Wei
- College of Chemical Engineering; State Key Laboratory of Materials-Oriented Chemical Engineering; Nanjing Tech University; Nanjing 210009 P.R. China
| | - Weilong Zhao
- Department of Polymer Science; University of Akron; Akron OH 44325-3909 USA
| | - Yang Yang
- Department of Chemistry; Haverford College; Haverford PA 19041 USA
| | - Beiliang Cui
- Network Information Center; Nanjing Tech University; Nanjing 210009 P.R. China
| | - Zhijun Xu
- College of Chemical Engineering; State Key Laboratory of Materials-Oriented Chemical Engineering; Nanjing Tech University; Nanjing 210009 P.R. China
| | - Xiaoning Yang
- College of Chemical Engineering; State Key Laboratory of Materials-Oriented Chemical Engineering; Nanjing Tech University; Nanjing 210009 P.R. China
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21
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Remsing RC, Xi E, Patel AJ. Protein Hydration Thermodynamics: The Influence of Flexibility and Salt on Hydrophobin II Hydration. J Phys Chem B 2018; 122:3635-3646. [DOI: 10.1021/acs.jpcb.7b12060] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Richard C. Remsing
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Erte Xi
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Amish J. Patel
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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22
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Pantawane S, Bandyopadhyay D, Choudhury N. Generic Mechanism for Pattern Formation in the Solvation Shells of Buckminsterfullerene. ACS OMEGA 2018; 3:1060-1068. [PMID: 31457948 PMCID: PMC6641439 DOI: 10.1021/acsomega.7b01858] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 01/16/2018] [Indexed: 06/10/2023]
Abstract
Accurate description of solvation structure of a hydrophobic nanomaterial is of immense importance to understand protein folding, molecular recognition, drug binding, and many related phenomena. Moreover, spontaneous pattern formation through self-organization of solvent molecules around a nanoscopic solute is fascinating and useful in making template-directed nanostructures of desired morphologies. Recently, it has been shown using polarizable atomistic models that the hydration shell of a buckminsterfullerene can have atomically resolved ordered structure, in which C60 atomic arrangement is imprinted. In analyzing any peculiar behavior of water, traditionally, emphasis has been placed on the long-ranged and orientation-dependent interactions in it. Here, we show through molecular dynamics simulation that the patterned solvation layer with the imprints of the hydrophobic surface atoms of the buckminsterfullerene can be obtained from a completely different mechanism arising from a spherically symmetric, short-ranged interaction having two characteristic lengthscales. The nature of the pattern can be modified by adjusting solvent density or pressure. Although solute-solvent dispersion interaction is the key to such pattern formation adjacent to the solute surface, the ordering at longer lengthscale is a consequence of mutual influence of short-range correlations among successive layers. The present study thus demonstrates that the formation of such patterned solvation shells around the buckminsterfullerene is not restricted to water, but encompasses a large class of anomalous fluids represented by two-lengthscale potential.
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Affiliation(s)
- Sanwardhini Pantawane
- Theoretical
Chemistry Section and Heavy water Division, Bhabha
Atomic Research Centre, Mumbai 400085, India
| | - Dibyendu Bandyopadhyay
- Theoretical
Chemistry Section and Heavy water Division, Bhabha
Atomic Research Centre, Mumbai 400085, India
| | - Niharendu Choudhury
- Theoretical
Chemistry Section and Heavy water Division, Bhabha
Atomic Research Centre, Mumbai 400085, India
- Homi
Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
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23
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van der Vegt NFA, Nayar D. The Hydrophobic Effect and the Role of Cosolvents. J Phys Chem B 2017; 121:9986-9998. [DOI: 10.1021/acs.jpcb.7b06453] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Nico F. A. van der Vegt
- Eduard-Zintl-Institut für
Anorganische und Physikalische Chemie, Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, 64287 Darmstadt, Germany
| | - Divya Nayar
- Eduard-Zintl-Institut für
Anorganische und Physikalische Chemie, Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, 64287 Darmstadt, Germany
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24
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Galib M, Duignan TT, Misteli Y, Baer MD, Schenter GK, Hutter J, Mundy CJ. Mass density fluctuations in quantum and classical descriptions of liquid water. J Chem Phys 2017; 146:244501. [DOI: 10.1063/1.4986284] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Mirza Galib
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Timothy T. Duignan
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Yannick Misteli
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Marcel D. Baer
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Gregory K. Schenter
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Jürg Hutter
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Christopher J. Mundy
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
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25
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Weiß RG, Setny P, Dzubiella J. Principles for Tuning Hydrophobic Ligand–Receptor Binding Kinetics. J Chem Theory Comput 2017; 13:3012-3019. [DOI: 10.1021/acs.jctc.7b00216] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- R. Gregor Weiß
- Institut
für Physik, Humboldt-Universität zu Berlin, Newtonstr. 15, D-12489 Berlin, Germany
- Institut
für Weiche Materie and Funktionale Materialen, Helmholtz-Zentrum Berlin, Hahn-Meitner Platz 1, D-14109 Berlin, Germany
| | - Piotr Setny
- Centre
of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Joachim Dzubiella
- Institut
für Physik, Humboldt-Universität zu Berlin, Newtonstr. 15, D-12489 Berlin, Germany
- Institut
für Weiche Materie and Funktionale Materialen, Helmholtz-Zentrum Berlin, Hahn-Meitner Platz 1, D-14109 Berlin, Germany
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26
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Starek G, Freites JA, Bernèche S, Tobias DJ. Gating energetics of a voltage-dependent K + channel pore domain. J Comput Chem 2017; 38:1472-1478. [PMID: 28211063 DOI: 10.1002/jcc.24742] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 01/03/2017] [Accepted: 01/05/2017] [Indexed: 01/14/2023]
Abstract
We used targeted molecular dynamics, informed by experimentally determined inter-atomic distances defining the pore region of open and closed states of the KvAP voltage-gated potassium channel, to generate a gating pathway of the pore domain in the absence of the voltage-sensing domains. We then performed umbrella sampling simulations along this pathway to calculate a potential of mean force that describes the free energy landscape connecting the closed and open conformations of the pore domain. The resulting energetic landscape displays three minima, corresponding to stable open, closed, and intermediate conformations with roughly similar stabilities. We found that the extent of hydration of the interior of the pore domain could influence the free energy landscape for pore opening/closing. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Greg Starek
- Swiss Institute of Bioinformatics and Biozentrum, University of Basel, Klingelbergstrasse 50/70, Basel, CH-4056, Switzerland.,Department of Chemistry, University of California, Irvine, California, 92697-2025
| | - J Alfredo Freites
- Department of Chemistry, University of California, Irvine, California, 92697-2025
| | - Simon Bernèche
- Swiss Institute of Bioinformatics and Biozentrum, University of Basel, Klingelbergstrasse 50/70, Basel, CH-4056, Switzerland
| | - Douglas J Tobias
- Department of Chemistry, University of California, Irvine, California, 92697-2025
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27
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Colloidal crystals with diamond symmetry at optical lengthscales. Nat Commun 2017; 8:14173. [PMID: 28194025 PMCID: PMC5316806 DOI: 10.1038/ncomms14173] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 12/05/2016] [Indexed: 11/08/2022] Open
Abstract
Future optical materials promise to do for photonics what semiconductors did for electronics, but the challenge has long been in creating the structure they require—a regular, three-dimensional array of transparent microspheres arranged like the atoms in a diamond crystal. Here we demonstrate a simple approach for spontaneously growing double-diamond (or B32) crystals that contain a suitable diamond structure, using DNA to direct the self-assembly process. While diamond symmetry crystals have been grown from much smaller nanoparticles, none of those previous methods suffice for the larger particles needed for photonic applications, whose size must be comparable to the wavelength of visible light. Intriguingly, the crystals we observe do not readily form in previously validated simulations; nor have they been predicted theoretically. This finding suggests that other unexpected microstructures may be accessible using this approach and bodes well for future efforts to inexpensively mass-produce metamaterials for an array of photonic applications. Colloidal crystals arranged in a diamond lattice are desirable for photonic applications, yet are challenging to create. Here, Wang et al. show the self-assembly of a binary system composed of two interlocked diamond structures with lattice spacing comparable to the wavelength of visible light.
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28
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Zanjani MB, Jenkins IC, Crocker JC, Sinno T. Colloidal Cluster Assembly into Ordered Superstructures via Engineered Directional Binding. ACS NANO 2016; 10:11280-11289. [PMID: 27936578 DOI: 10.1021/acsnano.6b06415] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Recent experimental studies have demonstrated a facile route for fabricating large numbers of geometrically uniform colloidal clusters out of submicron DNA-functionalized spheres. These clusters are ideally suited for use as anisotropic building blocks for hierarchical assembly of superstructures with symmetries that are otherwise inaccessible with simple spherical particles. We study computationally the self-assembly of cubic, tetrahedral, and octahedral clusters mediated by "bond spheres" that dock with the clusters at specific preferential sites, providing robust and well-defined directional bonding. We analyze the assembly process with a combination of direct molecular dynamics simulations of superstructure growth and state-of-the-art umbrella sampling techniques to compute nucleation free energy profiles. The simulations confirm the versatility and robustness of hierarchical cluster assembly but also reveal potential obstacles in the form of energetically accessible defect states. We find and study solutions for bypassing these defects that rely on appropriate selection of particle size and interparticle interaction as a function of building block shape and, therefore, provide operational guidelines for future experimental demonstrations.
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Affiliation(s)
- Mehdi B Zanjani
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Ian C Jenkins
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - John C Crocker
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Talid Sinno
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
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29
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Gianti E, Delemotte L, Klein ML, Carnevale V. On the role of water density fluctuations in the inhibition of a proton channel. Proc Natl Acad Sci U S A 2016; 113:E8359-E8368. [PMID: 27956641 PMCID: PMC5206518 DOI: 10.1073/pnas.1609964114] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Hv1 is a transmembrane four-helix bundle that transports protons in a voltage-controlled manner. Its crucial role in many pathological conditions, including cancer and ischemic brain damage, makes Hv1 a promising drug target. Starting from the recently solved crystal structure of Hv1, we used structural modeling and molecular dynamics simulations to characterize the channel's most relevant conformations along the activation cycle. We then performed computational docking of known Hv1 inhibitors, 2-guanidinobenzimidazole (2GBI) and analogs. Although salt-bridge patterns and electrostatic potential profiles are well-defined and distinctive features of activated versus nonactivated states, the water distribution along the channel lumen is dynamic and reflects a conformational heterogeneity inherent to each state. In fact, pore waters assemble into intermittent hydrogen-bonded clusters that are replaced by the inhibitor moieties upon ligand binding. The entropic gain resulting from releasing these conformationally restrained waters to the bulk solvent is likely a major contributor to the binding free energy. Accordingly, we mapped the water density fluctuations inside the pore of the channel and identified the regions of maximum fluctuation within putative binding sites. Two sites appear as outstanding: One is the already known binding pocket of 2GBI, which is accessible to ligands from the intracellular side; the other is a site located at the exit of the proton permeation pathway. Our analysis of the waters confined in the hydrophobic cavities of Hv1 suggests a general strategy for drug discovery that can be applied to any ion channel.
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Affiliation(s)
- Eleonora Gianti
- Institute for Computational Molecular Science, Department of Chemistry, Temple University, Philadelphia, PA 19122
| | - Lucie Delemotte
- Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Michael L Klein
- Institute for Computational Molecular Science, Department of Chemistry, Temple University, Philadelphia, PA 19122;
| | - Vincenzo Carnevale
- Institute for Computational Molecular Science, Department of Chemistry, Temple University, Philadelphia, PA 19122;
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