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Oh H, Tu YM, Samineni L, De Respino S, Mehrafrooz B, Joshi H, Massenburg L, Lopez-Marques H, Elessawy N, Song W, Behera H, Dhiman R, Boorla VS, Kher K, Lin YC, Maranas C, Aksimentiev A, D Freeman B, Kumar M. Dehydrated Biomimetic Membranes with Skinlike Structure and Function. ACS APPLIED MATERIALS & INTERFACES 2024. [PMID: 38598825 DOI: 10.1021/acsami.3c19572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
Novel vapor-permeable materials are sought after for applications in protective wear, energy generation, and water treatment. Current impermeable protective materials effectively block harmful agents but trap heat due to poor water vapor transfer. Here we present a new class of materials, vapor permeable dehydrated nanoporous biomimetic membranes (DBMs), based on channel proteins. This application for biomimetic membranes is unexpected as channel proteins and biomimetic membranes were assumed to be unstable under dry conditions. DBMs mimic human skin's structure to offer both high vapor transport and small molecule exclusion under dry conditions. DBMs feature highly organized pores resembling sweat pores in human skin, but at super high densities (>1012 pores/cm2). These DBMs achieved exceptional water vapor transport rates, surpassing commercial breathable fabrics by up to 6.2 times, despite containing >2 orders of magnitude smaller pores (1 nm vs >700 nm). These DBMs effectively excluded model biological agents and harmful chemicals both in liquid and vapor phases, again in contrast with the commercial breathable fabrics. Remarkably, while hydrated biomimetic membranes were highly permeable to liquid water, they exhibited higher water resistances after dehydration at values >38 times that of commercial breathable fabrics. Molecular dynamics simulations support our hypothesis that dehydration induced protein hydrophobicity increases which enhanced DBM performance. DBMs hold promise for various applications, including membrane distillation, dehumidification, and protective barriers for atmospheric water harvesting materials.
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Affiliation(s)
- Hyeonji Oh
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Yu-Ming Tu
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Laximicharan Samineni
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Sophie De Respino
- Maseeh Department of Civil, Architectural and Environmental Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Behzad Mehrafrooz
- Center for Biophysics and Quantitative Biology, The University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Physics and Beckman Institute for Advanced Science and Technology, The University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Himanshu Joshi
- Department of Biotechnology, Indian Institute of Technology, Hyderabad 502285, India
| | - Lynnicia Massenburg
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Horacio Lopez-Marques
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Nada Elessawy
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Woochul Song
- Division of Environmental Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea
| | - Harekrushna Behera
- Maseeh Department of Civil, Architectural and Environmental Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Raman Dhiman
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Veda Sheersh Boorla
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Kartik Kher
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Yi-Chih Lin
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Costas Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Aleksei Aksimentiev
- Center for Biophysics and Quantitative Biology, The University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Physics and Beckman Institute for Advanced Science and Technology, The University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Benny D Freeman
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Manish Kumar
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
- Maseeh Department of Civil, Architectural and Environmental Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
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Deng H, Luo Z, Imbrogno J, Swenson TM, Jiang Z, Wang X, Zhang S. Machine Learning Guided Polyamide Membrane with Exceptional Solute-Solute Selectivity and Permeance. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:17841-17850. [PMID: 36576929 DOI: 10.1021/acs.est.2c05571] [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: 06/17/2023]
Abstract
Designing polymeric membranes with high solute-solute selectivity and permeance is important but technically challenging. Existing industrial interfacial polymerization (IP) process to fabricate polyamide-based polymeric membranes is largely empirical, which requires enormous trial-and-error experimentations to identify optimal fabrication conditions from a wide candidate space for separating a given solute pair. Herein, we developed a novel multitask machine learning (ML) model based on an artificial neural network (ANN) with skip connections and selectivity regularization to guide the design of polyamide membranes. We used limited sets of lab-collected data to obtain satisfactory model performance over four iterations by introducing human expert experience in the online learning process. Four membranes under fabrication conditions guided by the model exceeded the present upper bound for mono/divalent ion selectivity and permeance of the polymeric membranes. Moreover, we obtained new mechanistic insights into the membrane design through feature analysis of the model. Our work demonstrates a ML approach that represents a paradigm shift for high-performance polymeric membranes design.
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Affiliation(s)
- Hao Deng
- Department Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University, Binhai New City, Fuzhou350207, China
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore117576, Singapore
| | - Zhiyao Luo
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore117576, Singapore
| | - Joe Imbrogno
- Pfizer Inc., 235 East 42nd Street, New York, New York10017, United States
| | - Tim M Swenson
- Pfizer Inc., 235 East 42nd Street, New York, New York10017, United States
| | - Zhongyi Jiang
- Department Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University, Binhai New City, Fuzhou350207, China
| | - Xiaonan Wang
- Department of Chemical Engineering, Tsinghua University, Beijing100084, China
| | - Sui Zhang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore117576, Singapore
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3
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Bodrenko I, Ceccarelli M, Acosta-Gutierrez S. The mechanism of an electrostatic nanofilter: overcoming entropy with electrostatics. Phys Chem Chem Phys 2023; 25:26497-26506. [PMID: 37772905 DOI: 10.1039/d3cp02895j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
General porins are nature's sieving machinery in the outer membrane of Gram-negative bacteria. Their unique hourglass-shaped architecture is highly conserved among different bacterial membrane proteins and other biological channels. These biological nanopores have been designed to protect the interior of the bacterial cell from leakage of toxic compounds while selectively allowing the entry of the molecules needed for cell growth and function. The mechanism of transport through porins is of utmost and direct interest for drug discovery, extending toward nanotechnology applications for blue energy, separations, and sequencing. Here we present a theoretical framework for analysing the filter of general porins in relation to translocating molecules with the aid of enhanced molecular simulations quantitatively. Using different electrostatic probes in the form of a series of related molecules, we describe the nature of this filter and how to finely tune permeability by exploiting electrostatic interactions between the pore and the translocating molecule. Eventually, we show how enhanced simulations constitute today a valid tool for characterising the mechanism and quantifying energetically the transport of molecules through nanopores.
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Affiliation(s)
- Igor Bodrenko
- École Normale Supérieure, Département de Chimie - Laboratoire PASTEUR, Paris, France
- CNR-IOM, Sezione di Cagliari, Cittadella Universitaria di Monserrato, S.P.8 - km 0.700, 09042 Monserrato (CA), Italy
| | - Matteo Ceccarelli
- CNR-IOM, Sezione di Cagliari, Cittadella Universitaria di Monserrato, S.P.8 - km 0.700, 09042 Monserrato (CA), Italy
- Department of Physics, University of Cagliari, Cittadella Universitaria di Monserrato, S.P.8 - km 0.700, 09042 Monserrato (CA), Italy.
| | - Silvia Acosta-Gutierrez
- Institute for Bioengineering of Catalonia, Carrer Baldiri Reixac 10-12, 080028 Barcelona, Spain.
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4
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Samineni L, Acharya B, Behera H, Oh H, Kumar M, Chowdhury R. Protein engineering of pores for separation, sensing, and sequencing. Cell Syst 2023; 14:676-691. [PMID: 37591205 DOI: 10.1016/j.cels.2023.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/13/2023] [Accepted: 07/19/2023] [Indexed: 08/19/2023]
Abstract
Proteins are critical to cellular function and survival. They are complex molecules with precise structures and chemistries, which allow them to serve diverse functions for maintaining overall cell homeostasis. Since the discovery of the first enzyme in 1833, a gamut of advanced experimental and computational tools has been developed and deployed for understanding protein structure and function. Recent studies have demonstrated the ability to redesign/alter natural proteins for applications in industrial processes of interest and to make customized, novel synthetic proteins in the laboratory through protein engineering. We comprehensively review the successes in engineering pore-forming proteins and correlate the amino acid-level biochemistry of different pore modification strategies to the intended applications limited to nucleotide/peptide sequencing, single-molecule sensing, and precise molecular separations.
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Affiliation(s)
- Laxmicharan Samineni
- Department of Civil, Architectural and Environmental Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Bibek Acharya
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50011, USA
| | - Harekrushna Behera
- Department of Civil, Architectural and Environmental Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Hyeonji Oh
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Manish Kumar
- Department of Civil, Architectural and Environmental Engineering, University of Texas at Austin, Austin, TX 78712, USA; McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Ratul Chowdhury
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50011, USA.
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5
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Fei J, Wang Y, Cheng H, Wang H, Wu M, Sun F, Sun C. An Aquaporin Gene ( KoPIP2;1) Isolated from Mangrove Plant Kandelia obovata Had Enhanced Cold Tolerance of Transgenic Arabidopsis thaliana. Bioengineering (Basel) 2023; 10:878. [PMID: 37508905 PMCID: PMC10376877 DOI: 10.3390/bioengineering10070878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/20/2023] [Accepted: 07/22/2023] [Indexed: 07/30/2023] Open
Abstract
Aquaporins (AQPs) are essential channel proteins that play central roles in maintaining water homeostasis. Here, a novel aquaporin gene, named KoPIP2;1, was cloned from the mangrove plant Kandelia obovata by RACE technology. The KoPIP2;1 gene was 1404 bp in length with an open reading frame (ORF) of 852 bp, encoded with 283 amino acids. Database comparisons revealed that KoPIP2;1 protein shared the highest identity (91.26%) with the aquaporin HbPIP2;2, which was isolated from Hevea brasiliensis. Gene expression analysis revealed that the KoPIP2;1 gene was induced higher in leaves than in stems and roots of K. obovata under cold stress. Transient expression of KoPIP2;1 in Nicotiana benthamiana epidermal cells revealed that the KoPIP2;1 protein was localized to the plasma membrane. Overexpressing KoPIP2;1 in Arabidopsis significantly enhanced the lateral root number of the transgenic lines. KoPIP2;1 transgenic Arabidopsis demonstrated better growth, elevated proline content, increased superoxide dismutase (SOD) and peroxidase (POD) activities, and reduced malondialdehyde (MDA) content compared with the wild-type Arabidopsis when exposed to cold stress. The findings suggest that overexpression of KoPIP2;1 probably conferred cold tolerance of transgenic Arabidopsis by enhancing osmoregulation and antioxidant capacity. This present data presents a valuable gene resource that contributes to the advancement of our understanding of aquaporins and their potential application in enhancing plant stress tolerance.
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Affiliation(s)
- Jiao Fei
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Youshao Wang
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Hao Cheng
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Hui Wang
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Meilin Wu
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Fulin Sun
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Cuici Sun
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China
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6
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Recent progress in the synthesis of advanced biofuel and bioproducts. Curr Opin Biotechnol 2023; 80:102913. [PMID: 36854202 DOI: 10.1016/j.copbio.2023.102913] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/20/2023] [Accepted: 01/30/2023] [Indexed: 02/27/2023]
Abstract
Energy is one of the most complex fields of study and an issue that influences nearly every aspect of modern life. Over the past century, combustion of fossil fuels, particularly in the transportation sector, has been the dominant form of energy release. Refining of petroleum and natural gas into liquid transportation fuels is also the centerpiece of the modern chemical industry used to produce materials, solvents, and other consumer goods. In the face of global climate change, the world is searching for alternative, sustainable means of producing energy carriers and chemical building blocks. The use of biofuels in engines predates modern refinery optimization and today represents a small but significant fraction of liquid transportation fuels burnt each year. Similarly, white biotechnology has been used to produce many natural products through fermentation. The evolution of recombinant DNA technology into modern synthetic biology has expanded the scope of biofuels and bioproducts that can be made by biocatalysts. This opinion examines the current trends in this research space, highlighting the substantial growth in computational tools and the growing influence of renewable electricity in the design of metabolic engineering strategies. In short, advanced biofuel and bioproduct synthesis remains a vibrant and critically important field of study whose focus is shifting away from the conversion of lignocellulosic biomass toward a broader consideration of how to reduce carbon dioxide to fuels and chemical products.
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7
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Biophysical quantification of unitary solute and solvent permeabilities to enable translation to membrane science. J Memb Sci 2022. [DOI: 10.1016/j.memsci.2022.121308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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8
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Shefer I, Lopez K, Straub AP, Epsztein R. Applying Transition-State Theory to Explore Transport and Selectivity in Salt-Rejecting Membranes: A Critical Review. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:7467-7483. [PMID: 35549171 DOI: 10.1021/acs.est.2c00912] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Membrane technologies using reverse osmosis (RO) and nanofiltration (NF) have been widely implemented in water purification and desalination processes. Separation between species at the molecular level is achievable in RO and NF membranes due to a complex and poorly understood combination of transport mechanisms that have attracted the attention of researchers within and beyond the membrane community for many years. Minimizing existing knowledge gaps in transport through these membranes can improve the sustainability of current water-treatment processes and expand the use of RO and NF membranes to other applications that require high selectivity between species. Since its establishment in 1949, and with growing popularity in recent years, Eyring's transition-state theory (TST) for transmembrane permeation has been applied in numerous studies to mechanistically explore molecular transport in membranes including RO and NF. In this review, we critically assess TST applied to transmembrane permeation in salt-rejecting membranes, focusing on mechanistic insights into transport under confinement that can be gained from this framework and the key limitations associated with the method. We first demonstrate and discuss the limited ability of the commonly used solution-diffusion model to mechanistically explain transport and selectivity trends observed in RO and NF membranes. Next, we review important milestones in the development of TST, introduce its underlying principles and equations, and establish the connection to transmembrane permeation with a focus on molecular-level enthalpic and entropic barriers that govern water and solute transport under confinement. We then critically review the application of TST to explore transport in RO and NF membranes, analyzing trends in measured enthalpic and entropic barriers and synthesizing new data to highlight important phenomena associated with the temperature-dependent measurement of the activation parameters. We also discuss major limitations of the experimental application of TST and propose specific solutions to minimize the uncertainties surrounding the current approach. We conclude with identifying future research needs to enhance the implementation and maximize the benefit of TST application to transmembrane permeation.
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Affiliation(s)
- Idit Shefer
- Faculty of Civil and Environmental Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Kian Lopez
- Department of Civil, Environmental and Architectural Engineering, University of Colorado Boulder, Boulder, Colorado 80309-0428, United States
| | - Anthony P Straub
- Department of Civil, Environmental and Architectural Engineering, University of Colorado Boulder, Boulder, Colorado 80309-0428, United States
| | - Razi Epsztein
- Faculty of Civil and Environmental Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel
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9
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Acharya A, Prajapati JD, Kleinekathöfer U. Atomistic Simulation of Molecules Interacting with Biological Nanopores: From Current Understanding to Future Directions. J Phys Chem B 2022; 126:3995-4008. [PMID: 35616602 DOI: 10.1021/acs.jpcb.2c01173] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biological nanopores have been at the focus of numerous studies due to their role in many biological processes as well as their (prospective) technological applications. Among many other topics, recent studies on nanopores have addressed two key areas: antibiotic permeation through bacterial channels and sensing of analytes. Although the two areas are quite far apart in terms of their objectives, in both cases atomistic simulations attempt to understand the solute dynamics and the solute-protein interactions within the channel lumen. While decades of studies on various channels have culminated in an improved understanding of the key molecular factors and led to practical applications in some cases, successful utilization is limited. In this Perspective we summarize recent progress in understanding key issues in molecular simulations of antibiotic translocation and in the development of nanopore sensors. Moreover, we comment on possible advancements in computational algorithms that can potentially resolve some of the issues.
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Affiliation(s)
- Abhishek Acharya
- Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany
| | | | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany
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10
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Lim YJ, Goh K, Wang R. The coming of age of water channels for separation membranes: from biological to biomimetic to synthetic. Chem Soc Rev 2022; 51:4537-4582. [PMID: 35575174 DOI: 10.1039/d1cs01061a] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Water channels are one of the key pillars driving the development of next-generation desalination and water treatment membranes. Over the past two decades, the rise of nanotechnology has brought together an abundance of multifunctional nanochannels that are poised to reinvent separation membranes with performances exceeding those of state-of-the-art polymeric membranes within the water-energy nexus. Today, these water nanochannels can be broadly categorized into biological, biomimetic and synthetic, owing to their different natures, physicochemical properties and methods for membrane nanoarchitectonics. Furthermore, against the backdrop of different separation mechanisms, different types of nanochannel exhibit unique merits and limitations, which determine their usability and suitability for different membrane designs. Herein, this review outlines the progress of a comprehensive amount of nanochannels, which include aquaporins, pillar[5]arenes, I-quartets, different types of nanotubes and their porins, graphene-based materials, metal- and covalent-organic frameworks, porous organic cages, MoS2, and MXenes, offering a comparative glimpse into where their potential lies. First, we map out the background by looking into the evolution of nanochannels over the years, before discussing their latest developments by focusing on the key physicochemical and intrinsic transport properties of these channels from the chemistry standpoint. Next, we put into perspective the fabrication methods that can nanoarchitecture water channels into high-performance nanochannel-enabled membranes, focusing especially on the distinct differences of each type of nanochannel and how they can be leveraged to unlock the as-promised high water transport potential in current mainstream membrane designs. Lastly, we critically evaluate recent findings to provide a holistic qualitative assessment of the nanochannels with respect to the attributes that are most strongly valued in membrane engineering, before discussing upcoming challenges to share our perspectives with researchers for pathing future directions in this coming of age of water channels.
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Affiliation(s)
- Yu Jie Lim
- Singapore Membrane Technology Center, Nanyang Environment and Water Research Institute, Nanyang Technological University, 637141, Singapore. .,School of Civil and Environmental Engineering, Nanyang Technological University, 639798, Singapore.,Interdisciplinary Graduate Programme, Graduate College, Nanyang Technological University, 637553, Singapore
| | - Kunli Goh
- Singapore Membrane Technology Center, Nanyang Environment and Water Research Institute, Nanyang Technological University, 637141, Singapore.
| | - Rong Wang
- Singapore Membrane Technology Center, Nanyang Environment and Water Research Institute, Nanyang Technological University, 637141, Singapore. .,School of Civil and Environmental Engineering, Nanyang Technological University, 639798, Singapore
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11
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Bodrenko IV, Milenkovic S, Ceccarelli M. Diffusion of molecules through nanopores under confinement: Time-scale bridging and crowding effects via Markov state model. Biomol Concepts 2022; 13:207-219. [PMID: 35417112 DOI: 10.1515/bmc-2022-0019] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/14/2022] [Indexed: 11/15/2022] Open
Abstract
Passive transport of molecules through nanopores is characterized by the interaction of molecules with pore internal walls and by a general crowding effect due to the constricted size of the nanopore itself, which limits the presence of molecules in its interior. The molecule-pore interaction is treated within the diffusion approximation by introducing the potential of mean force and the local diffusion coefficient for a correct statistical description. The crowding effect can be handled within the Markov state model approximation. By combining the two methods, one can deal with complex free energy surfaces taking into account crowding effects. We recapitulate the equations bridging the two models to calculate passive currents assuming a limited occupancy of the nanopore in a wide range of molecular concentrations. Several simple models are analyzed to clarify the consequences of the model. Eventually, a biologically relevant case of transport of an antibiotic molecule through a bacterial porin is used to draw conclusions (i) on the effects of crowding on transport of small molecules through biological channels, and (ii) to demonstrate its importance for modelling of cellular transport.
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Affiliation(s)
- Igor V Bodrenko
- CNR/IOM, Section of Cagliari, c/o Department of Physics, S.P. Monserrato-Sestu km 0.700, 09042 Monserrato, Italy.,Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Stefan Milenkovic
- CNR/IOM, Section of Cagliari, c/o Department of Physics, S.P. Monserrato-Sestu km 0.700, 09042 Monserrato, Italy
| | - Matteo Ceccarelli
- CNR/IOM, Section of Cagliari, c/o Department of Physics, S.P. Monserrato-Sestu km 0.700, 09042 Monserrato, Italy.,Department of Physics, University of Cagliari, S.P. Monserrato-Sestu km 0.700, 09042 Monserrato, Italy
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12
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Sun Y, Yi F, Li RH, Min X, Qin H, Cheng SQ, Liu Y. Inorganic-Organic Hybrid Membrane Based on Pillararene-Intercalated MXene Nanosheets for Efficient Water Purification. Angew Chem Int Ed Engl 2022; 61:e202200482. [PMID: 35099850 DOI: 10.1002/anie.202200482] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Indexed: 01/14/2023]
Abstract
Discharge of antibiotic-containing wastewater causes environmental pollution and threatens biological and human health. An efficient treatment method for this wastewater is urgently required. We prepared inorganic-organic hybrid MXene-pillararene nanosheets with a large lateral size (5-8 μm). The hybrid nanosheets were stacked on supports via vacuum-assisted filtration to prepare membranes with regular parallel slits and an interlayer spacing of 1.36 nm, which were used to purify antibiotic-containing water. Permeance through the membrane increased 100-fold compared with most polymeric and other two-dimensional nanofiltration membranes with similar rejection. This high permeance and rejection was attributed to the large lateral size of the nanosheets, regular interlayer spacing, and electrostatic interaction between the membrane and antibiotics. These membranes will broaden the applications of lamellar materials for the separation of high-value-added drugs in academia and industry.
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Affiliation(s)
- Yue Sun
- State Key Laboratory of Separation Membrane and Membrane Process, School of Chemistry, Tiangong University, 300387, Tianjin, China.,Hubei Key Laboratory of Catalysis and Materials Science, College of Chemistry and Material Sciences, South-Central University for Nationalities, 430074, Wuhan, China
| | - Fan Yi
- Hubei Key Laboratory of Catalysis and Materials Science, College of Chemistry and Material Sciences, South-Central University for Nationalities, 430074, Wuhan, China
| | - Run-Hao Li
- Hubei Key Laboratory of Catalysis and Materials Science, College of Chemistry and Material Sciences, South-Central University for Nationalities, 430074, Wuhan, China
| | - Xuehong Min
- Hubei Key Laboratory of Catalysis and Materials Science, College of Chemistry and Material Sciences, South-Central University for Nationalities, 430074, Wuhan, China
| | - Huan Qin
- Hubei Key Laboratory of Catalysis and Materials Science, College of Chemistry and Material Sciences, South-Central University for Nationalities, 430074, Wuhan, China
| | - Shi-Qi Cheng
- Hubei Key Laboratory of Catalysis and Materials Science, College of Chemistry and Material Sciences, South-Central University for Nationalities, 430074, Wuhan, China
| | - Yi Liu
- State Key Laboratory of Separation Membrane and Membrane Process, School of Chemistry, Tiangong University, 300387, Tianjin, China
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13
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Sun Y, Yi F, Li R, Min X, Qin H, Cheng S, Liu Y. Inorganic–Organic Hybrid Membrane Based on Pillararene‐Intercalated MXene Nanosheets for Efficient Water Purification. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202200482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yue Sun
- State Key Laboratory of Separation Membrane and Membrane Process School of Chemistry Tiangong University 300387 Tianjin China
- Hubei Key Laboratory of Catalysis and Materials Science College of Chemistry and Material Sciences South-Central University for Nationalities 430074 Wuhan China
| | - Fan Yi
- Hubei Key Laboratory of Catalysis and Materials Science College of Chemistry and Material Sciences South-Central University for Nationalities 430074 Wuhan China
| | - Run‐Hao Li
- Hubei Key Laboratory of Catalysis and Materials Science College of Chemistry and Material Sciences South-Central University for Nationalities 430074 Wuhan China
| | - Xuehong Min
- Hubei Key Laboratory of Catalysis and Materials Science College of Chemistry and Material Sciences South-Central University for Nationalities 430074 Wuhan China
| | - Huan Qin
- Hubei Key Laboratory of Catalysis and Materials Science College of Chemistry and Material Sciences South-Central University for Nationalities 430074 Wuhan China
| | - Shi‐Qi Cheng
- Hubei Key Laboratory of Catalysis and Materials Science College of Chemistry and Material Sciences South-Central University for Nationalities 430074 Wuhan China
| | - Yi Liu
- State Key Laboratory of Separation Membrane and Membrane Process School of Chemistry Tiangong University 300387 Tianjin China
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14
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The energetic barrier to single-file water flow through narrow channels. Biophys Rev 2022; 13:913-923. [PMID: 35035593 PMCID: PMC8724168 DOI: 10.1007/s12551-021-00875-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 10/26/2021] [Indexed: 10/30/2022] Open
Abstract
Various nanoscopic channels of roughly equal diameter and length facilitate single-file diffusion at vastly different rates. The underlying variance of the energetic barriers to transport is poorly understood. First, water partitioning into channels so narrow that individual molecules cannot overtake each other incurs an energetic penalty. Corresponding estimates vary widely depending on how the sacrifice of two out of four hydrogen bonds is accounted for. Second, entropy differences between luminal and bulk water may arise: additional degrees of freedom caused by dangling OH-bonds increase entropy. At the same time, long-range dipolar water interactions decrease entropy. Here, we dissect different contributions to Gibbs free energy of activation, ΔG ‡, for single-file water transport through narrow channels by analyzing experimental results from water permeability measurements on both bare lipid bilayers and biological water channels that (i) consider unstirred layer effects and (ii) adequately count the channels in reconstitution experiments. First, the functional relationship between water permeabilities and Arrhenius activation energies indicates negligible differences between the entropies of intraluminal water and bulk water. Second, we calculate ΔG ‡ from unitary water channel permeabilities using transition state theory. Plotting ΔG ‡ as a function of the number of H-bond donating or accepting pore-lining residues results in a 0.1 kcal/mol contribution per residue. The resulting upper limit for partial water dehydration amounts to 2 kcal/mol. In the framework of biomimicry, our analysis provides valuable insights for the design of synthetic water channels. It thus may aid in the urgent endeavor towards combating global water scarcity.
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15
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Lang C, Kumar M, Hickey RJ. Current status and future directions of self-assembled block copolymer membranes for molecular separations. SOFT MATTER 2021; 17:10405-10415. [PMID: 34768280 DOI: 10.1039/d1sm01368h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
One of the most efficient and promising separation alternatives to thermal methods such as distillation is the use of polymeric membranes that separate mixtures based on molecular size or chemical affinity. Self-assembled block copolymer membranes have gained considerable attention within the membrane field due to precise control over nanoscale structure, pore size, and chemical versatility. Despite the rapid progress and excitement, a significant hurdle in using block copolymer membranes for nanometer and sub-nanometer separations such as nanofiltration and reverse osmosis is the lower limit on domain size features. Strategies such as polymer post-functionalization, self-assembly of oligomers, liquid crystals, and random copolymers, or incorporation of artificial/natural channels within block copolymer materials are future directions with the potential to overcome current limitations with respect to separation size.
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Affiliation(s)
- Chao Lang
- South China Advanced Institute for Soft Matter Science and Technology, School of Molecular Science and Engineering, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, South China University of Technology, Guangzhou 510640, China
- Department of Materials Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania, 16801, USA.
| | - Manish Kumar
- Department of Civil, Architectural, and Environmental Engineering, The University of Texas at Austin, Austin, TX, 78712, USA.
| | - Robert J Hickey
- Department of Materials Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania, 16801, USA.
- Materials Research Institute, The Pennsylvania State University, University Park, Pennsylvania, 16801, USA
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16
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Roy A, Shen J, Joshi H, Song W, Tu YM, Chowdhury R, Ye R, Li N, Ren C, Kumar M, Aksimentiev A, Zeng H. Foldamer-based ultrapermeable and highly selective artificial water channels that exclude protons. NATURE NANOTECHNOLOGY 2021; 16:911-917. [PMID: 34017100 DOI: 10.1038/s41565-021-00915-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 04/06/2021] [Indexed: 06/12/2023]
Abstract
The outstanding capacity of aquaporins (AQPs) for mediating highly selective superfast water transport1-7 has inspired recent development of supramolecular monovalent ion-excluding artificial water channels (AWCs). AWC-based bioinspired membranes are proposed for desalination, water purification and other separation applications8-18. While some recent progress has been made in synthesizing AWCs that approach the water permeability and ion selectivity of AQPs, a hallmark feature of AQPs-high water transport while excluding protons-has not been reproduced. We report a class of biomimetic, helically folded pore-forming polymeric foldamers that can serve as long-sought-after highly selective ultrafast water-conducting channels with performance exceeding those of AQPs (1.1 × 1010 water molecules per second for AQP1), with high water-over-monovalent-ion transport selectivity (~108 water molecules over Cl- ion) conferred by the modularly tunable hydrophobicity of the interior pore surface. The best-performing AWC reported here delivers water transport at an exceptionally high rate, namely, 2.5 times that of AQP1, while concurrently rejecting salts (NaCl and KCl) and even protons.
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Affiliation(s)
- Arundhati Roy
- Department of Chemistry, College of Science, Hainan University, Haikou, Hainan, China
- NanoBio Lab, 31 Biopolis Way, The Nanos, Singapore
| | - Jie Shen
- Department of Chemistry, College of Science, Hainan University, Haikou, Hainan, China
| | - Himanshu Joshi
- Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Woochul Song
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Yu-Ming Tu
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Ratul Chowdhury
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Ruijuan Ye
- Department of Chemistry, College of Science, Hainan University, Haikou, Hainan, China
| | - Ning Li
- NanoBio Lab, 31 Biopolis Way, The Nanos, Singapore
| | | | - Manish Kumar
- Department of Civil, Architectural and Environmental Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Aleksei Aksimentiev
- Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Huaqiang Zeng
- Department of Chemistry, College of Science, Hainan University, Haikou, Hainan, China.
- Institute of Advanced Synthesis, Northwestern Polytechnical University, Xi'an, Shaanxi, China.
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17
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Madhavan A, Arun KB, Binod P, Sirohi R, Tarafdar A, Reshmy R, Kumar Awasthi M, Sindhu R. Design of novel enzyme biocatalysts for industrial bioprocess: Harnessing the power of protein engineering, high throughput screening and synthetic biology. BIORESOURCE TECHNOLOGY 2021; 325:124617. [PMID: 33450638 DOI: 10.1016/j.biortech.2020.124617] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/19/2020] [Accepted: 12/22/2020] [Indexed: 05/13/2023]
Abstract
Biocatalysts have wider applications in various industries. Biocatalysts are generating bigger attention among researchers due to their unique catalytic properties like activity, specificity and stability. However the industrial use of many enzymes is hindered by low catalytic efficiency and stability during industrial processes. Properties of enzymes can be altered by protein engineering. Protein engineers are increasingly study the structure-function characteristics, engineering attributes, design of computational tools for enzyme engineering, and functional screening processes to improve the design and applications of enzymes. The potent and innovative techniques of enzyme engineering deliver outstanding opportunities for tailoring industrially important enzymes for the versatile production of biochemicals. An overview of the current trends in enzyme engineering is explored with important representative examples.
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Affiliation(s)
- Aravind Madhavan
- Rajiv Gandhi Centre for Biotechnology, Trivandrum 695 014, India
| | - K B Arun
- Rajiv Gandhi Centre for Biotechnology, Trivandrum 695 014, India
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695 019, India
| | - Ranjna Sirohi
- The Center for Energy and Environmental Sustainability, Lucknow 226 010, Uttar Pradesh, India
| | - Ayon Tarafdar
- Division of Livestock Production and Management, ICAR - Indian Veterinary Research Institute, Izatnagar, Bareilly 243 122, Uttar Pradesh, India
| | - R Reshmy
- Post Graduate and Research Department of Chemistry, Bishop Moore College, Mavelikara 690 110, Kerala, India
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, North West A & F University, Yangling, Shaanxi 712 100, China
| | - Raveendran Sindhu
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695 019, India.
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18
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Tu YM, Samineni L, Ren T, Schantz AB, Song W, Sharma S, Kumar M. Prospective applications of nanometer-scale pore size biomimetic and bioinspired membranes. J Memb Sci 2021. [DOI: 10.1016/j.memsci.2020.118968] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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19
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Abstract
Protein engineering can yield new molecular tools for nanotechnology and therapeutic applications through modulating physiochemical and biological properties. Engineering membrane proteins is especially attractive because they perform key cellular processes including transport, nutrient uptake, removal of toxins, respiration, motility, and signaling. In this chapter, we describe two protocols for membrane protein engineering with the Rosetta software: (1) ΔΔG calculations for single point mutations and (2) sequence optimization in different membrane lipid compositions. These modular protocols are easily adaptable for more complex problems and serve as a foundation for efficient membrane protein engineering calculations.
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Affiliation(s)
- Rebecca F Alford
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jeffrey J Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA. .,Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, USA.
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20
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Zielinski DC, Patel A, Palsson BO. The Expanding Computational Toolbox for Engineering Microbial Phenotypes at the Genome Scale. Microorganisms 2020; 8:E2050. [PMID: 33371386 PMCID: PMC7767376 DOI: 10.3390/microorganisms8122050] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/07/2020] [Accepted: 12/16/2020] [Indexed: 02/06/2023] Open
Abstract
Microbial strains are being engineered for an increasingly diverse array of applications, from chemical production to human health. While traditional engineering disciplines are driven by predictive design tools, these tools have been difficult to build for biological design due to the complexity of biological systems and many unknowns of their quantitative behavior. However, due to many recent advances, the gap between design in biology and other engineering fields is closing. In this work, we discuss promising areas of development of computational tools for engineering microbial strains. We define five frontiers of active research: (1) Constraint-based modeling and metabolic network reconstruction, (2) Kinetics and thermodynamic modeling, (3) Protein structure analysis, (4) Genome sequence analysis, and (5) Regulatory network analysis. Experimental and machine learning drivers have enabled these methods to improve by leaps and bounds in both scope and accuracy. Modern strain design projects will require these tools to be comprehensively applied to the entire cell and efficiently integrated within a single workflow. We expect that these frontiers, enabled by the ongoing revolution of big data science, will drive forward more advanced and powerful strain engineering strategies.
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Affiliation(s)
- Daniel Craig Zielinski
- Department of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA; (D.C.Z.); (A.P.)
| | - Arjun Patel
- Department of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA; (D.C.Z.); (A.P.)
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA; (D.C.Z.); (A.P.)
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
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21
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Pritzl SD, Urban P, Prasselsperger A, Konrad DB, Frank JA, Trauner D, Lohmüller T. Photolipid Bilayer Permeability is Controlled by Transient Pore Formation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:13509-13515. [PMID: 33143416 DOI: 10.1021/acs.langmuir.0c02229] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Controlling the release or uptake of (bio-) molecules and drugs from liposomes is critically important for a range of applications in bioengineering, synthetic biology, and drug delivery. In this paper, we report how the reversible photoswitching of synthetic lipid bilayer membranes made from azobenzene-containing phosphatidylcholine (azo-PC) molecules (photolipids) leads to increased membrane permeability. We show that cell-sized, giant unilamellar vesicles (GUVs) prepared from photolipids display leakage of fluorescent dyes after irradiation with UV-A and visible light. Langmuir-Blodgett and patch-clamp measurements show that the permeability is the result of transient pore formation. By comparing the trans-to-cis and cis-to-trans isomerization process, we find that this pore formation is the result of area fluctuations and a change of the area cross-section between both photolipid isomers.
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Affiliation(s)
- Stefanie D Pritzl
- Chair for Photonics and Optoelectronics, Nano-Institute Munich, Department of Physics, Ludwig-Maximilians-Universität (LMU), Königinstraße 10, 80539 Munich, Germany
| | - Patrick Urban
- Chair for Photonics and Optoelectronics, Nano-Institute Munich, Department of Physics, Ludwig-Maximilians-Universität (LMU), Königinstraße 10, 80539 Munich, Germany
| | - Alexander Prasselsperger
- Chair for Photonics and Optoelectronics, Nano-Institute Munich, Department of Physics, Ludwig-Maximilians-Universität (LMU), Königinstraße 10, 80539 Munich, Germany
| | - David B Konrad
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377 Munich, Germany
- Department of Pharmacy, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377 Munich, Germany
| | - James A Frank
- Vollum Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - Dirk Trauner
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377 Munich, Germany
- Department of Chemistry, New York University, Silver Center, 100 Washington Square East, Room 712, New York 10003, United States
| | - Theobald Lohmüller
- Chair for Photonics and Optoelectronics, Nano-Institute Munich, Department of Physics, Ludwig-Maximilians-Universität (LMU), Königinstraße 10, 80539 Munich, Germany
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22
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Lynch C, Rao S, Sansom MSP. Water in Nanopores and Biological Channels: A Molecular Simulation Perspective. Chem Rev 2020; 120:10298-10335. [PMID: 32841020 PMCID: PMC7517714 DOI: 10.1021/acs.chemrev.9b00830] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Indexed: 12/18/2022]
Abstract
This Review explores the dynamic behavior of water within nanopores and biological channels in lipid bilayer membranes. We focus on molecular simulation studies, alongside selected structural and other experimental investigations. Structures of biological nanopores and channels are reviewed, emphasizing those high-resolution crystal structures, which reveal water molecules within the transmembrane pores, which can be used to aid the interpretation of simulation studies. Different levels of molecular simulations of water within nanopores are described, with a focus on molecular dynamics (MD). In particular, models of water for MD simulations are discussed in detail to provide an evaluation of their use in simulations of water in nanopores. Simulation studies of the behavior of water in idealized models of nanopores have revealed aspects of the organization and dynamics of nanoconfined water, including wetting/dewetting in narrow hydrophobic nanopores. A survey of simulation studies in a range of nonbiological nanopores is presented, including carbon nanotubes, synthetic nanopores, model peptide nanopores, track-etched nanopores in polymer membranes, and hydroxylated and functionalized nanoporous silica. These reveal a complex relationship between pore size/geometry, the nature of the pore lining, and rates of water transport. Wider nanopores with hydrophobic linings favor water flow whereas narrower hydrophobic pores may show dewetting. Simulation studies over the past decade of the behavior of water in a range of biological nanopores are described, including porins and β-barrel protein nanopores, aquaporins and related polar solute pores, and a number of different classes of ion channels. Water is shown to play a key role in proton transport in biological channels and in hydrophobic gating of ion channels. An overall picture emerges, whereby the behavior of water in a nanopore may be predicted as a function of its hydrophobicity and radius. This informs our understanding of the functions of diverse channel structures and will aid the design of novel nanopores. Thus, our current level of understanding allows for the design of a nanopore which promotes wetting over dewetting or vice versa. However, to design a novel nanopore, which enables fast, selective, and gated flow of water de novo would remain challenging, suggesting a need for further detailed simulations alongside experimental evaluation of more complex nanopore systems.
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Affiliation(s)
- Charlotte
I. Lynch
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Shanlin Rao
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
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23
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Chowdhury R, Grisewood MJ, Boorla VS, Yan Q, Pfleger BF, Maranas CD. IPRO+/-: Computational Protein Design Tool Allowing for Insertions and Deletions. Structure 2020; 28:1344-1357.e4. [PMID: 32857964 DOI: 10.1016/j.str.2020.08.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 07/01/2020] [Accepted: 08/07/2020] [Indexed: 12/30/2022]
Abstract
Insertions and deletions (indels) in protein sequences alter the residue spacing along the polypeptide backbone and consequently open up possibilities for tuning protein function in a way that is inaccessible by amino acid substitution alone. We describe an optimization-based computational protein redesign approach centered around predicting beneficial combinations of indels along with substitutions and also obtain putative substrate-docked structures for these protein variants. This modified algorithmic capability would be of interest for enzyme engineering and broadly inform other protein design tasks. We highlight this capability by (1) identifying active variants of a bacterial thioesterase enzyme ('TesA) with experimental corroboration, (2) recapitulating existing active TEM-1 β-Lactamase sequences of different sizes, and (3) identifying shorter 4-Coumarate:CoA ligases with enhanced in vitro activities toward non-native substrates. A separate PyRosetta-based open-source tool, Indel-Maker (http://www.maranasgroup.com/software.htm), has also been created to construct computational models of user-defined protein variants with specific indels and substitutions.
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Affiliation(s)
- Ratul Chowdhury
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Matthew J Grisewood
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Veda Sheersh Boorla
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Qiang Yan
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA.
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24
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Abstract
Contaminants, organic or inorganic, represent a threat for the environment and human health and in recent years their presence and persistence has increased rapidly. For this reason, several technologies including bioremediation in combination with nanotechnology have been explored to identify more systemic approaches for their removal from environmental matrices. Understanding the interaction between the contaminant, the microorganism, and the nanomaterials (NMs) is of crucial importance since positive and negative effects may be produced. For example, some nanomaterials are stimulants for microorganisms, while others are toxic. Thus, proper selection is of paramount importance. The main objective of this review was to analyze the principles of bioremediation assisted by nanomaterials, nanoparticles (NPs) included, and their interaction with environmental matrices. It also analyzed the response of living organisms employed to remediate the contaminants in the presence of nanomaterials. Besides, we discuss the international regulatory frame applicable to these technologies and how they might contribute to sustainability.
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25
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Protein Structure Prediction and Design in a Biologically Realistic Implicit Membrane. Biophys J 2020; 118:2042-2055. [PMID: 32224301 DOI: 10.1016/j.bpj.2020.03.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 02/04/2020] [Accepted: 03/09/2020] [Indexed: 11/19/2022] Open
Abstract
Protein design is a powerful tool for elucidating mechanisms of function and engineering new therapeutics and nanotechnologies. Although soluble protein design has advanced, membrane protein design remains challenging because of difficulties in modeling the lipid bilayer. In this work, we developed an implicit approach that captures the anisotropic structure, shape of water-filled pores, and nanoscale dimensions of membranes with different lipid compositions. The model improves performance in computational benchmarks against experimental targets, including prediction of protein orientations in the bilayer, ΔΔG calculations, native structure discrimination, and native sequence recovery. When applied to de novo protein design, this approach designs sequences with an amino acid distribution near the native amino acid distribution in membrane proteins, overcoming a critical flaw in previous membrane models that were prone to generating leucine-rich designs. Furthermore, the proteins designed in the new membrane model exhibit native-like features including interfacial aromatic side chains, hydrophobic lengths compatible with bilayer thickness, and polar pores. Our method advances high-resolution membrane protein structure prediction and design toward tackling key biological questions and engineering challenges.
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26
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Thinking the future of membranes: Perspectives for advanced and new membrane materials and manufacturing processes. J Memb Sci 2020. [DOI: 10.1016/j.memsci.2019.117761] [Citation(s) in RCA: 187] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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27
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Tu YM, Song W, Ren T, Shen YX, Chowdhury R, Rajapaksha P, Culp TE, Samineni L, Lang C, Thokkadam A, Carson D, Dai Y, Mukthar A, Zhang M, Parshin A, Sloand JN, Medina SH, Grzelakowski M, Bhattacharya D, Phillip WA, Gomez ED, Hickey RJ, Wei Y, Kumar M. Rapid fabrication of precise high-throughput filters from membrane protein nanosheets. NATURE MATERIALS 2020; 19:347-354. [PMID: 31988513 DOI: 10.1038/s41563-019-0577-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 12/02/2019] [Indexed: 05/22/2023]
Abstract
Biological membranes are ideal for separations as they provide high permeability while maintaining high solute selectivity due to the presence of specialized membrane protein (MP) channels. However, successful integration of MPs into manufactured membranes has remained a significant challenge. Here, we demonstrate a two-hour organic solvent method to develop 2D crystals and nanosheets of highly packed pore-forming MPs in block copolymers (BCPs). We then integrate these hybrid materials into scalable MP-BCP biomimetic membranes. These MP-BCP nanosheet membranes maintain the molecular selectivity of the three types of β-barrel MP channels used, with pore sizes of 0.8 nm, 1.3 nm, and 1.5 nm. These biomimetic membranes demonstrate water permeability that is 20-1,000 times greater than that of commercial membranes and 1.5-45 times greater than that of the latest research membranes with comparable molecular exclusion ratings. This approach could provide high performance alternatives in the challenging sub-nanometre to few-nanometre size range.
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Affiliation(s)
- Yu-Ming Tu
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, USA
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Woochul Song
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, USA
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Tingwei Ren
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, USA
| | - Yue-Xiao Shen
- Department of Civil, Environmental, & Construction Engineering, Texas Tech University, Lubbock, TX, USA
| | - Ratul Chowdhury
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, USA
| | | | - Tyler E Culp
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, USA
| | - Laxmicharan Samineni
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, USA
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Chao Lang
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, USA
- Department of Materials Science and Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Alina Thokkadam
- Department of Chemical and Biochemical Engineering, Rutgers University, Piscataway, NJ, USA
| | - Drew Carson
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, USA
| | - Yuxuan Dai
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, USA
| | - Arwa Mukthar
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Miaoci Zhang
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, USA
| | | | - Janna N Sloand
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
| | - Scott H Medina
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
| | | | - Dibakar Bhattacharya
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY, USA
| | - William A Phillip
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, USA
| | - Enrique D Gomez
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, USA
| | - Robert J Hickey
- Department of Materials Science and Engineering, The Pennsylvania State University, University Park, PA, USA
- Materials Research Institute, Pennsylvania State University, University Park, PA, USA
| | - Yinai Wei
- Department of Chemistry, University of Kentucky, Lexington, KY, USA
| | - Manish Kumar
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, USA.
- Materials Research Institute, Pennsylvania State University, University Park, PA, USA.
- Department of Civil and Environmental Engineering, Pennsylvania State University, University Park, PA, USA.
- Department of Civil, Architectural and Environmental Engineering, The University of Texas at Austin, Austin, TX, USA.
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28
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Song W, Joshi H, Chowdhury R, Najem JS, Shen YX, Lang C, Henderson CB, Tu YM, Farell M, Pitz ME, Maranas CD, Cremer PS, Hickey RJ, Sarles SA, Hou JL, Aksimentiev A, Kumar M. Artificial water channels enable fast and selective water permeation through water-wire networks. NATURE NANOTECHNOLOGY 2020; 15:73-79. [PMID: 31844288 PMCID: PMC7008941 DOI: 10.1038/s41565-019-0586-8] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Accepted: 11/04/2019] [Indexed: 05/09/2023]
Abstract
Artificial water channels are synthetic molecules that aim to mimic the structural and functional features of biological water channels (aquaporins). Here we report on a cluster-forming organic nanoarchitecture, peptide-appended hybrid[4]arene (PAH[4]), as a new class of artificial water channels. Fluorescence experiments and simulations demonstrated that PAH[4]s can form, through lateral diffusion, clusters in lipid membranes that provide synergistic membrane-spanning paths for a rapid and selective water permeation through water-wire networks. Quantitative transport studies revealed that PAH[4]s can transport >109 water molecules per second per molecule, which is comparable to aquaporin water channels. The performance of these channels exceeds the upper bound limit of current desalination membranes by a factor of ~104, as illustrated by the water/NaCl permeability-selectivity trade-off curve. PAH[4]'s unique properties of a high water/solute permselectivity via cooperative water-wire formation could usher in an alternative design paradigm for permeable membrane materials in separations, energy production and barrier applications.
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Affiliation(s)
- Woochul Song
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Himanshu Joshi
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ratul Chowdhury
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Joseph S Najem
- Department of Mechanical, Aerospace, and Biomedical Engineering, The University of Tennessee, Knoxville, TN, USA
- Department of Mechanical Engineering, The Pennsylvania State University, UniversityPark, PA, USA
| | - Yue-Xiao Shen
- Department of Civil, Environmental, & Construction Engineering, Texas Tech University, Lubbock, TX, USA
| | - Chao Lang
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Codey B Henderson
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Yu-Ming Tu
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Megan Farell
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Megan E Pitz
- Department of Mechanical, Aerospace, and Biomedical Engineering, The University of Tennessee, Knoxville, TN, USA
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Paul S Cremer
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Robert J Hickey
- Department of Materials Science and Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Stephen A Sarles
- Department of Mechanical, Aerospace, and Biomedical Engineering, The University of Tennessee, Knoxville, TN, USA
| | - Jun-Li Hou
- Department of Chemistry, Fudan University, Shanghai, China
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Manish Kumar
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA.
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, USA.
- Department of Civil and Environmental Engineering, The Pennsylvania State University, University Park, PA, USA.
- Department of Civil, Architectural and Environmental Engineering, The University of Texas at Austin, Austin, TX, USA.
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Chowdhury R, Maranas CD. From directed evolution to computational enzyme engineering—A review. AIChE J 2019. [DOI: 10.1002/aic.16847] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Ratul Chowdhury
- Department of Chemical Engineering The Pennsylvania State University University Park Pennsylvania
| | - Costas D. Maranas
- Department of Chemical Engineering The Pennsylvania State University University Park Pennsylvania
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30
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Samineni L, Xiong B, Chowdhury R, Pei A, Kuehster L, Wang H, Dickey R, Soto PE, Massenburg L, Nguyen TH, Maranas C, Velegol D, Kumar M, Velegol S. 7 Log Virus Removal in a Simple Functionalized Sand Filter. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:12706-12714. [PMID: 31593449 DOI: 10.1021/acs.est.9b03734] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Viral contamination of drinking water due to fecal contamination is difficult to detect and treat effectively, leading to frequent outbreaks worldwide. The purpose of this paper is to report on the molecular mechanism for unprecedented high virus removal from a practical sand filter. Sand filters functionalized using a water extract of Moringa oleifera (MO) seeds, functionalized sand (f-sand) filters, achieved a ∼7 log10 virus removal. These tests were conducted with MS2 bacteriophage, a recognized surrogate for pathogenic norovirus and rotavirus. We studied the molecular mechanism of this high removal since it can have important implications for sand filtration, the most common water treatment technology worldwide. Our data reveal that the virus removal activity of f-sand is due to the presence of a chitin-binding protein, M. oleifera chitin-binding protein (MoCBP) on f-sand. Standard column experiments were supported by proteomic analysis and molecular docking simulations. Our simulations show that MoCBP binds preferentially to MS2 capsid proteins demonstrating that specific molecular interactions are responsible for enhanced virus removal. In addition, we simplified the process of making f-sand and evinced how it could be regenerated using saline water. At present, no definitive solution exists for the challenge of treating fecally contaminated drinking and irrigation water for viruses without using technologies that demand high energy or chemical consumption. We propose functionalized sand (f-sand) filters as a highly effective, energy-efficient, and practical technology for virus removal applicable to both developing and developed countries.
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Affiliation(s)
| | | | | | | | - Louise Kuehster
- School of Chemical, Biological, and Materials Engineering , University of Oklahoma , Norman , Oklahoma 73019-1004 , United States
| | | | | | | | | | - Thanh H Nguyen
- Department of Civil and Environmental Engineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | | | | | - Manish Kumar
- Department of Civil and Environmental Engineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
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31
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Synthetic protein-conductive membrane nanopores built with DNA. Nat Commun 2019; 10:5018. [PMID: 31685824 PMCID: PMC6828756 DOI: 10.1038/s41467-019-12639-y] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Accepted: 09/23/2019] [Indexed: 11/08/2022] Open
Abstract
AbstractNanopores are key in portable sequencing and research given their ability to transport elongated DNA or small bioactive molecules through narrow transmembrane channels. Transport of folded proteins could lead to similar scientific and technological benefits. Yet this has not been realised due to the shortage of wide and structurally defined natural pores. Here we report that a synthetic nanopore designed via DNA nanotechnology can accommodate folded proteins. Transport of fluorescent proteins through single pores is kinetically analysed using massively parallel optical readout with transparent silicon-on-insulator cavity chips vs. electrical recordings to reveal an at least 20-fold higher speed for the electrically driven movement. Pores nevertheless allow a high diffusive flux of more than 66 molecules per second that can also be directed beyond equillibria. The pores may be exploited to sense diagnostically relevant proteins with portable analysis technology, to create molecular gates for drug delivery, or to build synthetic cells.
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32
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Throckmorton K, Vinnik V, Chowdhury R, Cook T, Chevrette MG, Maranas C, Pfleger B, Thomas MG. Directed Evolution Reveals the Functional Sequence Space of an Adenylation Domain Specificity Code. ACS Chem Biol 2019; 14:2044-2054. [PMID: 31430120 DOI: 10.1021/acschembio.9b00532] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nonribosomal peptides are important natural products biosynthesized by nonribosomal peptide synthetases (NRPSs). Adenylation (A) domains of NRPSs are highly specific for the substrate they recognize. This recognition is determined by 10 residues in the substrate-binding pocket, termed the specificity code. This finding led to the proposal that nonribosomal peptides could be altered by specificity code swapping. Unfortunately, this approach has proven, with few exceptions, to be unproductive; changing the specificity code typically results in broadened specificity or poor function. To enhance our understanding of A domain substrate selectivity, we carried out a detailed analysis of the specificity code from the A domain of EntF, an NRPS involved in enterobactin biosynthesis in Escherichia coli. Using directed evolution and a genetic selection, we determined which sites in the code have strict residue requirements and which are tolerant of variation. We showed that the EntF A domain, and other l-Ser-specific A domains, have a functional sequence space for l-Ser recognition, rather than a single code. This functional space is more expansive than the aggregate of all characterized l-Ser-specific A domains: we identified 152 new l-Ser specificity codes. Together, our data provide essential insights into how to overcome the barriers that prevent rational changes to A domain specificity.
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Affiliation(s)
- Kurt Throckmorton
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Vladimir Vinnik
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Ratul Chowdhury
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Taylor Cook
- Department of Chemical and Biological Engineering, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Marc G. Chevrette
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
- Department of Genetics, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Costas Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Brian Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Michael George Thomas
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
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Sutisna B, Musteata V, Pulido B, Puspasari T, Smilgies DM, Hadjichristidis N, Nunes SP. High flux membranes, based on self-assembled and H-bond linked triblock copolymer nanospheres. J Memb Sci 2019. [DOI: 10.1016/j.memsci.2019.04.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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34
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A heuristic derived from analysis of the ion channel structural proteome permits the rapid identification of hydrophobic gates. Proc Natl Acad Sci U S A 2019; 116:13989-13995. [PMID: 31235590 PMCID: PMC6628796 DOI: 10.1073/pnas.1902702116] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Ion channels are nanoscale protein pores in cell membranes. An exponentially increasing number of structures for channels means that computational methods for predicting their functional state are needed. Hydrophobic gates in ion channels result in local dewetting of pores, which functionally closes them to water and ion permeation. We use simulations of water behavior within nearly 200 different ion channel structures to explore how the radius and hydrophobicity of pores determine their hydration vs. dewetting behavior. Machine learning-assisted analysis of these simulations allowed us to propose a simple model for this relationship and present an easy method for rapidly predicting the functional state of new channel structures as they emerge. Ion channel proteins control ionic flux across biological membranes through conformational changes in their transmembrane pores. An exponentially increasing number of channel structures captured in different conformational states are now being determined; however, these newly resolved structures are commonly classified as either open or closed based solely on the physical dimensions of their pore, and it is now known that more accurate annotation of their conductive state requires additional assessment of the effect of pore hydrophobicity. A narrow hydrophobic gate region may disfavor liquid-phase water, leading to local dewetting, which will form an energetic barrier to water and ion permeation without steric occlusion of the pore. Here we quantify the combined influence of radius and hydrophobicity on pore dewetting by applying molecular dynamics simulations and machine learning to nearly 200 ion channel structures. This allows us to propose a simple simulation-free heuristic model that rapidly and accurately predicts the presence of hydrophobic gates. This not only enables the functional annotation of new channel structures as soon as they are determined, but also may facilitate the design of novel nanopores controlled by hydrophobic gates.
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35
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Bodrenko IV, Salis S, Acosta-Gutierrez S, Ceccarelli M. Diffusion of large particles through small pores: From entropic to enthalpic transport. J Chem Phys 2019; 150:211102. [PMID: 31176312 DOI: 10.1063/1.5098868] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a statistical model for solving and predicting the transport of large molecules through small flexible channels. The average radius of the channel and the average radius of the molecule are the only two quantities determining the steric part of the potential of mean force for the translocation, in the case of a small rigid particle and a large rigid channel: the barrier is completely entropic and is described by the Fick-Jacobs model. However, the flexibility of the channel's cross section and that of the molecule's size have a significant effect on transport, especially when a large molecule goes through a narrow channel. In this case, the steric barrier changes its statistical nature becoming enthalpic, and we predict a strong temperature enhancement of the diffusion current through the channel. The flexibility is described in terms of the equilibrium fluctuations of the channel and of the molecule. The model is compared with the all-atom MD simulations of the transport of hard spheres of various radii and of drug molecules through a biological nanochannel. For the case of Gaussian fluctuations, we derived a simple analytical expression for the steric barrier, which can be quantified using average size and fluctuations of the channel and of the molecule.
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Affiliation(s)
- Igor V Bodrenko
- Department of Physics, University of Cagliari, S.P. Monserrato-Sestu km 0.700, 09042 Monserrato, Italy
| | - Samuele Salis
- Department of Physics, University of Cagliari, S.P. Monserrato-Sestu km 0.700, 09042 Monserrato, Italy
| | - Silvia Acosta-Gutierrez
- Department of Physics, University of Cagliari, S.P. Monserrato-Sestu km 0.700, 09042 Monserrato, Italy
| | - Matteo Ceccarelli
- Department of Physics, University of Cagliari, S.P. Monserrato-Sestu km 0.700, 09042 Monserrato, Italy
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36
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Wilson J, Sarthak K, Si W, Gao L, Aksimentiev A. Rapid and Accurate Determination of Nanopore Ionic Current Using a Steric Exclusion Model. ACS Sens 2019; 4:634-644. [PMID: 30821441 DOI: 10.1021/acssensors.8b01375] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Nanopore sensing has emerged as a versatile approach to detection and identification of biomolecules. Presently, researchers rely on experience and intuition for choosing or modifying the nanopores to detect a target analyte. The field would greatly benefit from a computational method that could relate the atomic-scale geometry of the nanopores and analytes to the blockade nanopore currents they produce. Existing computational methods are either computationally too expensive to be used routinely in experimental laboratories or not sensitive enough to account for the atomic structure of the pore and the analytes. Here, we demonstrate a robust and inexpensive computational approach-the steric exclusion model (SEM) of nanopore conductance-that is orders of magnitude more efficient than all-atom MD and yet is sensitive enough to account for the atomic structure of the nanopore and the analyte. The method combines the computational efficiency of a finite element solver with the atomic precision of a nanopore conductance map to yield unprecedented speed and accuracy of ionic current prediction. We validate our SEM approach through comparison with the current blockades computed using the all-atom molecular dynamics method for a range of proteins confined to a solid-state nanopore, biological channels embedded in a lipid bilayer membranes, and blockade currents produced by DNA homopolymers in MspA. We illustrate potential applications of SEM by computing blockade currents produced by nucleosome proteins in a solid-state nanopore, individual amino acids in MspA, and by testing the effect of point mutations on amino acid distinguishability. We expect our SEM approach to become an integral part of future development of the nanopore sensing field.
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Affiliation(s)
| | | | - Wei Si
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments and School of Mechanical Engineering, Southeast University, Nanjing, 210096, China
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37
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Song W, Tu YM, Oh H, Samineni L, Kumar M. Hierarchical Optimization of High-Performance Biomimetic and Bioinspired Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:589-607. [PMID: 30577695 DOI: 10.1021/acs.langmuir.8b03655] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Biomimetic and bioinspired membranes have emerged as an innovative platform for water purification and aqueous separations. They are inspired by the exceptional water permeability (∼109 water molecules per second per channel) and perfect selectivity of biological water channels, aquaporins. However, only few successes have been reported for channel-based membrane fabrication due to inherent challenges of realizing coherence between channel design at the angstrom level and development of scalable membranes that maintain these molecular properties at practice-relevant scales. In this article, we feature recent progress toward practical biomimetic membranes, with the review organized along a hierarchical structural perspective that biomimetic membranes commonly share. These structures range from unitary pore shapes and tubular hydrophobic channel geometries to self-assembled bilayer structures and finally to macroscale membranes covering a size range from the angstrom, to the micrometer scale, and finally to the centimeter and larger scales. To maximize the advantage of water channel implementation into membranes, each feature needs to be optimized in an appropriate manner that provides a path to successful scale-up to achieve high performance in practical biomimetic and bioinspired membranes.
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38
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Diep P, Mahadevan R, Yakunin AF. Heavy Metal Removal by Bioaccumulation Using Genetically Engineered Microorganisms. Front Bioeng Biotechnol 2018; 6:157. [PMID: 30420950 PMCID: PMC6215804 DOI: 10.3389/fbioe.2018.00157] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 10/09/2018] [Indexed: 11/25/2022] Open
Abstract
Wastewater effluents from mines and metal refineries are often contaminated with heavy metal ions, so they pose hazards to human and environmental health. Conventional technologies to remove heavy metal ions are well-established, but the most popular methods have drawbacks: chemical precipitation generates sludge waste, and activated carbon and ion exchange resins are made from unsustainable non-renewable resources. Using microbial biomass as the platform for heavy metal ion removal is an alternative method. Specifically, bioaccumulation is a natural biological phenomenon where microorganisms use proteins to uptake and sequester metal ions in the intracellular space to utilize in cellular processes (e.g., enzyme catalysis, signaling, stabilizing charges on biomolecules). Recombinant expression of these import-storage systems in genetically engineered microorganisms allows for enhanced uptake and sequestration of heavy metal ions. This has been studied for over two decades for bioremediative applications, but successful translation to industrial-scale processes is virtually non-existent. Meanwhile, demands for metal resources are increasing while discovery rates to supply primary grade ores are not. This review re-thinks how bioaccumulation can be used and proposes that it can be developed for bioextractive applications-the removal and recovery of heavy metal ions for downstream purification and refining, rather than disposal. This review consolidates previously tested import-storage systems into a biochemical framework and highlights efforts to overcome obstacles that limit industrial feasibility, thereby identifying gaps in knowledge and potential avenues of research in bioaccumulation.
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Affiliation(s)
| | | | - Alexander F. Yakunin
- BioZone - Centre for Applied Biosciences and Bioengineering, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
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