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Chang HJ, Choi H, Na S. Predicting the self-assembly film structure of class II hydrophobin NC2 and estimating its structural characteristics. Colloids Surf B Biointerfaces 2020; 195:111269. [DOI: 10.1016/j.colsurfb.2020.111269] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/15/2020] [Accepted: 07/21/2020] [Indexed: 11/24/2022]
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2
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Yang J, Wang B, Ge L, Yang X, Wang X, Dai Y, Niu B, Xu H, Qiao M. The enhancement of surface activity and nanoparticle stability through the alteration of charged amino acids of HGFI. Colloids Surf B Biointerfaces 2019; 175:703-712. [DOI: 10.1016/j.colsurfb.2018.12.044] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 12/15/2018] [Accepted: 12/17/2018] [Indexed: 11/24/2022]
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3
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Fungal Hydrophobins and Their Self-Assembly into Functional Nanomaterials. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1174:161-185. [DOI: 10.1007/978-981-13-9791-2_5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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4
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Abstract
Surfaces and interfaces are ubiquitous in nature and are involved in many biological processes. Due to this, natural organisms have evolved a number of methods to control interfacial and surface properties. Many of these methods involve the use of specialised protein biosurfactants, which due to the competing demands of high surface activity, biocompatibility, and low solution aggregation may take structures that differ from the traditional head–tail structure of small molecule surfactants. As well as their biological functions, these proteins have also attracted interest for industrial applications, in areas including food technology, surface modification, and drug delivery. To understand the biological functions and technological applications of protein biosurfactants, it is necessary to have a molecular level description of their behaviour, in particular at surfaces and interfaces, for which molecular simulation is well suited to investigate. In this review, we will give an overview of simulation studies of a number of examples of protein biosurfactants (hydrophobins, surfactin, and ranaspumin). We will also outline some of the key challenges and future directions for molecular simulation in the investigation of protein biosurfactants and how this can help guide future developments.
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5
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Noble AJ, Dandey VP, Wei H, Brasch J, Chase J, Acharya P, Tan YZ, Zhang Z, Kim LY, Scapin G, Rapp M, Eng ET, Rice WJ, Cheng A, Negro CJ, Shapiro L, Kwong PD, Jeruzalmi D, des Georges A, Potter CS, Carragher B. Routine single particle CryoEM sample and grid characterization by tomography. eLife 2018; 7:e34257. [PMID: 29809143 PMCID: PMC5999397 DOI: 10.7554/elife.34257] [Citation(s) in RCA: 172] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 05/17/2018] [Indexed: 12/11/2022] Open
Abstract
Single particle cryo-electron microscopy (cryoEM) is often performed under the assumption that particles are not adsorbed to the air-water interfaces and in thin, vitreous ice. In this study, we performed fiducial-less tomography on over 50 different cryoEM grid/sample preparations to determine the particle distribution within the ice and the overall geometry of the ice in grid holes. Surprisingly, by studying particles in holes in 3D from over 1000 tomograms, we have determined that the vast majority of particles (approximately 90%) are adsorbed to an air-water interface. The implications of this observation are wide-ranging, with potential ramifications regarding protein denaturation, conformational change, and preferred orientation. We also show that fiducial-less cryo-electron tomography on single particle grids may be used to determine ice thickness, optimal single particle collection areas and strategies, particle heterogeneity, and de novo models for template picking and single particle alignment.
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Affiliation(s)
- Alex J Noble
- National Resource for Automated Molecular MicroscopySimons Electron Microscopy Center, New York Structural Biology CenterNew YorkUnited States
| | - Venkata P Dandey
- National Resource for Automated Molecular MicroscopySimons Electron Microscopy Center, New York Structural Biology CenterNew YorkUnited States
| | - Hui Wei
- National Resource for Automated Molecular MicroscopySimons Electron Microscopy Center, New York Structural Biology CenterNew YorkUnited States
| | - Julia Brasch
- National Resource for Automated Molecular MicroscopySimons Electron Microscopy Center, New York Structural Biology CenterNew YorkUnited States
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew YorkUnited States
| | - Jillian Chase
- Department of Chemistry and BiochemistryCity College of New YorkNew YorkUnited States
- Program in BiochemistryThe Graduate Center of the City University of New YorkNew YorkUnited States
| | - Priyamvada Acharya
- National Resource for Automated Molecular MicroscopySimons Electron Microscopy Center, New York Structural Biology CenterNew YorkUnited States
- Vaccine Research CenterNational Institute of Allergy and Infectious Diseases, National Institutes of HealthMarylandUnited States
| | - Yong Zi Tan
- National Resource for Automated Molecular MicroscopySimons Electron Microscopy Center, New York Structural Biology CenterNew YorkUnited States
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew YorkUnited States
| | - Zhening Zhang
- National Resource for Automated Molecular MicroscopySimons Electron Microscopy Center, New York Structural Biology CenterNew YorkUnited States
| | - Laura Y Kim
- National Resource for Automated Molecular MicroscopySimons Electron Microscopy Center, New York Structural Biology CenterNew YorkUnited States
| | - Giovanna Scapin
- National Resource for Automated Molecular MicroscopySimons Electron Microscopy Center, New York Structural Biology CenterNew YorkUnited States
- Department of Structural Chemistry and Chemical BiotechnologyMerck & Co., IncNew JerseyUnited States
| | - Micah Rapp
- National Resource for Automated Molecular MicroscopySimons Electron Microscopy Center, New York Structural Biology CenterNew YorkUnited States
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew YorkUnited States
| | - Edward T Eng
- National Resource for Automated Molecular MicroscopySimons Electron Microscopy Center, New York Structural Biology CenterNew YorkUnited States
| | - William J Rice
- National Resource for Automated Molecular MicroscopySimons Electron Microscopy Center, New York Structural Biology CenterNew YorkUnited States
| | - Anchi Cheng
- National Resource for Automated Molecular MicroscopySimons Electron Microscopy Center, New York Structural Biology CenterNew YorkUnited States
| | - Carl J Negro
- National Resource for Automated Molecular MicroscopySimons Electron Microscopy Center, New York Structural Biology CenterNew YorkUnited States
| | - Lawrence Shapiro
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew YorkUnited States
| | - Peter D Kwong
- Vaccine Research CenterNational Institute of Allergy and Infectious Diseases, National Institutes of HealthMarylandUnited States
| | - David Jeruzalmi
- Department of Chemistry and BiochemistryCity College of New YorkNew YorkUnited States
- Program in BiochemistryThe Graduate Center of the City University of New YorkNew YorkUnited States
- Program in BiologyThe Graduate Center of the City University of New YorkNew YorkUnited States
- Program in ChemistryThe Graduate Center of the City University of New YorkNew YorkUnited States
| | - Amedee des Georges
- Department of Chemistry and BiochemistryCity College of New YorkNew YorkUnited States
- Program in BiochemistryThe Graduate Center of the City University of New YorkNew YorkUnited States
- Program in ChemistryThe Graduate Center of the City University of New YorkNew YorkUnited States
- Advanced Science Research CenterThe Graduate Center of the City University of New YorkNew YorkUnited States
| | - Clinton S Potter
- National Resource for Automated Molecular MicroscopySimons Electron Microscopy Center, New York Structural Biology CenterNew YorkUnited States
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew YorkUnited States
| | - Bridget Carragher
- National Resource for Automated Molecular MicroscopySimons Electron Microscopy Center, New York Structural Biology CenterNew YorkUnited States
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew YorkUnited States
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6
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Deckers SM, Venken T, Khalesi M, Gebruers K, Baggerman G, Lorgouilloux Y, Shokribousjein Z, Ilberg V, Schönberger C, Titze J, Verachtert H, Michiels C, Neven H, Delcour J, Martens J, Derdelinckx G, De Maeyer M. Combined Modeling and Biophysical Characterisation of CO2 Interaction with Class II Hydrophobins: New Insight into the Mechanism Underpinning Primary Gushing. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-2012-0905-01] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Sylvie M. Deckers
- KU Leuven, Department of Microbial and Molecular Systems (M2S), and Leuven Food Science and Nutrition Research Centre (LFoRCe), BE-3001 Heverlee, Belgium
| | - Tom Venken
- KU Leuven, Department of Chemistry, Division of Chemistry, section: Molecular and Structural Biology, Laboratory for Biomolecular Modelling and BioMacS, BE-3001 Heverlee, Belgium
| | - Mohammadreza Khalesi
- KU Leuven, Department of Microbial and Molecular Systems (M2S), and Leuven Food Science and Nutrition Research Centre (LFoRCe), BE-3001 Heverlee, Belgium
| | - Kurt Gebruers
- KU Leuven, Department of Microbial and Molecular Systems (M2S), and Leuven Food Science and Nutrition Research Centre (LFoRCe), BE-3001 Heverlee, Belgium
| | - Geert Baggerman
- KU Leuven, Facility for Systems Biology based Mass Spectrometry (SyBioMa), BE-3000 Leuven, Belgium
| | - Yannick Lorgouilloux
- KU Leuven, Facility for Systems Biology based Mass Spectrometry (SyBioMa), BE-3000 Leuven, Belgium
| | - Zahra Shokribousjein
- KU Leuven, Department of Microbial and Molecular Systems (M2S), and Leuven Food Science and Nutrition Research Centre (LFoRCe), BE-3001 Heverlee, Belgium
| | - Vladimir Ilberg
- Hochschule Weihenstephan-Triesdorf, Fakultät Gartenbau und Lebensmitteltechnologie, D-85350 Freisinig, Germany
| | - Christina Schönberger
- KU Leuven, Department of Microbial and Molecular Systems (M2S), and Leuven Food Science and Nutrition Research Centre (LFoRCe), BE-3001 Heverlee, Belgium
| | - Jean Titze
- Barth-Haas Group, Barth Innovations, D-90482 Nuremberg, Germany
| | - Hubert Verachtert
- KU Leuven, Department of Microbial and Molecular Systems (M2S), and Leuven Food Science and Nutrition Research Centre (LFoRCe), BE-3001 Heverlee, Belgium
| | - Chris Michiels
- National University of Ireland, University College Cork, School of Food and Nutritional Sciences, Cork, Ireland
| | - Hedwig Neven
- KU Leuven, Department of Microbial and Molecular Systems (M2S), and Leuven Food Science and Nutrition Research Centre (LFoRCe), BE-3001 Heverlee, Belgium
| | - Jan Delcour
- KU Leuven, Department of Microbial and Molecular Systems (M2S), and Leuven Food Science and Nutrition Research Centre (LFoRCe), BE-3001 Heverlee, Belgium
| | - Johan Martens
- KU Leuven, Department of Microbial and Molecular Systems (M2S), and Leuven Food Science and Nutrition Research Centre (LFoRCe), BE-3001 Heverlee, Belgium
| | - Guy Derdelinckx
- KU Leuven, Department of Microbial and Molecular Systems (M2S), and Leuven Food Science and Nutrition Research Centre (LFoRCe), BE-3001 Heverlee, Belgium
| | - Marc De Maeyer
- KU Leuven, Department of Microbial and Molecular Systems (M2S), and Leuven Food Science and Nutrition Research Centre (LFoRCe), BE-3001 Heverlee, Belgium
- KU Leuven, Department of Chemistry, Division of Chemistry, section: Molecular and Structural Biology, Laboratory for Biomolecular Modelling and BioMacS, BE-3001 Heverlee, Belgium
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7
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Arooj M, Gandhi NS, Kreck CA, Arrigan DWM, Mancera RL. Adsorption and Unfolding of Lysozyme at a Polarized Aqueous–Organic Liquid Interface. J Phys Chem B 2016; 120:3100-12. [DOI: 10.1021/acs.jpcb.6b00536] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mahreen Arooj
- School of Biomedical Sciences, CHIRI Biosciences and Curtin Institute
for Computation, ‡Department of Chemistry and Nanochemistry Research Institute, Curtin University, GPO
Box U1987, Perth, WA 6845, Australia
| | - Neha S. Gandhi
- School of Biomedical Sciences, CHIRI Biosciences and Curtin Institute
for Computation, ‡Department of Chemistry and Nanochemistry Research Institute, Curtin University, GPO
Box U1987, Perth, WA 6845, Australia
| | - Cara A. Kreck
- School of Biomedical Sciences, CHIRI Biosciences and Curtin Institute
for Computation, ‡Department of Chemistry and Nanochemistry Research Institute, Curtin University, GPO
Box U1987, Perth, WA 6845, Australia
| | - Damien W. M. Arrigan
- School of Biomedical Sciences, CHIRI Biosciences and Curtin Institute
for Computation, ‡Department of Chemistry and Nanochemistry Research Institute, Curtin University, GPO
Box U1987, Perth, WA 6845, Australia
| | - Ricardo L. Mancera
- School of Biomedical Sciences, CHIRI Biosciences and Curtin Institute
for Computation, ‡Department of Chemistry and Nanochemistry Research Institute, Curtin University, GPO
Box U1987, Perth, WA 6845, Australia
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8
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9
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Ettelaie R, Murray BS. Evolution of bubble size distribution in particle stabilised bubble dispersions: Competition between particle adsorption and dissolution kinetics. Colloids Surf A Physicochem Eng Asp 2015. [DOI: 10.1016/j.colsurfa.2014.10.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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10
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Abstract
The behaviour of complex molecules, such as nanoparticles, polymers, and proteins, at liquid interfaces is of increasing importance in a number of areas of science and technology. It has long been recognised that solid particles adhere to liquid interfaces, which provides a convenient method for the preparation of nanoparticle structures or to modify interfacial properties. The adhesion of proteins at liquid interfaces is important in many biological processes and in a number of materials applications of biomolecules. While the reduced dimensions of these particles make experimental investigation challenging, molecular simulations provide a natural means for the study of these systems. In this paper I will give an overview of some recent work using molecular simulation to investigate the behaviour of complex molecules at liquid interfaces, focusing on the relationship between interfacial adsorption and molecular structure, and outline some avenues for future research.
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11
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On the link between surface rheology and foam disproportionation in mixed hydrophobin HFBII and whey protein systems. Colloids Surf A Physicochem Eng Asp 2013. [DOI: 10.1016/j.colsurfa.2012.12.040] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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12
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Walther A, Müller AHE. Janus Particles: Synthesis, Self-Assembly, Physical Properties, and Applications. Chem Rev 2013; 113:5194-261. [DOI: 10.1021/cr300089t] [Citation(s) in RCA: 1328] [Impact Index Per Article: 120.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Andreas Walther
- DWI at RWTH Aachen University − Institute for Interactive Materials Research, D-52056 Aachen, Germany
| | - Axel H. E. Müller
- Institute of Organic Chemistry, Johannes Gutenberg University Mainz, D-55099 Mainz,
Germany
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13
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Gobbo C, Li M, Mali KS, van Esch JH, De Feyter S. Preprogrammed 2D folding of conformationally flexible oligoamides: foldamers with multiple turn elements. ACS NANO 2012; 6:10684-10698. [PMID: 23214464 DOI: 10.1021/nn303868q] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Controlling the molecular conformation of oligomers on surfaces through noncovalent interactions symbolizes an important approach in the bottom-up patterning of surfaces with nanoscale precision. Here we report on the design, synthesis, and scanning tunneling microscopy (STM) investigation of linear oligoamides adsorbed at the liquid-solid interface. A new class of extended foldamers comprising as many as four turn elements based on a structural design "rule" adapted from a mimic foldamer was successfully synthesized. The self-assembly of these progressively complex oligomeric structures was scrutinized at the liquid-solid interface by employing STM. Submolecularly resolved STM images of foldamers reveal characteristic in-plane folding and self-assembly behavior of these conformationally flexible molecules. The complexity of the supramolecular architectures increases with increasing number of turn elements. The dissimilarity in the adsorption behavior of different foldamers is discussed qualitatively in light of enthalpic and entropic factors. The modular construction of these oligomeric foldamers with integrated functionalities provides a simple, efficient, and versatile approach to surface patterning with molecular precision.
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Affiliation(s)
- Cristian Gobbo
- Department of Chemistry, Laboratory of Self-assembling Systems, Delft University of Technology, Julianalaan 136, 2628 BL Delft, The Netherlands
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14
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Liu Y, Wu M, Feng X, Shao X, Cai W. Adsorption Behavior of Hydrophobin Proteins on Polydimethylsiloxane Substrates. J Phys Chem B 2012; 116:12227-34. [DOI: 10.1021/jp304796p] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Yingzhe Liu
- College of Chemistry, Nankai University, Tianjin, 300071, People's Republic
of China
| | - Ming Wu
- College of Life
Science, Nankai University, Tianjin, 300071,
People's Republic
of China
| | - Xizeng Feng
- College of Life
Science, Nankai University, Tianjin, 300071,
People's Republic
of China
| | - Xueguang Shao
- College of Chemistry, Nankai University, Tianjin, 300071, People's Republic
of China
| | - Wensheng Cai
- College of Chemistry, Nankai University, Tianjin, 300071, People's Republic
of China
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15
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Cheung DL. Molecular simulation of hydrophobin adsorption at an oil-water interface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:8730-8736. [PMID: 22591377 DOI: 10.1021/la300777q] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Hydrophobins are small, amphiphilic proteins expressed by strains of filamentous fungi. They fulfill a number of biological functions, often related to adsorption at hydrophobic interfaces, and have been investigated for a number of applications in materials science and biotechnology. In order to understand the biological function and applications of these proteins, a microscopic picture of the adsorption of these proteins at interfaces is needed. Using molecular dynamics simulations with a chemically detailed coarse-grained potential, the behavior of typical hydrophobins at the water-octane interface is studied. Calculation of the interfacial adsorption strengths indicates that the adsorption is essentially irreversible, with adsorption strengths of the order of 100 k(B)T (comparable to values determined for synthetic nanoparticles but significantly larger than small molecule surfactants and biomolecules). The protein structure at the interface is unchanged at the interface, which is consistent with the biological function of these proteins. Comparison of native proteins with pseudoproteins that consist of uniform particles shows that the surface structure of these proteins has a large effect on the interfacial adsorption strengths, as does the flexibility of the protein.
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Affiliation(s)
- David L Cheung
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry CV4 7AL, UK.
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16
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Li JL, Geng CY, Bu Y, Huang XR, Sun CC. Conformational transition pathway in the allosteric process of calcium-induced recoverin: Molecular dynamics simulations. J Comput Chem 2009; 30:1135-45. [DOI: 10.1002/jcc.21144] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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17
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Houmadi S, Ciuchi F, De Santo MP, De Stefano L, Rea I, Giardina P, Armenante A, Lacaze E, Giocondo M. Langmuir-Blodgett film of hydrophobin protein from Pleurotus ostreatus at the air-water interface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:12953-12957. [PMID: 18925762 DOI: 10.1021/la802306r] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We present results concerning the formation of Langmuir-Blodgett (LB) films of a class I hydrophobin from Pleurotus ostreatus at the air-water interface, and their structure as Langmuir-Blodgett (LB) films when deposited on silicon substrates. LB films of the hydrophobin were investigated by atomic force microscopy (AFM). We observed that the compressed film at the air-water interface exhibits a molecular depletion even at low surface pressure. In order to estimate the surface molecular concentration, we fit the experimental isotherm with Volmer's equation describing the equation of state for molecular monolayers. We found that about (1)/ 10 of the molecules contribute to the surface film formation. When transferred on silicon substrates, compact and uniform monomolecular layers about 2.5 nm thick, comparable to a typical molecular size, were observed. The monolayers coexist with protein aggregates, under the typical rodlet form with a uniform thickness of about 5.0 nm. The observed rodlets appear to be a hydrophilic bilayer and can then be responsible for the surface molecular depletion.
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Affiliation(s)
- S Houmadi
- CNR-INFM LICRYL-Liquid Crystals Laboratory c/o Dipartimento di Fisica, Universita della Calabria, 87036 Rende, Italy
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18
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Uribe A, Zariñán T, Pérez-Solis MA, Gutiérrez-Sagal R, Jardón-Valadez E, Piñeiro A, Dias JA, Ulloa-Aguirre A. Functional and structural roles of conserved cysteine residues in the carboxyl-terminal domain of the follicle-stimulating hormone receptor in human embryonic kidney 293 cells. Biol Reprod 2008; 78:869-82. [PMID: 18199880 DOI: 10.1095/biolreprod.107.063925] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
The carboxyl-terminal segment of G protein-coupled receptors has one or more conserved cysteine residues that are potential sites for palmitoylation. This posttranslational modification contributes to membrane association, internalization, and membrane targeting of proteins. In contrast to other members of the glycoprotein hormone receptor family (the LH and thyroid-stimulating hormone receptors), it is not known whether the follicle-stimulating hormone receptor (FSHR) is palmitoylated and what are the effects of abolishing its potential palmitoylation sites. In the present study, a functional analysis of the FSHR carboxyl-terminal segment cysteine residues was carried out. We constructed a series of mutant FSHRs by substituting cysteine residues with alanine, serine, or threonine individually and together at positions 629 and 655 (conserved cysteines) and 627 (nonconserved). The results showed that all three cysteine residues are palmitoylated but that only modification at Cys629 is functionally relevant. The lack of palmitoylation does not appear to greatly impair coupling to G(s) but, when absent at position 629, does significantly impair cell surface membrane expression of the partially palmitoylated receptor. All FSHR Cys mutants were capable of binding agonist with the same affinity as the wild-type receptor and internalizing on agonist stimulation. Molecular dynamics simulations at a time scale of approximately 100 nsec revealed that replacement of Cys629 resulted in structures that differed significantly from that of the wild-type receptor. Thus, deviations from wild-type conformation may potentially contribute to the severe impairment in plasma membrane expression and the modest effects on signaling exhibited by the receptors modified in this particular position.
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Affiliation(s)
- Aída Uribe
- Research Unit in Reproductive Medicine, Hospital de Ginecobstetricia "Luis Castelazo Ayala," Instituto Mexicano del Seguro Social, Mexico
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Karttunen M, Rottler J, Vattulainen I, Sagui C. Chapter 2 Electrostatics in Biomolecular Simulations: Where Are We Now and Where Are We Heading? CURRENT TOPICS IN MEMBRANES 2008. [DOI: 10.1016/s1063-5823(08)00002-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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20
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Hektor HJ, Scholtmeijer K. Hydrophobins: proteins with potential. Curr Opin Biotechnol 2007; 16:434-9. [PMID: 15950452 DOI: 10.1016/j.copbio.2005.05.004] [Citation(s) in RCA: 142] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2005] [Revised: 05/01/2005] [Accepted: 05/26/2005] [Indexed: 11/28/2022]
Abstract
Hydrophobins are self-assembling proteins of fungal origin. Their ability to self-assemble into an amphipathic membrane is of interest for many different applications, ranging from medical and technical coatings to the production of proteinaceous glue and cosmetics. Assembled hydrophobins can modify surface characteristics, thus controling the binding properties of the surface; for example, enzymes can be actively and non-covalently immobilized on electrode surfaces and medical coatings can be improved for biocompatibility. Over the past few years research on hydrophobins has contributed to a better understanding of the self-assembly process and is generating more handles to control and manipulate the process. This knowledge could have an immediate effect on production levels, which are not yet adequate, and provide the boost needed for hydrophobins to reach their full potential.
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Affiliation(s)
- Harm J Hektor
- BiOMaDe Technology Foundation, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
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21
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Corvis Y, Walcarius A, Rink R, Mrabet NT, Rogalska E. Preparing catalytic surfaces for sensing applications by immobilizing enzymes via hydrophobin layers. Anal Chem 2007; 77:1622-30. [PMID: 15762565 DOI: 10.1021/ac048897w] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Simple and reliable immobilization techniques that preserve the activity of enzymes are of interest in many technologies based on catalysis. Here, two redox enzymes, glucose oxidase from Aspergillus niger and horseradish peroxidase, were immobilized by physisorption on glassy carbon electrodes coated with Schizophyllum commune hydrophobin. Hydrophobins are small, interfacially active proteins that have the remarkable property of adhering to almost any surface. We showed recently that these proteins can be used to immobilize small, electroactive molecules. The results obtained in this work show a way to easily manufacture stable, enzyme-based catalytic surfaces for applications in biosensing.
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Affiliation(s)
- Yohann Corvis
- Groupe d'Etude des Vecteurs Supramoléculaires du Médicament UMR 7565 CNRS/Université Henri Poincaré Nancy 1, Faculté des Sciences, BP 239, 54506 Vandoeuvre-lès-Nancy Cedex, France
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22
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Makrodimitris K, Fernandez EJ, Woolf TB, O'Connell JP. Mesoscopic simulation of adsorption of peptides in a hydrophobic chromatography system. Anal Chem 2007; 77:1243-52. [PMID: 15732903 DOI: 10.1021/ac048812r] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mesoscopic simulations using Langevin dipoles on a lattice for the solvent and calculated partial charges for the solute have been used to estimate free energies of adsorption from data on reversed-phase chromatography on nine protected peptides covering a wide range of structures. There is a single parameter, the effective solvent dipole moment, that is fit to data for one peptide and used to predict properties of the other eight peptides. Good agreement of adsorption chemical potentials, including order of chromatographic retention times, is found for calculations that are Boltzmann-averaged over a set of orientations. In addition, the results suggest that there are preferential orientations for each peptide at the model hydrophobic chromatographic surface. Estimation methods for adsorption based on molecular descriptors and hydrophobicity scales are shown to be unreliable for these systems. With refinements and extensions, this simulation method should be applicable to solvents containing salt, such as in hydrophobic interaction chromatography, and to larger solutes including proteins.
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Affiliation(s)
- Kosta Makrodimitris
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22904, USA
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23
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Yang K, Deng Y, Zhang C, Elasri M. Identification of new members of hydrophobin family using primary structure analysis. BMC Bioinformatics 2006; 7 Suppl 4:S16. [PMID: 17217508 PMCID: PMC1780129 DOI: 10.1186/1471-2105-7-s4-s16] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background Hydrophobins are fungal proteins that can turn into amphipathic membranes at hydrophilic/hydrophobic interfaces by self-assembly. The assemblages by Class I hydrophobins are extremely stable and possess the remarkable ability to change the polarity of the surface. One of its most important industrial applications is its usage as paint. Without detailed knowledge of the 3D structure and self-assembly principles of hydrophobins, it is difficult to make significant progress in furthering its research. Results In order to provide useful information to hydrophobin researchers, we analyzed primary structure of hydrophobins to gain more insight about these proteins. In this paper, we presented an in-depth primary sequence analysis using batch BLAST search of the database, sequence filtering by programming and motif finding by MEME. We used batch BLAST to find similar sequences in the NCBI nr database. Then we used MEME to find out motifs. Based on the newly found motifs and the well-known C-CC-C-C-CC-C pattern we used MAST to search the entire nr database. At the end, domain search and phylogenetic analysis were conducted to confirm the result. After searching the nr database with the new PSSM-format motifs identified by MEME, many sequences from various species were found by MAST. Filtering process by pattern, domain and length left 9 qualified candidates. Conclusion All of 9 newly identified potential hydrophobins possess the common pattern and hydrophobin domain. From the multiple sequence alignment result, we can see that some of them are grouped very close to other known hydrophobins, which means their phylogenetic relationship is very close and it is highly plausible that they are indeed hydrophobin proteins.
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Affiliation(s)
- Kuan Yang
- Department of Biological Sciences, University of SouthernMississippi, Hattiesburg, Mississippi 39406, USA
| | - Youping Deng
- Department of Biological Sciences, University of SouthernMississippi, Hattiesburg, Mississippi 39406, USA
| | - Chaoyang Zhang
- School of Computing, University of Southern Mississippi, Hattiesburg, Mississippi 39406, USA
| | - Mohamed Elasri
- Department of Biological Sciences, University of SouthernMississippi, Hattiesburg, Mississippi 39406, USA
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24
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Zhang J, Li C, Chen K, Zhu W, Shen X, Jiang H. Conformational transition pathway in the allosteric process of human glucokinase. Proc Natl Acad Sci U S A 2006; 103:13368-73. [PMID: 16938872 PMCID: PMC1569170 DOI: 10.1073/pnas.0605738103] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2006] [Indexed: 12/25/2022] Open
Abstract
Glucokinase (GK) is an important enzyme for regulating blood glucose levels and a potentially attractive target for diabetes of the young type 2 and persistent hyperinsulinemic hypoglycemia of infancy. To characterize the conformational transition of GK from the closed state to the superopen state, a series of conventional molecular dynamics (MD) and target MD (TMD) simulations were performed on both the wild-type enzyme and its mutants. Two 10-ns conventional MD simulations showed that, although the allosteric site of GK is approximately 20 A away from the active site, the activator is able to enhance the activity of the enzyme through conformational restriction. Fourteen TMD simulations on GK and five of its mutants revealed a reliably conformational transition pathway. The overall conformational transition includes three stages, and three likely stable intermediate states were identified by free energy scanning for the snapshots throughout the pathway. The conformational transition feature revealed by our TMD simulations rationalized several important mutagenesis and kinetic data. Remarkably, the TMD simulations predicted that Y61S, I159A, A201R, V203E, and V452S mutations, which have not been investigated so far, may facilitate the opening process of GK. These predictions also have been verified by mutagenesis and kinetic analyses in this study. These observations are beneficial to understanding the mechanism of GK regulation and designing the compounds for treating metabolic diseases.
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Affiliation(s)
- Jian Zhang
- Center for Drug Discovery and Design, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, and Graduate School, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; and
| | - Chenjing Li
- Center for Drug Discovery and Design, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, and Graduate School, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; and
| | - Kaixian Chen
- Center for Drug Discovery and Design, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, and Graduate School, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; and
| | - Weiliang Zhu
- Center for Drug Discovery and Design, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, and Graduate School, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; and
| | - Xu Shen
- Center for Drug Discovery and Design, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, and Graduate School, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; and
| | - Hualiang Jiang
- Center for Drug Discovery and Design, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, and Graduate School, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; and
- School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
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25
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Hakanpää J, Szilvay GR, Kaljunen H, Maksimainen M, Linder M, Rouvinen J. Two crystal structures of Trichoderma reesei hydrophobin HFBI--the structure of a protein amphiphile with and without detergent interaction. Protein Sci 2006; 15:2129-40. [PMID: 16882996 PMCID: PMC2242604 DOI: 10.1110/ps.062326706] [Citation(s) in RCA: 131] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2006] [Revised: 06/05/2006] [Accepted: 06/08/2006] [Indexed: 10/24/2022]
Abstract
Hydrophobins are small fungal proteins that are highly surface active and possess a unique ability to form amphiphilic membranes through spontaneous self-assembly. The first crystal structure of a hydrophobin, Trichoderma reesei HFBII, revealed the structural basis for the function of this amphiphilic protein--a patch consisting of hydrophobic side chains on the protein surface. Here, the crystal structures of a native and a variant T. reesei hydrophobin HFBI are presented, revealing the same overall structure and functional hydrophobic patch as in the HFBII structure. However, some structural flexibility was found in the native HFBI structure: The asymmetric unit contained four molecules, and, in two of these, an area of seven residues was displaced as compared to the two other HFBI molecules and the previously determined HFBII structure. This structural change is most probably induced by multimer formation. Both the native and the N-Cys-variant of HFBI were crystallized in the presence of detergents, but an association between the protein and a detergent was only detected in the variant structure. There, the molecules were arranged into an extraordinary detergent-associated octamer and the solvent content of the crystals was 75%. This study highlights the conservation of the fold of class II hydrophobins in spite of the low sequence identity and supports our previous suggestion that concealment of the hydrophobic surface areas of the protein is the driving force in the formation of multimers and monolayers in the self-assembly process.
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26
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Szilvay GR, Nakari-Setälä T, Linder MB. Behavior of Trichoderma reesei Hydrophobins in Solution: Interactions, Dynamics, and Multimer Formation. Biochemistry 2006; 45:8590-8. [PMID: 16834333 DOI: 10.1021/bi060620y] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Filamentous fungi utilize small amphiphilic proteins called hydrophobins in their adaptation to the environment. The hydrophobins are used to form coatings on various fungal structures, lower the surface tension of water, and to mediate surface attachment. Hydrophobins function through self-assembly at interfaces, for example, at the air-water interface, and at fungal cellular structures. Despite their high tendency to self assemble at interfaces, hydrophobins can be very soluble in water. To understand the mechanism of hydrophobin self-assembly, in this work, we have studied the behavior of two Trichoderma reesei hydrophobins, HFBI and HFBII in aqueous solution. The main methods used were Förster resonance energy transfer (FRET) and size exclusion chromatography. A genetically engineered HFBI variant, NCys-HFBI, was utilized for the site-specific labeling of dyes for the FRET experiments. We observed the multimerization of HFBI in a concentration-dependent manner. A change from monomers to tetramers was seen when the hydrophobin concentration was increased. Interaction studies between HFBI and HFBII suggested that at low concentrations homodimers are preferred, and at higher concentrations, the heterotetramers of HFBI and HFBII are formed. In conclusion, the results support the model where hydrophobins in aqueous solutions form multimers by hydrophobic interactions. In contrast to micelles formed by detergents, the hydrophobin multimers are defined in size and involve specific protein-protein interactions.
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Affiliation(s)
- Géza R Szilvay
- VTT Biotechnology, Tietotie 2, P.O. Box 1000, FIN-02044 VTT, Finland.
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27
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Fan H, Wang X, Zhu J, Robillard GT, Mark AE. Molecular dynamics simulations of the hydrophobin SC3 at a hydrophobic/hydrophilic interface. Proteins 2006; 64:863-73. [PMID: 16770796 DOI: 10.1002/prot.20936] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Hydrophobins are small ( approximately 100 aa) proteins that have an important role in the growth and development of mycelial fungi. They are surface active and, after secretion by the fungi, self-assemble into amphipathic membranes at hydrophobic/hydrophilic interfaces, reversing the hydrophobicity of the surface. In this study, molecular dynamics simulation techniques have been used to model the process by which a specific class I hydrophobin, SC3, binds to a range of hydrophobic/hydrophilic interfaces. The structure of SC3 used in this investigation was modeled based on the crystal structure of the class II hydrophobin HFBII using the assumption that the disulfide pairings of the eight conserved cysteine residues are maintained. The proposed model for SC3 in aqueous solution is compact and globular containing primarily beta-strand and coil structures. The behavior of this model of SC3 was investigated at an air/water, an oil/water, and a hydrophobic solid/water interface. It was found that SC3 preferentially binds to the interfaces via the loop region between the third and fourth cysteine residues and that binding is associated with an increase in alpha-helix formation in qualitative agreement with experiment. Based on a combination of the available experiment data and the current simulation studies, we propose a possible model for SC3 self-assembly on a hydrophobic solid/water interface.
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Affiliation(s)
- Hao Fan
- Groningen Biomolecular Sciences and Biotechnology Institute (GBB), Department of Biophysical Chemistry, University of Groningen, Groningen, the Netherlands
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28
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Corvis Y, Brezesinski G, Rink R, Walcarius A, Van der Heyden A, Mutelet F, Rogalska E. Analytical Investigation of the Interactions between SC3 Hydrophobin and Lipid Layers: Elaborating of Nanostructured Matrixes for Immobilizing Redox Systems. Anal Chem 2006; 78:4850-64. [PMID: 16841903 DOI: 10.1021/ac0602064] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrophobins are highly tensioactive fungal proteins with a pronounced affinity for interfaces and a propensity for self-assembly. Recently, these proteins were shown to be useful in retaining different molecules on solid surfaces. This finding offers a possibility for developing new functional materials, while creating the necessity of further research at a deeper mechanistic level. In this work, the mechanisms governing the surface phenomena were studied using native Schizophyllum commune hydrophobin (SC3) and lipid mono- and bilayers; the soft matter systems were used to get a handle on the interactive protein/interface effects at a molecular level. The results obtained indicated that the SC3/lipid membrane interactions were adjusted by protein conformational adaptation, allowing its incorporation into lipid matrixes; the incorporation of a chelating SC3 hydrophobin (PFA-SC3) in a monoolein cubic phase yielded a biomimetic, cell-like system of Cu(II) cation immobilization. This system, which is suitable for modifying electrode surface and monitoring the Cu(II)/Cu(0) redox process, may be of practical interest in switching and sensing.
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Affiliation(s)
- Yohann Corvis
- Groupe d'Etude des Vecteurs Supramoléculaires du Médicament UMR 7565 CNRS/Université Henri Poincaré Nancy 1, Faculté des Sciences, BP 239, 54506 Vandoeuvre-lès-Nancy Cedex, France
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29
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Linder MB, Szilvay GR, Nakari-Setälä T, Penttilä ME. Hydrophobins: the protein-amphiphiles of filamentous fungi. FEMS Microbiol Rev 2005; 29:877-96. [PMID: 16219510 DOI: 10.1016/j.femsre.2005.01.004] [Citation(s) in RCA: 412] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2004] [Revised: 12/20/2004] [Accepted: 01/21/2005] [Indexed: 11/22/2022] Open
Abstract
Hydrophobins are surface active proteins produced by filamentous fungi. They have a role in fungal growth as structural components and in the interaction of fungi with their environment. They have, for example, been found to be important for aerial growth, and for the attachment of fungi to solid supports. Hydrophobins also render fungal structures, such as spores, hydrophobic. The biophysical properties of the isolated proteins are remarkable, such as strong adhesion, high surface activity and the formation of various self-assembled structures. The first high resolution three dimensional structure of a hydrophobin, HFBII from Trichoderma reesei, was recently solved. In this review, the properties of hydrophobins are analyzed in light of these new data. Various application possibilities are also discussed.
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Affiliation(s)
- Markus B Linder
- VTT Biotechnology, Tietotie 2, P.O.Box 1500, FIN-02044 VTT, Finland.
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30
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Xu Y, Shen J, Luo X, Zhu W, Chen K, Ma J, Jiang H. Conformational transition of amyloid beta-peptide. Proc Natl Acad Sci U S A 2005; 102:5403-7. [PMID: 15800039 PMCID: PMC556260 DOI: 10.1073/pnas.0501218102] [Citation(s) in RCA: 206] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2004] [Indexed: 12/19/2022] Open
Abstract
The amyloid beta-peptides (Abetas), containing 39-43 residues, are the key protein components of amyloid deposits in Alzheimer's disease. To structurally characterize the dynamic behavior of Abeta(40), 12 independent long-time molecular dynamics (MD) simulations for a total of 850 ns were performed on both the wide-type peptide and its mutant in both aqueous solution and a biomembrane environment. In aqueous solution, an alpha-helix to beta-sheet conformational transition for Abeta(40) was observed, and an entire unfolding process from helix to coil was traced by MD simulation. Structures with beta-sheet components were observed as intermediates in the unfolding pathway of Abeta(40). Four glycines (G(25), G(29), G(33), and G(37)) are important for Abeta(40) to form beta-sheet in aqueous solution; mutations of these glycines to alanines almost abolished the beta-sheet formation and increased the content of the helix component. In the dipalmitoyl phosphatidylcholine (DPPC) bilayer, the major secondary structure of Abeta(40) is a helix; however, the peptide tends to exit the membrane environment and lie down on the surface of the bilayer. The dynamic feature revealed by our MD simulations rationalized several experimental observations for Abeta(40) aggregation and amyloid fibril formation. The results of MD simulations are beneficial to understanding the mechanism of amyloid formation and designing the compounds for inhibiting the aggregation of Abeta and amyloid fibril formation.
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Affiliation(s)
- Yechun Xu
- Center for Drug Discovery and Design, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Graduate School of Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
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31
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Nichols MR, Moss MA, Reed DK, Hoh JH, Rosenberry TL. Rapid assembly of amyloid-beta peptide at a liquid/liquid interface produces unstable beta-sheet fibers. Biochemistry 2005; 44:165-73. [PMID: 15628857 DOI: 10.1021/bi048846t] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Accumulation of aggregated amyloid-beta peptide (Abeta) in the brain is a pathological hallmark of Alzheimer's disease (AD). In vitro studies indicate that the 40- to 42-residue Abeta peptide in solution will undergo self-assembly leading to the transient appearance of soluble protofibrils and ultimately to insoluble fibrils. The Abeta peptide is amphiphilic and accumulates preferentially at a hydrophilic/hydrophobic interface. Solid surfaces and air-water interfaces have been shown previously to promote Abeta aggregation, but detailed characterization of these aggregates has not been presented. In this study Abeta(1-40) introduced to aqueous buffer in a two-phase system with chloroform aggregated 1-2 orders of magnitude more rapidly than Abeta in the buffer alone. The interface-induced aggregates were released into the aqueous phase and persisted for 24-72 h before settling as a visible precipitate at the interface. Thioflavin T fluorescence and circular dichroism analyses confirmed that the Abeta aggregates had a beta-sheet secondary structure. However, these aggregates were far less stable than Abeta(1-40) protofibrils prepared in buffer alone and disaggregated completely within 3 min on dilution. Atomic force microscopy revealed that the aggregates consisted of small globules 4-5 nm in height and long flexible fibers composed of these globules aligned roughly along a longitudinal axis, a morphology distinct from that of Abeta protofibrils prepared in buffer alone. The relative instability of the fibers was supported by fiber interruptions apparently introduced by brief washing of the AFM grids. To our knowledge, unstable aggregates of Abeta with beta-sheet structure and fibrous morphology have not been reported previously. Our results provide the clearest evidence yet that the intrinsic beta-sheet structure of an in vitro Abeta aggregate depends on the aggregation conditions and is reflected in the stability of the aggregate and the morphology observed by atomic force microscopy. Resolution of these structural differences at the molecular level may provide important clues to the further understanding of amyloid formation in vivo.
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Affiliation(s)
- Michael R Nichols
- Department of Neuroscience, Mayo Clinic College of Medicine, 4500 San Pablo Road, Jacksonville, Florida 32224, USA.
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32
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Wang X, Permentier HP, Rink R, Kruijtzer JAW, Liskamp RMJ, Wösten HAB, Poolman B, Robillard GT. Probing the self-assembly and the accompanying structural changes of hydrophobin SC3 on a hydrophobic surface by mass spectrometry. Biophys J 2005; 87:1919-28. [PMID: 15345568 PMCID: PMC1304595 DOI: 10.1529/biophysj.104.041616] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The fungal class I hydrophobin SC3 self-assembles into an amphipathic membrane at hydrophilic-hydrophobic interfaces such as the water-air and water-Teflon interface. During self-assembly, the water-soluble state of SC3 proceeds via the intermediate alpha-helical state to the stable end form called the beta-sheet state. Self-assembly of the hydrophobin at the Teflon surface is arrested in the alpha-helical state. The beta-sheet state can be induced at elevated temperature in the presence of detergent. The structural changes of SC3 were monitored by various mass spectrometry techniques. We show that the so-called second loop of SC3 (C39-S72) has a high affinity for Teflon. Binding of this part of SC3 to Teflon was accompanied by the formation of alpha-helical structure and resulted in low solvent accessibility. The solvent-protected region of the second loop extended upon conversion to the beta-sheet state. In contrast, the C-terminal part of SC3 became more exposed to the solvent. The results indicate that the second loop of class I hydrophobins plays a pivotal role in self-assembly at the hydrophilic-hydrophobic interface. Of interest, this loop is much smaller in case of class II hydrophobins, which may explain the differences in their assembly.
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Affiliation(s)
- X Wang
- Department of Biochemistry and Mass Spectrometry Core Facility, University of Groningen, Groningen, The Netherlands
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33
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Ash WL, Zlomislic MR, Oloo EO, Tieleman DP. Computer simulations of membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2005; 1666:158-89. [PMID: 15519314 DOI: 10.1016/j.bbamem.2004.04.012] [Citation(s) in RCA: 204] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2004] [Accepted: 04/29/2004] [Indexed: 11/30/2022]
Abstract
Computer simulations are rapidly becoming a standard tool to study the structure and dynamics of lipids and membrane proteins. Increasing computer capacity allows unbiased simulations of lipid and membrane-active peptides. With the increasing number of high-resolution structures of membrane proteins, which also enables homology modelling of more structures, a wide range of membrane proteins can now be simulated over time spans that capture essential biological processes. Longer time scales are accessible by special computational methods. We review recent progress in simulations of membrane proteins.
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Affiliation(s)
- Walter L Ash
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary AB, Canada T2N 1N4
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34
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Expression and Engineering of Fungal Hydrophobins. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/s1874-5334(05)80012-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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35
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Fuchs U, Czymmek KJ, Sweigard JA. Five hydrophobin genes in Fusarium verticillioides include two required for microconidial chain formation. Fungal Genet Biol 2004; 41:852-64. [PMID: 15288021 DOI: 10.1016/j.fgb.2004.04.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2003] [Accepted: 04/27/2004] [Indexed: 10/26/2022]
Abstract
Five hydrophobin genes have been identified in the fungal corn pathogen Fusarium verticillioides. HYD1, HYD2, and HYD3 encode Class I hydrophobins. The predicted structures of Hyd1p and Hyd2p are 80% similar, while Hyd3p has an unusually small number of amino acids between the third and fourth cysteines. HYD4 and HYD5 encode Class II hydrophobins. Mutants with HYD1-5 individually deleted and a hyd1deltahyd2delta double mutant were similar to wild-type strains in the amount of disease caused in a corn seedling infection assay and in the number of microconidia produced. Microconidial chains were rare in hyd1delta and hyd2delta mutants as microconidia were present almost exclusively as false heads. Transformation of hyd1delta and hyd2delta mutants with HYD1 and HYD2, respectively, restored microconidial chain formation, but transformation with HYD1::AcGFP and HYD2::AcGFP did not complement the mutation. HYD1::AcGFP and HYD2::AcGFP localized to the outside of conidia in false heads and in chains.
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MESH Headings
- Amino Acid Sequence
- Consensus Sequence
- Cryoelectron Microscopy
- DNA, Fungal/chemistry
- Fungal Proteins/genetics
- Fungal Proteins/physiology
- Fusarium/cytology
- Fusarium/genetics
- Fusarium/physiology
- Fusarium/ultrastructure
- Gene Deletion
- Genes, Fungal
- Genes, Reporter
- Genetic Complementation Test
- Green Fluorescent Proteins
- Luminescent Proteins/genetics
- Luminescent Proteins/metabolism
- Microscopy
- Microscopy, Confocal
- Molecular Sequence Data
- Morphogenesis/genetics
- Morphogenesis/physiology
- Mutagenesis, Insertional
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology
- Spores, Fungal/cytology
- Spores, Fungal/genetics
- Spores, Fungal/growth & development
- Spores, Fungal/ultrastructure
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Affiliation(s)
- Uta Fuchs
- Max-Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, D-35043 Marburg, Germany
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36
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Patra M, Karttunen M, Hyvönen MT, Falck E, Vattulainen I. Lipid Bilayers Driven to a Wrong Lane in Molecular Dynamics Simulations by Subtle Changes in Long-Range Electrostatic Interactions. J Phys Chem B 2004. [DOI: 10.1021/jp031281a] [Citation(s) in RCA: 168] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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37
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Hakanpää J, Paananen A, Askolin S, Nakari-Setälä T, Parkkinen T, Penttilä M, Linder MB, Rouvinen J. Atomic resolution structure of the HFBII hydrophobin, a self-assembling amphiphile. J Biol Chem 2003; 279:534-9. [PMID: 14555650 DOI: 10.1074/jbc.m309650200] [Citation(s) in RCA: 190] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Hydrophobins are proteins specific to filamentous fungi. Hydrophobins have several important roles in fungal physiology, for example, adhesion, formation of protective surface coatings, and the reduction of the surface tension of water, which allows growth of aerial structures. Hydrophobins show remarkable biophysical properties, for example, they are the most powerful surface-active proteins known. To this point the molecular basis of the function of this group of proteins has been largely unknown. We have now determined the crystal structure of the hydrophobin HFBII from Trichoderma reesei at 1.0 A resolution. HFBII has a novel, compact single domain structure containing one alpha-helix and four antiparallel beta-strands that completely envelop two disulfide bridges. The protein surface is mainly hydrophilic, but two beta-hairpin loops contain several conserved aliphatic side chains that form a flat hydrophobic patch that makes the molecule amphiphilic. The amphiphilicity of the HFBII molecule is expected to be a source for surface activity, and we suggest that the behavior of this surfactant is greatly enhanced by the self-assembly that is favored by the combination of size and rigidity. This mechanism of function is supported by atomic force micrographs that show highly ordered arrays of HFBII at the air water interface. The data presented show that much of the current views on structure function relations in hydrophobins must be re-evaluated.
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Affiliation(s)
- Johanna Hakanpää
- Department of Chemistry, University of Joensuu, PO Box 111, 80101 Joensuu, Finland
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38
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Stroud PA, Goodwin JS, Butko P, Cannon GC, McCormick CL. Experimental evidence for multiple assembled states of Sc3 from Schizophyllum commune. Biomacromolecules 2003; 4:956-67. [PMID: 12857079 DOI: 10.1021/bm034045e] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The hydrophobin Sc3 from the fungus Schizophyllum commune assembles from the aqueous phase into ordered structures with substantially different characteristics depending upon experimental conditions. Under the first condition, a vortexing procedure widely reported in the literature, interfacial assembly yields highly ordered, stacked beta-sheets. We have also observed a previously unreported assembly of Sc3 under a second condition, which occurs in a time-dependent manner from quiescent solution. The resulting types of assembled states have been compared utilizing fluorescence techniques, sodium dodecyl sulfate polyacrylamide gel electrophoresis, immunoblotting, density gradient centrifugation, and phase contrast and atomic force microscopy. A model based on this study and previous literature is proposed that suggests three distinct states of Sc3: (1) soluble Sc3 consisting of unimers or multimers in micelle-like association, (2) interfacially assembled I-Sc3 with highly ordered, stacked beta-sheets, presumably formed in a templated manner at the air/water interface of microscopic bubbles generated by vortexing, and (3) solution-assembled S-Sc3, a less-ordered structure formed in a time-dependent manner in the absence of an interface.
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Affiliation(s)
- Paul A Stroud
- Department of Polymer Science and Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, Mississippi 39406-0076, USA
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