34 results on '"Heymann, J. B."'
Search Results
2. Structural aspects of the cytochromeb 6 f complex; structure of the lumen-side domain of cytochromef
- Author
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Cramer, W. A., Martinez, S. E., Huang, D., Tae, G. -S., Everly, R. M., Heymann, J. B., Cheng, R. H., Baker, T. S., and Smith, J. L.
- Published
- 1994
- Full Text
- View/download PDF
3. Sampling effects influence heights measured with atomic force microscopy
- Author
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Heymann, J. B., Möller, C., and Müller, D. J.
- Published
- 2002
4. Imaging streptavidin 2D crystals on biotinylated lipid monolayers at high resolution with the atomic force microscope
- Author
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SCHEURING, S., MÜLLER, D. J., RINGLER, P., HEYMANN, J. B., and ENGEL, A.
- Published
- 1999
5. Organising multi-dimensional biological image information: The BioImage Database
- Author
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Carazo, J. M., Stelzer, E. H. K., Engel, A., Fita, I., Henn, C., Machtynger, J., McNeil, P., Shotton, D. M., Chagoyen, M., de Alarcón, P. A., Fritsch, R., Heymann, J. B., Kalko, S., Pittet, J. J., Rodriguez-Tomé, P., Boudier, T., Carazo, J. M., Stelzer, E. H. K., Engel, A., Fita, I., Henn, C., Machtynger, J., McNeil, P., Shotton, D. M., Chagoyen, M., de Alarcón, P. A., Fritsch, R., Heymann, J. B., Kalko, S., Pittet, J. J., Rodriguez-Tomé, P., and Boudier, T.
- Abstract
Nowadays it is possible to unravel complex information at all levels of cellular organization by obtaining multi-dimensional image information. at the macromolecular level, three-dimensional (3D) electron microscopy, together with other techniques, is able to reach resolutions at the nanometer or subnanometer level. The information is delivered in the form of 3D volumes containing samples of a given function, for example, the electron density distribution within a given macromolecule. The same situation happens at the cellular level with the new forms of light microscopy, particularly confocal microscopy, all of which produce biological 3D volume information. Furthermore, it is possible to record sequences of images over time (videos), as well as sequences of volumes, bringing key information on the dynamics of living biological systems. It is in this context that work on bioimage started two years ago, and that its first version is now presented here. In essence, Bioimage is a database specifically designed to contain multi-dimensional images, perform queries and interactively work with the resulting multi-dimensional information on the World Wide Web, as well as accomplish the required cross-database links. Two sister home pages of bioimage can be accessed at http://www.bioimage.org and http://www-embl.bioimage.org
- Published
- 2017
6. Dynamics of the Protrusion Domain of Herpes Simplex Virus Capsid from Time-Resolved Cryo-EM and Molecular Modelling
- Author
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Heymann, J B, primary, Trus, B L, additional, and Steven, A C, additional
- Published
- 2005
- Full Text
- View/download PDF
7. Recent Advances in Electron Cryotomography and their Application to Imaging Purified Protein Complexes, Isolated Organelles, and Small Cells
- Author
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Iancu, C V, primary, Murphy, G E, additional, Wright, E R, additional, Benjamin, J, additional, Tivol, W F, additional, Dias, D P, additional, Heymann, J B, additional, and Jensen, G, additional
- Published
- 2005
- Full Text
- View/download PDF
8. Organising multi-dimensional biological image information: The BioImage Database
- Author
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Carazo, J. M., primary, Stelzer, E. H. K., additional, Engel, A., additional, Fita, I., additional, Henn, C., additional, Machtynger, J., additional, McNeil, P., additional, Shotton, D. M., additional, Chagoyen, M., additional, de Alarcon, P. A., additional, Fritsch, R., additional, Heymann, J. B., additional, Kalko, S., additional, Pittet, J. J., additional, Rodriguez-Tome, P., additional, and Boudier, T., additional
- Published
- 1999
- Full Text
- View/download PDF
9. Characterization of Electrostatic and Nonelectrostatic Components of Protein−Membrane Binding Interactions
- Author
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Heymann, J. B., primary, Zakharov, S. D., additional, Zhang, Y.-L., additional, and Cramer, W. A., additional
- Published
- 1996
- Full Text
- View/download PDF
10. Structure-Function of the Channel-Forming Colicins
- Author
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Cramer, W A, primary, Heymann, J B, additional, Schendel, S L, additional, Deriy, B N, additional, Cohen, F S, additional, Elkins, P A, additional, and Stauffacher, C V, additional
- Published
- 1995
- Full Text
- View/download PDF
11. Characterization of the Chloroplast Cytochrome b6f Complex as a Structural and Functional Dimer
- Author
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Huang, D., primary, Everly, R. M., additional, Cheng, R. H., additional, Heymann, J. B., additional, Schaegger, H., additional, Sled, V., additional, Ohnishi, T., additional, Baker, T. S., additional, and Cramer, W. A., additional
- Published
- 1994
- Full Text
- View/download PDF
12. Structural aspects of the cytochromeb6f complex; structure of the lumen-side domain of cytochromef
- Author
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Cramer, W. A., Martinez, S. E., Huang, D., Tae, G. -S., Everly, R. M., Heymann, J. B., Cheng, R. H., Baker, T. S., and Smith, J. L.
- Abstract
The following findings concerning the structure of the cytochromeb
6 f complex and its component polypeptides, cytb6 , subunit IV and cytochromef subunit are discussed:(1)Comparison of the amino acid sequences of 13 and 16 cytochromeb6 and subunit IV polypeptides, respectively, led to (a) reconsideration of the helix lengths and probable interface regions, (b) identification of two likely surface-seeking helices in cytb6 and one in SU IV, and (c) documentation of a high degree of sequence invariance compared to the mitochondrial cytochrome. The extent of identity is particularly high (88% for conserved and pseudoconserved residues) in the segments of cytb6 predicted to be extrinsic on then-side of the membrane.(2)The intramembrane attractive forces betweentrans-membrane helices that normally stabilize the packing of integral membrane proteins are relatively weak.(3)The complex isolated in dimeric form has been visualized, along with isolated monomer, by electron microscopy. The isolated dimer is much more active than the monomer, is the major form of the complex isolated and purified from chloroplasts, and is inferred to be a functional form in the membrane.(4)The isolated cytb6 f complex contains one molecule of chlorophylla.(5)The structure of the 252 residue lumen-side domain of cytochromef isolated from turnip chloroplasts has been solved by X-ray diffraction analysis to a resolution of 2.3 Å.- Published
- 1994
- Full Text
- View/download PDF
13. Organising multi-dimensional biological image information: The BioImage Database
- Author
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Carazo, J. M., Stelzer, E. H. K., Engel, A., Fita, I., Henn, C., Machtynger, J., McNeil, P., Shotton, D. M., Chagoyen, M., de Alarcón, P. A., Fritsch, R., Heymann, J. B., Kalko, S., Pittet, J. J., Rodriguez-Tomé, P., Boudier, T., Carazo, J. M., Stelzer, E. H. K., Engel, A., Fita, I., Henn, C., Machtynger, J., McNeil, P., Shotton, D. M., Chagoyen, M., de Alarcón, P. A., Fritsch, R., Heymann, J. B., Kalko, S., Pittet, J. J., Rodriguez-Tomé, P., and Boudier, T.
- Abstract
Nowadays it is possible to unravel complex information at all levels of cellular organization by obtaining multi-dimensional image information. at the macromolecular level, three-dimensional (3D) electron microscopy, together with other techniques, is able to reach resolutions at the nanometer or subnanometer level. The information is delivered in the form of 3D volumes containing samples of a given function, for example, the electron density distribution within a given macromolecule. The same situation happens at the cellular level with the new forms of light microscopy, particularly confocal microscopy, all of which produce biological 3D volume information. Furthermore, it is possible to record sequences of images over time (videos), as well as sequences of volumes, bringing key information on the dynamics of living biological systems. It is in this context that work on bioimage started two years ago, and that its first version is now presented here. In essence, Bioimage is a database specifically designed to contain multi-dimensional images, perform queries and interactively work with the resulting multi-dimensional information on the World Wide Web, as well as accomplish the required cross-database links. Two sister home pages of bioimage can be accessed at http://www.bioimage.org and http://www-embl.bioimage.org
14. The Isolation and Characterization of Volutin Granules as Subcellular Components Involved in Biological Phosphorus Removal
- Author
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Heymann, J. B., primary, Eagle, L. M., additional, Greben, H. A., additional, and Potgieter, D. J. J., additional
- Published
- 1989
- Full Text
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15. The Biochemistry of Enhanced Phosphorus Removal by Activated Sludge
- Author
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Heymann, J. B., primary
- Published
- 1985
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16. Retrovirus Capsid Assembly and Polymorphism Studied by Cryo-EM and Cryo-ET.
- Author
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Cardone, G., Cheng, N., Heymann, J. B., Butan, C., Winkler, D. C., Purdy, J. G., Craven, R. C., and Steven, A. C.
- Subjects
RETROVIRUSES - Abstract
Extended abstract of a paper presented at Microscopy and Microanalysis 2010 in Portland, Oregon, USA, August 1 – August 5, 2010. [ABSTRACT FROM PUBLISHER]
- Published
- 2010
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17. The isolation and characterization of volutin granules as subcellular components involved in biological phosphorus removal
- Author
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Greben, H. A., Eagle, L. M., Heymann, J. B., and Potgieter, D. J. J. Potgieter
- Subjects
PHOSPHORUS ,ACTIVATED sludge process - Published
- 1989
18. Local resolution estimates of cryoEM reconstructions.
- Author
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Vilas JL, Heymann JB, Tagare HD, Ramirez-Aportela E, Carazo JM, and Sorzano C
- Subjects
- Cryoelectron Microscopy, Algorithms
- Abstract
The field of cryoEM has quickly advanced in last years with the new biochemical, technological, methodological and computational developments. It has allowed significant progresses in Structural Biology, typically reaching quasi-atomic resolutions in the reconstructed maps. However, this rapid advance has also generated new questions relevant to resolution estimates. The global resolution metrics and their criteria have been deeply discussed in the last decade, but despite that, it remains as an important issue in the field. Recently, the introduction of local resolution measurements has changed how cryoEM reconstructions are interpreted, providing information about the existence of heterogeneity, flexibility, and angular assignment errors, and using it as a tool to aid in modeling. In this review we revisit the concept of local resolution and the different algorithms in the current state of the art. However, the concept of local resolution is not uniquely defined, and each implementation measures different features. This may lead to inappropriate interpretation of local resolution maps. Hence, a set of good practices is provided in this review to avoid misleading and over-interpretation of the reconstructions., (Copyright © 2020 Elsevier Ltd. All rights reserved.)
- Published
- 2020
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19. Capsid structure of Kaposi's sarcoma-associated herpesvirus, a gammaherpesvirus, compared to those of an alphaherpesvirus, herpes simplex virus type 1, and a betaherpesvirus, cytomegalovirus.
- Author
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Trus BL, Heymann JB, Nealon K, Cheng N, Newcomb WW, Brown JC, Kedes DH, and Steven AC
- Subjects
- Amino Acid Sequence, Capsid genetics, Capsid isolation & purification, Capsid metabolism, Cell Line, Cryoelectron Microscopy, Cytomegalovirus genetics, Cytomegalovirus metabolism, Herpesvirus 1, Human genetics, Herpesvirus 1, Human metabolism, Herpesvirus 8, Human genetics, Herpesvirus 8, Human metabolism, Humans, Molecular Sequence Data, Phylogeny, Capsid ultrastructure, Capsid Proteins, Cytomegalovirus ultrastructure, Herpesvirus 1, Human ultrastructure, Herpesvirus 8, Human ultrastructure
- Abstract
The capsid of Kaposi's sarcoma-associated herpesvirus (KSHV) was visualized at 24-A resolution by cryoelectron microscopy. Despite limited sequence similarity between corresponding capsid proteins, KSHV has the same T=16 triangulation number and much the same capsid architecture as herpes simplex virus (HSV) and cytomegalovirus (CMV). Its capsomers are hexamers and pentamers of the major capsid protein, forming a shell with a flat, close-packed, inner surface (the "floor") and chimney-like external protrusions. Overlying the floor at trigonal positions are (alpha beta(2)) heterotrimers called triplexes. The floor structure is well conserved over all three viruses, and the most variable capsid features reside on the outer surface, i.e., in the shapes of the protrusions and triplexes, in which KSHV resembles CMV and differs from HSV. Major capsid protein sequences from the three subfamilies have some similarity, which is closer between KSHV and CMV than between either virus and HSV. The triplex proteins are less highly conserved, but sequence analysis identifies relatively conserved tracts. In alphaherpesviruses, the alpha-subunit (VP19c in HSV) has a 100-residue N-terminal extension and an insertion near the C terminus. The small basic capsid protein sequences are highly divergent: whereas the HSV and CMV proteins bind only to hexons, difference mapping suggests that the KSHV protein, ORF65, binds around the tips of both hexons and pentons.
- Published
- 2001
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20. Bsoft: image and molecular processing in electron microscopy.
- Author
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Heymann JB
- Subjects
- Computer Systems, Documentation, Electronic Data Processing, Microscopy, Atomic Force, Microscopy, Electron methods, Molecular Structure, Image Processing, Computer-Assisted methods, Models, Molecular, Software
- Abstract
Software for the processing of electron micrographs in structural biology suffers from incompatibility between different packages, poor definition and choice of conventions, and a lack of coherence in software development. The solution lies in adopting a common philosophy of interaction and conventions between the packages. To understand the choices required to have such common interfaces, I am developing a package called "Bsoft." Its foundations lie in the variety of different image file formats used in electron microscopy-a continually frustrating experience to the user and programmer alike. In Bsoft, this problem is greatly diminished by support for many different formats (including MRC, SPIDER, IMAGIC, SUPRIM, and PIF) and by separating algorithmic issues from image format-specific issues. In addition, I implemented a generalized functionality for reading the tag-base STAR (self-defining text archiving and retrieval) parameter file format as a mechanism to exchanging parameters between different packages. Bsoft is written in highly portable code (tested on several Unix systems and under VMS) and offers a continually growing range of image processing functionality, such as Fourier transformation, cross-correlation, and interpolation. Finally, prerequisites for software collaboration are explored, which include agreements on information exchange and conventions, and tests to evaluate compatibility between packages., (Copyright 2001 Academic Press.)
- Published
- 2001
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- View/download PDF
21. Structural determinants of water permeation through aquaporin-1.
- Author
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Murata K, Mitsuoka K, Hirai T, Walz T, Agre P, Heymann JB, Engel A, and Fujiyoshi Y
- Subjects
- Amino Acid Sequence, Aquaporin 1, Cell Membrane Permeability, Crystallography methods, Electrons, Models, Molecular, Molecular Sequence Data, Protein Conformation, Protein Folding, Protons, Aquaporins chemistry, Water chemistry
- Abstract
Human red cell AQP1 is the first functionally defined member of the aquaporin family of membrane water channels. Here we describe an atomic model of AQP1 at 3.8A resolution from electron crystallographic data. Multiple highly conserved amino-acid residues stabilize the novel fold of AQP1. The aqueous pathway is lined with conserved hydrophobic residues that permit rapid water transport, whereas the water selectivity is due to a constriction of the pore diameter to about 3 A over a span of one residue. The atomic model provides a possible molecular explanation to a longstanding puzzle in physiology-how membranes can be freely permeable to water but impermeable to protons.
- Published
- 2000
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22. Atomic force microscopy of native purple membrane.
- Author
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Müller DJ, Heymann JB, Oesterhelt F, Möller C, Gaub H, Büldt G, and Engel A
- Subjects
- Bacteriorhodopsins chemistry, Bacteriorhodopsins ultrastructure, Crystallization, Halobacterium, Intracellular Membranes ultrastructure, Microscopy, Atomic Force, Models, Molecular, Molecular Structure, Purple Membrane ultrastructure, Purple Membrane chemistry
- Abstract
Atomic force microscopy (AFM) allows the observation of surface structures of purple membrane (PM) in buffer solution with subnanometer resolution. This offers the possibility to classify the major conformations of the native bacteriorhodopsin (BR) surfaces and to map the variability of individual polypeptide loops connecting transmembrane alpha-helices of BR. The position, the variability and the flexibility of these loops depend on the packing arrangement of BR molecules in the lipid bilayer with significant differences observed between the trigonal and orthorhombic crystal forms. Cleavage of the Schiff base bond leads to a disassembly of the trigonal PM crystal, which is restored by regenerating the bleached PM. The combination of single molecule AFM imaging and single molecule force-spectroscopy provides an unique insight into the interactions between individual BR molecules and the PM, and between secondary structure elements within BR.
- Published
- 2000
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23. The fold of human aquaporin 1.
- Author
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de Groot BL, Heymann JB, Engel A, Mitsuoka K, Fujiyoshi Y, and Grubmüller H
- Subjects
- Aquaporin 1, Aquaporins ultrastructure, Bacteriorhodopsins chemistry, Bacteriorhodopsins metabolism, Bacteriorhodopsins ultrastructure, Blood Group Antigens, Cryoelectron Microscopy, Humans, Models, Molecular, Peptide Fragments chemistry, Peptide Fragments metabolism, Peptide Fragments ultrastructure, Protein Structure, Secondary, Aquaporins chemistry, Aquaporins metabolism, Protein Folding
- Abstract
The fold of human aquaporin 1 is determined from cryo-electron microscopic data at 4.5 A resolution. The monomeric structure consists of two transmembrane triple helices arranged around a pseudo-2-fold axis connected by a long flexible extracellular loop. Each triplet contains between its second and third helix a functional loop containing the highly conserved fingerprint NPA motif. These functional loops are assumed to fold inwards between the two triplets, thereby forming the heart of the water channel. The helix topology was determined from the directionality pattern of each of the six transmembrane helices with respect to the membrane, together with constraints defined by the sequence and atomic force microscopy data. The directionality of the helices was determined by collecting the best-fitting orientations resulting from a search through the three-dimensional experimental map for a large number of alpha-helical fragments. Tests on cryo-electron crystallographic bacteriorhodopsin data suggest that our method is generally applicable to determine the topology of helical proteins for which only medium-resolution electron microscopy data are available., (Copyright 2000 Academic Press.)
- Published
- 2000
- Full Text
- View/download PDF
24. Conformations of the rhodopsin third cytoplasmic loop grafted onto bacteriorhodopsin.
- Author
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Heymann JB, Pfeiffer M, Hildebrandt V, Kaback HR, Fotiadis D, Groot B, Engel A, Oesterhelt D, and Müller DJ
- Subjects
- Amino Acid Sequence, Animals, Bacteriorhodopsins genetics, Bacteriorhodopsins ultrastructure, Cattle, Microscopy, Atomic Force, Models, Molecular, Molecular Sequence Data, Mutation, Protein Conformation, Protein Structure, Secondary, Recombinant Proteins chemistry, Recombinant Proteins genetics, Recombinant Proteins ultrastructure, Rhodopsin genetics, Rhodopsin ultrastructure, Bacteriorhodopsins chemistry, Rhodopsin chemistry
- Abstract
Background: The third cytoplasmic loop of rhodopsin (Rho EF) is important in signal transduction from the retinal in rhodopsin to its G protein, transducin. This loop also interacts with rhodopsin kinase, which phosphorylates light-activated rhodopsin, and arrestin, which displaces transducin from light-activated phosphorylated rhodopsin., Results: We replaced eight residues of the EF loop of bacteriorhodopsin (BR) with 24 residues from the third cytoplasmic loop of bovine Rho EF. The surfaces of purple membrane containing the mutant BR (called IIIN) were imaged by atomic force microscopy (AFM) under physiological conditions to a resolution of 0.5-0.7 nm. The crystallinity and extracellular surface of IIIN were not perturbed, and the cytoplasmic surface of IIIN increased in height compared with BR, consistent with the larger loop. Ten residues of Rho EF were excised by V8 protease, revealing helices E and F in the AFM topographs. Rho EF was modeled onto the BR structure, and the envelope derived from the AFM data of IIIN was used to select probable models., Conclusions: A likely conformation of Rho EF involves some extension of helices E and F, with the tip of the loop lying over helix C and projecting towards the C terminus. This is consistent with mutagenesis data showing the TTQ transducin-binding motif close to loop CD, and cysteine cross-linking data indicating the C-terminal part of Rho EF to be close to the CD loop.
- Published
- 2000
- Full Text
- View/download PDF
25. Structural clues in the sequences of the aquaporins.
- Author
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Heymann JB and Engel A
- Subjects
- Amino Acid Sequence, Aquaporin 1, Blood Group Antigens, Conserved Sequence, Crystallography, X-Ray, Humans, Macromolecular Substances, Models, Molecular, Molecular Sequence Data, Protein Structure, Quaternary, Protein Structure, Secondary, Aquaporins chemistry
- Abstract
The large number of sequences available for the aquaporin family represents a valuable source of information to incorporate into three-dimensional structure determination. Phylogenetic analysis was used to define type sequences to avoid extreme over-representation of some subfamilies, and as a measure of the quality of multiple sequence alignment. Inspection of the sequence alignment suggested eight conserved segments that define the core architecture of six transmembrane helices and two functional loops, B and E, projecting into the plane of the membrane. The sum of the core segments and the minimum lengths of the interlinking loops constitute the 208 residues necessary to satisfy the aquaporin architecture. Analysis of hydrophobic and conservation periodicity and of correlated mutations across the alignment indicated the likely assignment and orientation of the helices in the bilayer. This assignment is examined with respect to the structure of the erythrocyte aquaporin 1 determined by electron crystallography. The aquaporin 1 tetramer is described as three rings of helices, each ring with a different exposure to the lipid environment. The sequence analysis clearly suggests that two helices are exposed along their whole lengths, two helices are exposed only at their N termini, and two helices are not exposed to lipid. It is further proposed that, besides loops B and E, the highly conserved motifs on helices 1 and 4, ExxxTxxF/L, could line the water channel., (Copyright 2000 Academic Press.)
- Published
- 2000
- Full Text
- View/download PDF
26. Charting the surfaces of the purple membrane.
- Author
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Heymann JB, Müller DJ, Landau EM, Rosenbusch JP, Pebay-Peyroula E, Büldt G, and Engel A
- Subjects
- Amino Acid Motifs, Bacteriorhodopsins chemistry, Cell Size, Computer Graphics, Databases, Factual, Electron Probe Microanalysis, Microscopy, Atomic Force, Models, Molecular, Reproducibility of Results, X-Ray Diffraction, Purple Membrane chemistry
- Abstract
The preponderance of structural data of the purple membrane from X-ray diffraction (XRD), electron crystallography (EC), and atomic force microscopy (AFM) allows us to ask questions about the structure of bacteriorhodopsin itself, as well as about the information derived from the different techniques. The transmembrane helices of bacteriorhodopsin are quite similar in both EC and XRD models. In contrast, the loops at the surfaces of the purple membrane show the highest variability between the atomic models, comparable to the height variance measured by AFM. The excellent agreement of the AFM topographs with the atomic models from XRD builds confidence in the results. Small technical difficulties in EC lead to poorer resolution of the loop structures, although the combination of atomic models with AFM surfaces allows clear interpretation of the extent and flexibility of the loop structures. While XRD remains the premier technique to determine very-high-resolution structures, EC offers a method to determine loop structures unhindered by three-dimensional crystal contacts, and AFM provides information about surface structures and their flexibility under physiological conditions., (Copyright 1999 Academic Press.)
- Published
- 1999
- Full Text
- View/download PDF
27. The structure of aquaporin-1 at 4.5-A resolution reveals short alpha-helices in the center of the monomer.
- Author
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Mitsuoka K, Murata K, Walz T, Hirai T, Agre P, Heymann JB, Engel A, and Fujiyoshi Y
- Subjects
- Aquaporin 1, Crystallography methods, Electrons, Erythrocytes chemistry, Image Processing, Computer-Assisted, Membrane Proteins chemistry, Models, Molecular, Water chemistry, Aquaporins chemistry, Protein Structure, Secondary
- Abstract
Aquaporin-1 is a water channel found in mammalian red blood cells that is responsible for high water permeability of its membrane. Our electron crystallographic analysis of the three-dimensional structure of aquaporin-1 at 4.5-A resolution confirms the previous finding that each subunit consists of a right-handed bundle of six highly tilted transmembrane helices that surround a central X-shaped structure. In our new potential map, the rod-like densities for the transmembrane helices show helically arranged protrusions, indicating the positions of side chains. Thus, in addition to the six transmembrane helices, observation of helically arranged side-chain densities allowed the identification of two short alpha-helices representing the two branches of the central X-shaped structure that extend to the extracellular and cytoplasmic membrane surfaces. The other two branches are believed to be loops connecting the short alpha-helix to a neighboring transmembrane helix. A pore found close to the center of the aquaporin-1 monomer is suggested to be the course of water flow with implications for the water selectivity., (Copyright 1999 Academic Press.)
- Published
- 1999
- Full Text
- View/download PDF
28. Visualizing 3D data obtained from microscopy on the Internet.
- Author
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Pittet JJ, Henn C, Engel A, and Heymann JB
- Subjects
- Animals, Humans, Hypermedia, Image Processing, Computer-Assisted, Microscopy, Atomic Force, Models, Molecular, Models, Theoretical, Online Systems, Programming Languages, Data Display, Databases as Topic, Diagnostic Imaging, Internet, Microscopy, Molecular Structure, User-Computer Interface
- Abstract
The Internet is a powerful communication medium increasingly exploited by business and science alike, especially in structural biology and bioinformatics. The traditional presentation of static two-dimensional images of real-world objects on the limited medium of paper can now be shown interactively in three dimensions. Many facets of this new capability have already been developed, particularly in the form of VRML (virtual reality modeling language), but there is a need to extend this capability for visualizing scientific data. Here we introduce a real-time isosurfacing node for VRML, based on the marching cube approach, allowing interactive isosurfacing. A second node does three-dimensional (3D) texture-based volume-rendering for a variety of representations. The use of computers in the microscopic and structural biosciences is extensive, and many scientific file formats exist. To overcome the problem of accessing such data from VRML and other tools, we implemented extensions to SGI's IFL (image format library). IFL is a file format abstraction layer defining communication between a program and a data file. These technologies are developed in support of the BioImage project, aiming to establish a database prototype for multidimensional microscopic data with the ability to view the data within a 3D interactive environment., (Copyright 1999 Academic Press.)
- Published
- 1999
- Full Text
- View/download PDF
29. Progress on the structure and function of aquaporin 1.
- Author
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Heymann JB, Agre P, and Engel A
- Subjects
- Animals, Aquaporin 1, Blood Group Antigens, Cattle, Crystallization, Crystallography, X-Ray, Erythrocyte Membrane chemistry, Glycosylation, Humans, Ion Channels physiology, Multigene Family, Protein Processing, Post-Translational, Protein Structure, Secondary, Recombinant Fusion Proteins chemistry, Recombinant Fusion Proteins metabolism, Structure-Activity Relationship, Aquaporins, Ion Channels chemistry, Models, Molecular, Protein Conformation, Water metabolism
- Abstract
Life exists in water as universal solvent, and cells need to deal with its influx and efflux. Nature has accomplished the almost impossible, creating membrane channels with both a high flux and a high specificity for water. The first water channel was discovered in red blood cell membranes. Today known as aquaporin-1, this channel was found to be closely related to the major integral protein (MIP)1 of the eye lens. Cloning and sequencing of numerous related proteins of the MIP family revealed the widespread occurrence of such channels, suggesting an essential physiological function. Their structures hold the clues to the remarkable water channel activity, as well as to the arrangement of transmembrane segments in general. Recent medium-resolution three-dimensional electron microscopic studies determined a tetrameric complex with six tilted transmembrane helices per monomer. The helices within each monomer surround a central density formed by two interhelical loops implicated by mutagenesis in the water channel function. A combination of sequence analysis and assignment of the observed densities to predicted helices provides a basis for speculation on the nature of the water course through the protein. In particular, four highly conserved polar residues, E142-N192-N76-E17, are proposed to form a chain of key groups involved in the pathway of water flow through the channel.
- Published
- 1998
- Full Text
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30. 2D crystallization of membrane proteins: rationales and examples.
- Author
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Hasler L, Heymann JB, Engel A, Kistler J, and Walz T
- Subjects
- Bacterial Proteins chemistry, Bacterial Proteins isolation & purification, Crystallization, Crystallography, X-Ray, Detergents pharmacology, Humans, Hydrogen-Ion Concentration, Lipid Bilayers, Membrane Lipids chemistry, Membrane Proteins drug effects, Membrane Proteins isolation & purification, Protein Conformation drug effects, Membrane Proteins chemistry
- Abstract
The difficulty in crystallizing channel proteins in three dimensions limits the use of X-ray crystallography in solving their structures. In contrast, the amphiphilic character of integral membrane proteins promotes their integration into artificial lipid bilayers. Protein-protein interactions may lead to ordering of the proteins within the lipid bilayer into two-dimensional crystals that are amenable to structural studies by electron crystallography and atomic force microscopy. While reconstitution of membrane proteins with lipids is readily achieved, the mechanisms for crystal formation during or after reconstitution are not well understood. The nature of the detergent and lipid as well as pH and counter-ions is known to influence the crystal type and quality. Protein-protein interactions may also promote crystal stacking and aggregation of the sheet-like crystals, posing problems in data collection. Although highly promising, the number of well-studied examples is still too small to draw conclusions that would be applicable to any membrane protein of interest. Here we discuss parameters influencing the outcome of two-dimensional crystallization trials using prominent examples of channel protein crystals and highlight areas where further improvements to crystallization protocols can be made.
- Published
- 1998
- Full Text
- View/download PDF
31. Electron and atomic force microscopy of membrane proteins.
- Author
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Heymann JB, Müller DJ, Mitsuoka K, and Engel A
- Subjects
- Aquaporin 1, Bacteriorhodopsins ultrastructure, Crystallization, Ion Channels ultrastructure, Aquaporins, Membrane Proteins ultrastructure, Microscopy, Atomic Force methods, Microscopy, Electron methods
- Abstract
Electron crystallography is becoming a powerful tool for the resolution of membrane protein structures. The past year has seen the production of a bacteriorhodopsin model at 3.5 A and the structure of aquaporin 1 approaching atomic resolution. Determination of surface topographies of 2D crystals using the atomic force microscope is similarly advancing to a level that reveals submolecular details. As the latter is operated in solution, membrane proteins can be observed at work.
- Published
- 1997
- Full Text
- View/download PDF
32. The three-dimensional structure of aquaporin-1.
- Author
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Walz T, Hirai T, Murata K, Heymann JB, Mitsuoka K, Fujiyoshi Y, Smith BL, Agre P, and Engel A
- Subjects
- Animals, Aquaporin 1, Blood Proteins chemistry, Blood Proteins ultrastructure, Erythrocytes chemistry, Ion Channels ultrastructure, Membrane Proteins chemistry, Membrane Proteins ultrastructure, Models, Molecular, Recombinant Proteins chemistry, Xenopus, Aquaporins, Ion Channels chemistry, Protein Conformation
- Abstract
The entry and exit of water from cells is a fundamental process of life. Recognition of the high water permeability of red blood cells led to the proposal that specialized water pores exist in the plasma membrane. Expression in Xenopus oocytes and functional studies of an erythrocyte integral membrane protein of relative molecular mass 28,000, identified it as the mercury-sensitive water channel, aquaporin-1 (AQP1). Many related proteins, all belonging to the major intrinsic protein (MIP) family, are found throughout nature. AQP1 is a homotetramer containing four independent aqueous channels. When reconstituted into lipid bilayers, the protein forms two-dimensional lattices with a unit cell containing two tetramers in opposite orientation. Here we present the three-dimensional structure of AQP1 determined at 6A resolution by cryo-electron microscopy. Each AQP1 monomer has six tilted, bilayer-spanning alpha-helices which form a right-handed bundle surrounding a central density. These results, together with functional studies, provide a model that identifies the aqueous pore in the AQP1 molecule and indicates the organization of the tetrameric complex in the membrane.
- Published
- 1997
- Full Text
- View/download PDF
33. Membrane binding of the colicin E1 channel: activity requires an electrostatic interaction of intermediate magnitude.
- Author
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Zakharov SD, Heymann JB, Zhang YL, and Cramer WA
- Subjects
- Binding Sites, Biophysical Phenomena, Biophysics, Calcium metabolism, Cell Membrane chemistry, Cell Membrane metabolism, Colicins chemistry, Escherichia coli metabolism, Hydrogen-Ion Concentration, Ion Channels chemistry, Lipid Bilayers chemistry, Lipid Bilayers metabolism, Membrane Lipids chemistry, Membrane Lipids metabolism, Membrane Potentials, Models, Biological, Static Electricity, Thermodynamics, Colicins metabolism, Ion Channels metabolism
- Abstract
In vitro channel activity of the C-terminal colicin E1 channel polypeptide under conditions of variable electrostatic interaction with synthetic lipid membranes showed distinct maxima with respect to pH and membrane surface potential. The membrane binding energy was determined from fluorescence quenching of the intrinsic tryptophans of the channel polypeptide by liposomes containing N-trinitrophenyl-phosphatidylethanolamine. Maximum in vitro colicin channel activity correlated with an intermediate magnitude of the electrostatic interaction. For conditions associated with maximum activity (40% anionic lipid, I = 0.12 M, pH 4.0), the free energy of binding was delta G approximately -9 kcal/mol, with nonelectrostatic and electrostatic components, delta Gnel approximately -5 kcal/mol and delta Gel approximately -4 kcal/mol, and an effective binding charge of +7 at pH 4.0. Binding of the channel polypeptide to negative membranes at pH 8 is minimal, whereas initial binding at pH 4 followed by a shift to pH 8 causes only 3-10% reversal of binding, implying that it is kinetically trapped, probably by a hydrophobic interaction. It was inferred that membrane binding and insertion involves an initial electrostatic interaction responsible for concentration and binding to the membrane surface. This is followed by insertion into the bilayer driven by hydrophobic forces, which are countered in the case of excessive electrostatic binding.
- Published
- 1996
- Full Text
- View/download PDF
34. Characterization of electrostatic and nonelectrostatic components of protein--membrane binding interactions.
- Author
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Heymann JB, Zakharov SD, Zhang YL, and Cramer WA
- Subjects
- Colicins chemistry, Colicins metabolism, Electrochemistry, In Vitro Techniques, Liposomes, Membrane Potentials, Models, Chemical, Protein Binding, Proteins chemistry, Spectrophotometry, Thermodynamics, Tryptophan, Membranes, Artificial, Proteins metabolism
- Abstract
A general method was developed to determine the thermodynamic parameters for the interaction of protein with membranes. Protein intrinsic tryptophan fluorescence was quenched by titration with large unilamellar vesicles containing 9,10-dibrominated distearoylphosphatidylcholine (Br4-DSPC) or a small amount of trinitrophenylphosphatidylethanolamine (TNP-PE), Binding was modeled as a bimolecular reaction of free protein with a unit of "n" lipid molecules and a dissociation constant, Kd. The contribution of residual fluorescence and light scattering could be eliminated by using the second derivative of the titration function as the basis for calculations. For the binding of C-terminal channel domain polypeptides(178-190 residues) of the colicin El ion channel, n=50-60 and Kd=2-3 nM at pH 4, ionic strength, I=0.12 M, and anionic lipid content = 40% (surface potential, psi o =-30 mV), conditions for which the protein has high activity. Values of n = 95 and 210 for the binding of a C-terminal 293-residue colicin fragment and the 522 residue intact colicin E1 molecule scale qualitatively according to the increase in molecular size. General methods are presented to distinguish the electrostatic (delta G el) and nonelectrostatic (delta G nel) components of the total delta G for binding. Using Br4DSPC as the quencher, the binding of the channel polypeptide, P178, was characterized by delta G approximately -9.8 kcal/mol, and delta G el approximately -7.0 kcal/mol, and delta G el= -2.8 kcal/mol (psi o = -30 mV). Using TNP-PE as the quencher, similar values of delta G approximately -9.3 to -9.9 kcal/mol were determined, a somewhat smaller value for delta G nel approximately -5.0 kcal/mol, and a correspondingly larger value for deltaGnel approximately -4.9 kcal/mol. The existence of a delta G nel component of this magnitude may distinguish proteins that have the potential to insert into the membrane.
- Published
- 1996
- Full Text
- View/download PDF
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