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  • 1
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    Molecular architecture and electrostatic properties of a bacterial porin (1991)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1991-12-13
    Description: The integral membrane protein porin from Rhodobacter capsulatus consists of three tightly associated 16-stranded beta barrels that give rise to three distinct diffusion channels for small solutes through the outer membrane. The x-ray structure of this porin has revealed details of its shape, the residue distributions within the pore and at the membrane-facing surface, and the location of calcium sites. The electrostatic potential has been calculated and related to function. Moreover, potential calculations were found to predict the Ca2+ sites.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Weiss, M S -- Abele, U -- Weckesser, J -- Welte, W -- Schiltz, E -- Schulz, G E -- New York, N.Y. -- Science. 1991 Dec 13;254(5038):1627-30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Organische Chemie und Biochemie, Freiburg, Federal Republic of Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1721242" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Outer Membrane Proteins/*chemistry ; Calcium/metabolism ; Calcium-Binding Proteins/metabolism ; Computer Graphics ; Crystallography ; Ion Channels/*chemistry ; Ions ; Macromolecular Substances ; Models, Molecular ; Molecular Structure ; Porins ; Protein Conformation ; Rhodobacter capsulatus/*chemistry ; X-Ray Diffraction
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
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    Designed protein-protein association (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-01-12
    Description: The analysis of natural contact interfaces between protein subunits and between proteins has disclosed some general rules governing their association. We have applied these rules to produce a number of novel assemblies, demonstrating that a given protein can be engineered to form contacts at various points of its surface. Symmetry plays an important role because it defines the multiplicity of a designed contact and therefore the number of required mutations. Some of the proteins needed only a single side-chain alteration in order to associate to a higher-order complex. The mobility of the buried side chains has to be taken into account. Four assemblies have been structurally elucidated. Comparisons between the designed contacts and the results will provide useful guidelines for the development of future architectures.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Grueninger, Dirk -- Treiber, Nora -- Ziegler, Mathias O P -- Koetter, Jochen W A -- Schulze, Monika-Sarah -- Schulz, Georg E -- New York, N.Y. -- Science. 2008 Jan 11;319(5860):206-9. doi: 10.1126/science.1150421.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Organische Chemie und Biochemie, Albert-Ludwigs-Universitat, Albertstrasse 21, 79104 Freiburg im Breisgau, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18187656" target="_blank"〉PubMed〈/a〉
    Keywords: Aldehyde-Lyases/*chemistry/genetics ; Bacterial Proteins/*chemistry/genetics ; Crystallization ; Crystallography, X-Ray ; Cysteine Synthase/*chemistry/genetics ; Dimerization ; Glycoside Hydrolases/*chemistry/genetics ; Models, Molecular ; Mutagenesis, Site-Directed ; Mutant Proteins/chemistry ; Point Mutation ; Porins/*chemistry/genetics ; Protein Conformation ; *Protein Engineering ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Protein Subunits/*chemistry/genetics ; Urocanate Hydratase/*chemistry/genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
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    Structure and function of a squalene cyclase (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-09-20
    Description: The crystal structure of squalene-hopene cyclase from Alicyclobacillus acidocaldarius was determined at 2.9 angstrom resolution. The mechanism and sequence of this cyclase are closely related to those of 2,3-oxidosqualene cyclases that catalyze the cyclization step in cholesterol biosynthesis. The structure reveals a membrane protein with membrane-binding characteristics similar to those of prostaglandin-H2 synthase, the only other reported protein of this type. The active site of the enzyme is located in a large central cavity that is of suitable size to bind squalene in its required conformation and that is lined by aromatic residues. The structure supports a mechanism in which the acid starting the reaction by protonating a carbon-carbon double bond is an aspartate that is coupled to a histidine. Numerous surface alpha helices are connected by characteristic QW-motifs (Q is glutamine and W is tryptophan) that tighten the protein structure, possibly for absorbing the reaction energy without structural damage.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wendt, K U -- Poralla, K -- Schulz, G E -- New York, N.Y. -- Science. 1997 Sep 19;277(5333):1811-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Organische Chemie und Biochemie, Albertstrasse 21, D-79104 Freiburg im Breisgau, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9295270" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacillaceae/*enzymology ; Binding Sites ; Cell Membrane/enzymology ; Crystallization ; Crystallography, X-Ray ; Cyclization ; Dimerization ; Humans ; Hydrogen Bonding ; *Intramolecular Transferases ; Isomerases/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Recombinant Proteins/chemistry/metabolism ; Sequence Alignment ; Squalene/metabolism ; Thermodynamics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
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    Self-assembly of proteins into designed networks (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-10-04
    Description: A C4-symmetric tetrameric aldolase was used to produce a quadratic network consisting of the enzyme as a rigid four-way connector and stiff streptavidin rods as spacers. Each aldolase subunit was furnished with a His6 tag for oriented binding to a planar surface and two tethered biotins for binding streptavidin in an oriented manner. The networks were improved by starting with composite units and also by binding to nickel-nitrilotriacetic acid-lipid monolayers. The mesh was adjustable in 5-nanometer increments. The production of a net with switchable mesh was initiated with the use of a calcium ion-containing beta-helix spacer that denatured on calcium ion depletion.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ringler, Philippe -- Schulz, Georg E -- New York, N.Y. -- Science. 2003 Oct 3;302(5642):106-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Organische Chemie und Biochemie, Albert-Ludwigs-Universitat Freiburg, Albertstrasse 21, D-79104 Freiburg im Breisgau, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14526081" target="_blank"〉PubMed〈/a〉
    Keywords: Aldehyde-Lyases/*chemistry/genetics/metabolism ; Binding Sites ; Biotin/chemistry/metabolism ; Calcium/metabolism ; Edetic Acid ; *Glycoside Hydrolases ; Lipids/chemistry ; Macromolecular Substances ; Metalloendopeptidases/chemistry/metabolism ; Microscopy, Electron ; Models, Molecular ; Mutation ; Nitrilotriacetic Acid ; Protein Conformation ; Protein Denaturation ; *Protein Engineering ; Protein Structure, Secondary ; Recombinant Fusion Proteins/chemistry ; Streptavidin/*chemistry ; beta-Galactosidase/*chemistry
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
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    The structure of a mycobacterial outer-membrane channel (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-02-21
    Description: Mycobacteria have low-permeability outer membranes that render them resistant to most antibiotics. Hydrophilic nutrients can enter by way of transmembrane-channel proteins called porins. An x-ray analysis of the main porin from Mycobacterium smegmatis, MspA, revealed a homooctameric goblet-like conformation with a single central channel. This is the first structure of a mycobacterial outer-membrane protein. No structure-related protein was found in the Protein Data Bank. MspA contains two consecutive beta barrels with nonpolar outer surfaces that form a ribbon around the porin, which is too narrow to fit the thickness of the mycobacterial outer membrane in contemporary models.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Faller, Michael -- Niederweis, Michael -- Schulz, Georg E -- New York, N.Y. -- Science. 2004 Feb 20;303(5661):1189-92.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Organische Chemie und Biochemie, Albert-Ludwigs-Universitat, Albertstrasse 21, 79104 Freiburg im Breisgau, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14976314" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arginine/chemistry ; Cell Membrane Permeability ; Cloning, Molecular ; Crystallization ; Crystallography, X-Ray ; Electric Conductivity ; Escherichia coli/genetics ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Mycobacterium smegmatis/*chemistry/metabolism ; Porins/*chemistry/genetics/metabolism ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
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    The structure of a retinal-forming carotenoid oxygenase (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-04-12
    Description: Enzymes that produce retinal and related apocarotenoids constitute a sequence- and thus structure-related family, a member of which was analyzed by x-ray diffraction. This member is an oxygenase and contains an Fe2+-4-His arrangement at the axis of a seven-bladed beta-propeller chain fold covered by a dome formed by six large loops. The Fe2+ is accessible through a long nonpolar tunnel that holds a carotenoid derivative in one of the crystals. On binding, three consecutive double bonds of this carotenoid changed from a straight all-trans to a cranked cis-trans-cis conformation. The remaining trans bond is located at the dioxygen-ligated Fe2+ and cleaved by oxygen.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kloer, Daniel P -- Ruch, Sandra -- Al-Babili, Salim -- Beyer, Peter -- Schulz, Georg E -- R01 EY020551/EY/NEI NIH HHS/ -- New York, N.Y. -- Science. 2005 Apr 8;308(5719):267-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Organische Chemie und Biochemie, Albert-Ludwigs-Universitat, Albertstrasse 21, 79104 Freiburg im Breisgau, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15821095" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Cloning, Molecular ; Crystallography, X-Ray ; Escherichia coli ; Humans ; Molecular Sequence Data ; Oxygenases/*chemistry ; Protein Conformation ; Recombinant Proteins ; Retinaldehyde/*chemistry ; Synechocystis/*enzymology/genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
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    Structure of the thiamine- and flavin-dependent enzyme pyruvate oxidase (1993)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1993-02-12
    Description: Pyruvate oxidase from Lactobacillus plantarum is a tetrameric enzyme that decarboxylates pyruvate, producing hydrogen peroxide and the energy-storage metabolite acetylphosphate. Structure determination at 2.1 angstroms showed that the cofactors thiamine pyrophosphate (TPP) and flavin adenine dinucleotide (FAD) are bound at the carboxyl termini of six-stranded parallel beta sheets. The pyrophosphate moiety of TPP is bound to a metal ion and to a beta alpha alpha beta unit corresponding to an established sequence fingerprint. The spatial arrangement of TPP and FAD suggests that the oxidation of the oxyethyl intermediate does not occur by hydride displacement but rather by a two-step transfer of two electrons.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Muller, Y A -- Schulz, G E -- New York, N.Y. -- Science. 1993 Feb 12;259(5097):965-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Organische Chemie und Biochemie, Albert-Ludwigs-Universitat, Freiburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8438155" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Chemistry, Physical ; Crystallization ; Flavin-Adenine Dinucleotide/metabolism/*pharmacology ; Lactobacillus/*enzymology ; Macromolecular Substances ; Molecular Sequence Data ; Molecular Structure ; Physicochemical Phenomena ; Protein Structure, Secondary ; Pyruvate Oxidase/*chemistry/metabolism ; Thiamine Pyrophosphate/metabolism/*pharmacology ; X-Ray Diffraction
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
    Electronic Resource
    Electronic Resource
    A designed mutant of the enzyme glutathione reductase shortens the crystallization time by a factor of forty (1994)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 50 (1994), S. 228-231 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The packing of glutathione reductase from Escherichia coli in crystal form T showed a place where two molecules are at a distance of only 6 Å between the closest atoms, i.e. where a contact is almost made. In order to form this contact with hydrogen bonds, two amino-acid residues were exchanged. This mutation had no effect on molecular packing or the resolution limit of the X-ray diffraction, but facilitated crystal nucleation dramatically and possibly increased the crystal growth rate and shortened the crystallization time.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S090744499300993X
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  • 9
    Electronic Resource
    Electronic Resource
    Refined High-Resolution Structure of the Metal-Ion Dependent L-Fuculose-1-phosphate Aldolase (Class II) from Escherichia coli (1996)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 52 (1996), S. 1082-1091 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The structure of the class II zinc-ion dependent L-fuculose-1-phosphate aldolase from Escherichia coli in its tetragonal crystal form has been established at 1.92 Å resolution. The homotetrameric enzyme has a molecular mass of 4 × 24 kDa and follows C4 symmetry. The structure model is exactly symmetrical, which contradicts an observed birefringence anomaly of the crystals. The four catalytic centers are located in deep clefts at the interfaces of adjacent subunits. The zinc ion is coordinated by three histidines and one glutamate in an almost tetrahedral arrangement. In contrast to numerous other catalytically competent zinc ions, there is no water molecule in the ligand sphere. Replacement of zinc by a cobalt ion caused only small structural changes. A search through the Protein Data Bank indicated that the chain fold is novel. Sequence homology searches revealed a significant similarity to the bacterial L-ribulose-5-phosphate 4-epimerase.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444996009146
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  • 10
    Electronic Resource
    Electronic Resource
    Infinite Non-crystallographic Symmetries in Crystals of a Globular Protein (1997)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 53 (1997), S. 274-279 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The monomeric enzyme 6-phospho-β-galactosidase crystallized in three forms, all of which can be considered as fiber associations when judged from the packing contacts. In one case the internal fiber symmetry is a row of parallel twofold axes that are displaced by a′ along the fiber axis. In the crystal, these twofold axes are non-crystallographic, but they define the x axis by a = 2a′. Antiparallel and asymmetric fiber association along y and z, respectively, results in space group P21. The two other crystal forms contain fibers with internal 21 axes (translation c′) defining the z axis by c = 2c′. Antiparallel fiber association results in sheets with internal twofold and 21 axes defining the yz plane. These sheets associate along x in two ways; in one case the internal sheet symmetry becomes crystallographic, while it remains non-crystallographic in the other. All non-crystallographic fiber symmetries run infinitely through the crystal. In one case they cause exact systematic absences that mimic space group P212121 instead of the actual P21212. The relationship between contact areas and local symmetries is discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444996014977
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