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Structural Studies of Binding Proteins: Investigations of Flexibility, Specificity and Stability
Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology.
2003 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Binding proteins are present both in gram-negative and gram-positive bacteria. They are the recognition components of the ABC transport systems that transport different nutrients into the cell, and are in some cases also involved in chemotaxis. In gram-negative bacteria, they are present in the periplasm between the inner and the porous outer membrane. Here, these highly specific proteins can bind to a certain ligand such as ions, sugars and amino acids. The protein-ligand complex can then interact with permeases bound to the inner membrane that transport the nutrient into the cell. Gram-positive bacteria lack an outer membrane and the binding protein must therefore be anchored to the cell membrane.

In this thesis different aspects of three members of the super-family of the periplasmic binding proteins have been studied. In the case of the allose-binding protein (ALBP) from E. coli we focused on the movement of the protein when ligand is bound and released. This protein was also compared with the ribose-binding protein (RBP) which belongs to the same structural cluster and from which both open and closed structures are available. The leucine-binding protein (LBP) from E. coli was studied with regards to the structural basis of its specificity for different ligands as well as its conformational changes. The leucine-isoleucine-valine protein has 80% sequence identity with LBP but still exhibits a different preference for ligands. The structure of the maltose-binding protein (MBP) was obtained from a gram-positive thermoacidophile, A. acidocaldarius. Here, our goal was to study acid-stability of proteins. Since little is known about this and structures of the mesophilic counterpart in E. coli are available, as well as structures from two hyperthermophiles, we had an opportunity to study differences in their structural properties that could explain their differing stabilities.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis , 2003. , p. 53
Series
Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1104-232X ; 899
Keywords [en]
Molecular biology, Periplasmic binding protein, X-ray crystallography, conformational change, acidophile, protein specificity, protein structure
Keywords [sv]
Molekylärbiologi
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:uu:diva-3640ISBN: 91-554-5764-9 (print)OAI: oai:DiVA.org:uu-3640DiVA, id: diva2:163491
Public defence
2003-11-21, B21, Biomedical centre (BMC), Uppsala, 13:00
Opponent
Supervisors
Available from: 2003-10-30 Created: 2003-10-30Bibliographically approved
List of papers
1. Hinge-bending motion of D-allose-binding protein from Escherichia coli: three open conformations.
Open this publication in new window or tab >>Hinge-bending motion of D-allose-binding protein from Escherichia coli: three open conformations.
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2002 In: Journal of biological chemistry, Vol. 277, no 16, p. 14077-84Article in journal (Refereed) Published
Identifiers
urn:nbn:se:uu:diva-90953 (URN)
Available from: 2003-10-30 Created: 2003-10-30Bibliographically approved
2. X-ray structures of the maltose-maltodextrin binding protein of the thermoacidophilic bacterium Alicyclobacillus acidocaldarius provide insight into acid stability of proteins
Open this publication in new window or tab >>X-ray structures of the maltose-maltodextrin binding protein of the thermoacidophilic bacterium Alicyclobacillus acidocaldarius provide insight into acid stability of proteins
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2004 (English)In: Journal of Molecular Cell Biology, ISSN 1674-2788, E-ISSN 1759-4685, Vol. 335, no 1, p. 261-274Article in journal (Refereed) Published
Abstract [en]

Maltose-binding proteins act as primary receptors in bacterial transport and chemotaxis systems. We report here crystal structures of the thermoacidostable maltose-binding protein from Alicyclobacillus acidocaldarius, and explore its modes of binding to maltose and maltotriose. Further, comparison with the structures of related proteins from Escherichia coli (a mesophile), and two hyperthermophiles (Pyrococcus furiosus and Thermococcus litoralis) allows an investigation of the basis of thermo- and acidostability in this family of proteins.The thermoacidophilic protein has fewer charged residues than the other three structures, which is compensated by an increase in the number of polar residues. Although the content of acidic and basic residues is approximately equal, more basic residues are exposed on its surface whereas most acidic residues are buried in the interior. As a consequence, this protein has a highly positive surface charge. Fewer salt bridges are buried than in the other MBP structures, but the number exposed on its surface does not appear to be unusual. These features appear to be correlated with the acidostability of the A. acidocaldarius protein rather than its thermostability. An analysis of cavities within the proteins shows that the extremophile proteins are more closely packed than the mesophilic one. Proline content is slightly higher in the hyperthermophiles and thermoacidophiles than in mesophiles, and this amino acid is more common at the second position of beta-turns, properties that are also probably related to thermostability. Secondary structural content does not vary greatly in the different structures, and so is not a contributing factor.

National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-90954 (URN)10.1016/j.jmb.2003.10.042 (DOI)14659755 (PubMedID)
Available from: 2003-10-30 Created: 2003-10-30 Last updated: 2017-12-14Bibliographically approved
3. X-ray structures of the leucine-binding protein illustrate conformational changes, as well as ligand specificity
Open this publication in new window or tab >>X-ray structures of the leucine-binding protein illustrate conformational changes, as well as ligand specificity
Manuscript (Other academic)
Identifiers
urn:nbn:se:uu:diva-90955 (URN)
Available from: 2003-10-30 Created: 2003-10-30 Last updated: 2016-05-09Bibliographically approved

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