For example the recombinant production of many membrane proteins is a major challenge and purification and crystallization are also difficult steps. The result: although around 25 percent of all proteins are membrane proteins, they account for less than one percent of the total number of proteins with known structures.
Membrane protein structures are thus underrepresented fold. Given their medical relevance, they should be much better known.
Since the experimental analysis of a membrane protein can take up to several years, the NYCOMPS scientists applied a bioinformatics strategy, the so-called homology modeling. The basic assumption of this strategy is that proteins with common evolutionary predecessors resemble each other in their amino acid sequences, as well as in their three-dimensional structure. If the structure of one of the related proteins can be determined experimentally, the remaining ones can be predicted. In the case of the bacterial membrane protein TehA they could bring all pieces of the puzzle together.
Using a multistage selection process we chose 43 proteins from 38 different organisms," says TUM computational biologist Marco Punta. Scientists at Columbia University now succeeded in experimentally determining the tertiary structure of the membrane protein TehA of the bacterium Haemophilus influenzae using X-ray crystallography. With a resolution of 0. Furthermore, the experiment harbored a surprise: The TehA membrane protein has a hitherto entirely unknown fold. After getting to know the "TehA family," the scientists at Columbia University succeeded in deriving the structures of the individual proteins.
In particular, they modeled the structure of the plant membrane protein SLAC1. Comparing this to the protein structure of TehA derived experimentally, they could build a structural model for SLAC1 -- entirely without experimentation, using nothing but bioinformatics methods. The results at hand show that this strategy can work for membrane proteins, too," says Burkhard Rost. Ultimately, the three-dimensional structures are determined to identify the function of the proteins using mutagenesis tests.
Although the membrane proteins TehA and SLAC1 are only distantly related -- the overlap of the amino acid sequence is only 19 percent -- the predicted tertiary structure of SLAC1 was so good that a new hypothesis on the function of the SLAC1 membrane protein could be put forward. SLAC1 is found in the stomata of the plant Arabidopsis thaliana. Stomata control the exchange of water vapor and carbon dioxide between the plant and its environment.
This is very important in photosynthesis. The membrane protein SLAC1 plays a role in this process, as well, as part of the anion channel: It influences the turgor pressure -- the pressure of cell fluid on the cell wall -- and thus the gas exchange of the plant cell as a reaction to environmental influences such as aridity and high carbon dioxide concentration.
Coordinating the impact of structural genomics on the human α-helical transmembrane proteome
SLAC1 anion channels are entirely novel in structure and, apparently, in the mechanism for ion conductance. The SLAC1 pore has a relatively uniform diameter, but in the middle a Phenylalanine-group blocks the way. The results suggest that this amino acid is turned away when the ion channel is activated through binding of a triggering protein.
Materials provided by Technische Universitaet Muenchen. Note: Content may be edited for style and length. Protein Expression and Purification 25, Production and purification of novel secreted human proteins. Gene , The role of oil in macromolecular crystallization. Structure 5, Efficient Protein Crystallization. Structural Biology , Acta Crystallogr D 50, Highthroughput x-ray crystallography for structure-base drug design. Drug Discov. Today 6, SS The genesis of high-throughput structure-based drug discovery using protein crystallography. Highthroughput crystallization.
Microdispensing technologies in drug discovery. Today 5, Xray diffraction studies on enzymes in the glocolytic pathway.
Cold Spring Harbor Symp. Preparation and Analysis of Protein Crystals. Wiley, New York.
Solving the structure of human H ferritin by genetically engineering intermolecular crystal contacts. Nature , Studies on engineering crystallizability by mutation of surface residues of human thymidylate synthase.
- Good humor, bad taste : a sociology of the joke!
- The Family in the Western World from the Black Death to the Industrial Age.
- Structural genomics of membrane proteins!
- Structural Genomics Literature.
- Planet Hong Kong: Popular Cinema and the Art of Entertainment (Second edition);
Growth , Acta Crystallogr. D 55, Structure and function of the Bacillus hybrid enzyme GluXyn native-like jellyroll fold preserved after insertion of autonomous globular domain. USA 95, Creating a bifunctional protein by insertion of beta-lactamase into the maltodextrin-binding protein. An inverse correlation between loop length and stability in a fourhelix- bundle protein. Fold Des. Protein engineering loops in aspartic proteinases: site-directed mutagenesis, biochemical characterization and X-ray analysis of chymosin with a replaced loop for rhizopuspepsin.
Protein Eng. Transproteomic evidence of a loop-deletion mechanism for enhancing protein thermostability. In vitro evolution of thermodynamically stable turns. Structure at 2. USA 94, Preparation and crystallization of a human immunodeficiency virus pFab complex. Enzymatic proteins. D 50, Deglycosylation of proteins for crystallization using recombinant fusion protein glycosidases.
Protein Sci. Crystal structure of phytase from Aspergillus ficuum at 2. Structure of human neutral endopeptidase Neprilysis complexed with phosphoramidon. Structure 12, PNAS , Protein crystallization using incomplete factorial experiments. High-throughput crystallography for lead discovery in drug design. Drug Disc. The prospects of protein nanocrystallography.
D58, Towards the automated evaluation of crystallization trials. D 58, Semiautomatic protein crystallization system that allows in situ observation of x-ray diffraction from crystals in the drop. Automated crystal mounting and data collection in protein crystallography.
The Structural Genomics Consortium
Structure 58, Rigaku Journal. Cryocrystallography of biological macromolecules. B 44, Cool data: quantity and quality.
- Structural genomics accelerates protein structure determination;
- Foucault and the Iranian Revolution: Gender and the Seductions of Islamism.
- Becoming a Nazi Town: Culture and Politics in Göttingen between the World Wars.
- Nazi War Trials.
- Structural genomics on membrane proteins: mini review..
Automated protein model building combined with iterative structure refinement. Current State of automated crystallographic data analysis. Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction MAD : a vehicle for direct determination of threedimensional structure. EMBO J.
The New York Consortium on Membrane Protein Structure (NYCOMPS)
Phase determination from multiwavelength anomalous diffraction measurements. Methods Enzymol. Singlewavelength anomalous diffraction phasing revisited. D 56, Accounts of Chemical Research 36 , Maximum-likelihood density modification. Highthroughput x-ray crystallography for drug discovery. Drug Design Special Publication , Highthroughput screening of structural proteomics targets using NMR.
Structural Genomics on Membrane Proteins: 1st Edition (Paperback) - Routledge
FEBS Letters , Rapid classification of a protein fold family using a statistical analysis of dipolar couplings. Bioinformatics 19, Structural proteomics: a tool for genome annotation. Current Opinion in Chemical Biology 8, An integrated approach to structural genomics. Progress in Biophysics and Molecular Biology 73, Genetic Engineering News The next ice age: cryo-electron tomography of intact cells.
Trends Cell Biol. The structural basis of large ribosomal subunit function. Annu Rev Biochem. Structure prediction meta server. Bioinformatics 17, Extending the accuracy limits of prediction for side chain conformations. FUGUE: sequence-structure homology recognition using environmentspecific substitution tables and structure dependent gap penalties. Bioinformatics 16, Comparative modeling of CASP4 target proteins: combining results of sequence search with threedimensional structure assessment.
Proteins: Struct. USA 98, Comparative protein modelling by satisfaction of spatial restraints. Homology modeling with internal coordinate mechanics: deformation zone mapping and improvements of models via conformational search. ESyPred3D: prediction of protein 3D structures. Bioinformatics 18, Hidden Markov models for detecting remote protein homologies.
Bioinformatics 14, A tool for incrementing threading optimization T. Pcons: a neural-network-based consensus predictor that improves fold recognition. Rosetta in CASP4: progress in ab initio protein structure prediction. Ab initio protein structure prediction via a combination of threading, lattice folding, clustering, and structure refinement. Ab initio protein structure prediction. Ab initio fold prediction of small helical proteins using distance geometry and knowledge-based scoring functions.
Homology modeling and molecular dynamics study of NAD-dependent glycerol phosphate dehydrogenase from Trypanosoma brucei rhodesiense, a potential target enzyme for antisleeping sickness drug development. USA 99, Probing the structure of falcipain-3, a cysteine protease from Plasmodium falciparum: comparative protein modeling and docking studies.
Functional annotation of proteomic sequences based on consensus of sequence and structural analysis. Briefings in Bioinformatics 3, Fold recognition without folds. Ab initio protein structure prediction using physicochemical potentials and a simplified off-lattice model.
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