6 results match your criteria randomization solvent-exposed

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Measuring the hydrogen/deuterium exchange of proteins at high spatial resolution by mass spectrometry: overcoming gas-phase hydrogen/deuterium scrambling.

Acc Chem Res 2014 Oct 29;47(10):3018-27. Epub 2014 Aug 29.

Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen , DK-2100 Copenhagen, Denmark.

Proteins are dynamic molecules that exhibit conformational flexibility to function properly. Well-known examples of this are allosteric regulation of protein activity and ligand-induced conformational changes in protein receptors. Detailed knowledge of the conformational properties of proteins is therefore pertinent to both basic and applied research, including drug development, since the majority of drugs target protein receptors and a growing number of drugs introduced to the market are therapeutic peptides or proteins. Read More

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October 2014

Fine epitope mapping based on phage display and extensive mutagenesis of the target antigen.

Authors:
Gertrudis Rojas

Methods Mol Biol 2014 ;1131:447-76

Systems Biology Department, Center of Molecular Immunology, La Habana, Cuba.

The residues contributing to the formation of the epitope recognized by a monoclonal antibody can be defined in several ways. Mutagenesis on the target antigen, followed by screening of the reactivity of the new variants with the antibody, is particularly powerful to reveal the functional contribution of each amino acid in the context of the native antigen. The current protocol provides a relatively simple procedure to study the surface of the target antigen in the search for residues involved in recognition. Read More

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October 2014

Affilin-novel binding molecules based on human gamma-B-crystallin, an all beta-sheet protein.

J Mol Biol 2007 Sep 22;372(1):172-85. Epub 2007 Jun 22.

Scil Proteins GmbH, Heinrich Damerow Str. 1, 06120 Halle (Saale), Germany.

The concept of novel binding proteins as an alternative to antibodies has undergone rapid development and is now ready for practical use in a wide range of applications. Alternative binding proteins, based on suitable scaffolds with desirable properties, are selected from combinatorial libraries in vitro. Here, we describe an approach using a beta-sheet of human gamma-B-crystallin to generate a universal binding site through randomization of eight solvent-exposed amino acid residues selected according to structural and sequence analyses. Read More

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September 2007

Exploring sequence constraints on an interhelical turn using in vivo selection for catalytic activity.

Protein Sci 1998 Feb;7(2):325-35

Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, USA.

The role of interhelical turns in determining protein structure has been investigated previously in relatively simple four-helix-bundle proteins using combinatorial mutagenesis coupled with screening for functional variants. To assess the tolerance to sequence substitution of a short, interhelical turn in a larger, more complicated protein, we have exploited a more sensitive in vivo selection for catalytic activity. Randomization of three solvent-exposed turn residues in Escherichia coli chorismate mutase (Ala65, His66, and His67), followed by selection, indicated that >63% of tripeptides, including some with significantly altered backbone conformations, can functionally replace the native sequence. Read More

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February 1998

Core mutants of the immunoglobulin binding domain of streptococcal protein G: stability and structural integrity.

FEBS Lett 1996 Dec;398(2-3):312-6

Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA.

A library of core mutants of the GB1 domain of streptococcal protein G was created, and the structure and stability of selected members was assessed by 1H-15N heteronuclear correlation NMR spectroscopy and fluorescence. All mutants comprised changes in beta-sheet residues, with sidechains at positions 5 (Leu), 7 (Leu), 52 (Phe) and 54 (Val) forming the beta-sheet side of the sheet-helix core interface. A solvent exposed position Ile-6 was chosen as a control. Read More

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December 1996

A combinatorial library of an alpha-helical bacterial receptor domain.

Protein Eng 1995 Jun;8(6):601-8

Department of Biochemistry and Biotechnology, Royal Institute of Technology, Stockholm, Sweden.

The construction and characterization of a combinatorial library of a solvent-exposed surface of an alpha-helical domain derived from a bacterial receptor is described. Using a novel solid-phase approach, the library was assembled in a directed and successive manner utilizing single-stranded oligonucleotides containing multiple random substitutions for the variegated segments of the gene fragment. The simultaneous substitution of 13 residues to all 20 possible amino acids was carried out in a region spanning 81 nucleotides. Read More

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