Strong hydrophobic nature of cysteine residues in proteins

  title={Strong hydrophobic nature of cysteine residues in proteins},
  author={Nozomi Nagano and M. Ota and Ken Nishikawa},
  journal={FEBS Letters},
The differences between disulfide‐bonding cystine (Cys_SS) and free cysteine (Cys_SH) residues were examined by analyzing the statistical distribution of both types of residue in proteins of known structure. Surprisingly, Cys_SH residues display stronger hydrophobicity than Cys_SS residues. A detailed survey of atoms which come into contact with the sulfhydryl group (sulfur atom) of Cys_SH revealed those atoms are essentially the same in number and variety as those of the methyl group of… 
Mutation choice to eliminate buried free cysteines in protein therapeutics.
A comprehensive structure and stability study of Ala, Ser, Thr, and Val mutations at each of the three buried free-Cys positions in fibroblast growth factor-1 indicated a general optimization for the wild-type Cys, including van der Waals and H-bond interactions.
Hydrophobic Characteristic Is Energetically Preferred for Cysteine in a Model Membrane Protein
The results and observations from the thermodynamic analysis of the PagP barrel may explain why cysteine, despite possessing a polar sulfhydryl group, tends to behave as a hydrophobic residue in folded protein structures.
Engineering disulfide bonds within an antibody.
In heavy chain variable or light chain variable domains, the introduction of additional disulfide bonds into the framework region did not reduce antigen-binding affinity, suggesting that generating disulfIDE bonds may be a method for stabilizing IgG and antibody fragments, such as the antigen- binding fragment, and single-chain andsingle-domain antibodies.
Characterizing the relation of functional and Early Folding Residues in protein structures using the example of aminoacyl-tRNA synthetases
Abstract Proteins are chains of amino acids which adopt a three-dimensional structure and are then able to catalyze chemical reactions or propagate signals in organisms. Without external influence,
Role of introduced surface cysteine of NADH oxidase from Lactobacillus rhamnosus.
Results showed that exception of the sites on dimer interface, the activities of LrNox mutants were improved to vary degrees when the polar uncharged and alanine residues were mutated to cysteine, andStructural analysis suggested that even a single cySteine mutation on the specific non-conserved surface area of LRNox could induce changes on the conformation of catalytic Cysteine and lower the activation free energy to improve the catalytic activity.
Free energy calculations on the stability of the 14-3-3ζ protein.
In this work, the stability of selected Cys mutants of 14-3-3ζ was predicted by free-energy calculations and the obtained data were compared with experimentally determined stabilities and offers additional insight into the stability and dimerization of this important family of regulatory proteins.
Prediction of catalytic residues in enzymes based on known tertiary structure, stability profile, and sequence conservation.
This novel method exhibited better sensitivity in the prediction accuracy than traditional methods that consider only the residue conservation and was applied to some so-called "hypothetical" proteins, with known structures but undefined functions.
Stabilization of an Immunoglobulin Fold Domain by an Engineered Disulfide Bond at the Buried Hydrophobic Region*
We report for the first time the stabilization of an immunoglobulin fold domain by an engineered disulfide bond. In the llama single-domain antibody, which has human chorionic gonadotropin as its
Distinct Molecular Surfaces and Hydrophobicity of Amino Acid Residues in Proteins
  • L. Pacios
  • Chemistry, Computer Science
    J. Chem. Inf. Comput. Sci.
  • 2001
Hydrophobicity is a useful concept to rationalize the role played by amino acid residues in terms of buried or exposed conformation with regard to the aqueous environment in proteins. The
Effects of serine-to-cysteine mutations on beta-lactamase folding.
Spectroscopic, hydrodynamic, and chemical methods revealed that the mutations do not alter the native fold but distinctly change stability and the features of partially folded states and that both thiol groups become exposed simultaneously.


Hydrophobicity of amino acid residues in globular proteins.
In the experiment reported in this article, proteins of known structure were used to measure the average area that each residue buries upon folding, and this characteristic quantity, theaverage area buried, is correlated with residue hydrophobicity.
Disulphide bridges in globular proteins.
  • J. Thornton
  • Chemistry, Medicine
    Journal of molecular biology
  • 1981
There is a strong preference for shorter connections, with half-cystines separated by less than 24 residues in 49% of all disulphides.
Cluster analysis of amino acid indices for prediction of protein structure and function.
The relationship among 222 published indices representing various physicochemical and biochemical properties of amino acid residues has been investigated by hierarchical cluster analysis, finding the indices that best reproduce the amino acid mutation data matrix are searched against this collection.
Classification of proteins into groups based on amino acid composition and other characters. II. Grouping into four types.
The results indicate that amino acid composition is well correlated to location in an organism, biological function, folding type, and disulfideonding, and the findings are discussed from the protein-taxonomical point of view.
Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features
A set of simple and physically motivated criteria for secondary structure, programmed as a pattern‐recognition process of hydrogen‐bonded and geometrical features extracted from x‐ray coordinates is developed.
Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins.
The size of the database was increased, the single-linkage cluster analysis was re-performed and there was a relationship between the PAM units of Dayhoff's mutation matrix and the volume and hydrophobicity of amino acids.
The classification of amino acid conservation.
  • W. R. Taylor
  • Biology, Medicine
    Journal of theoretical biology
  • 1986
A classification of amino acid type is described which is based on a synthesis of physico-chemical and mutation data. This is organised in the form of a Venn diagram from which sub-sets are derived
Assessment of pseudo-energy potentials by the best-five test: a new use of the three-dimensional profiles of proteins.
The best-five test is a new use of the 3D profile table for assessing the ability of the pseudo-energy potentials, where the energy level of potential functions is adjusted by referring to the random-environmental state of the proteins.
Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins.
The helix, s Applequist, 1963) in which the Zimm-Bragg parameters u and s are defined respectively as the cooperativity factor for helix initiation, and the equi- librium constant for converting a
Protein disulfide bond synthesis: a possible intracellular mechanism
Abstract A mixed function (drug) oxidase located on the endoplasmic reticulum near the sites of protein synthesis can provide oxidizing equivalents ideal for protein disulfide bond formation. The