scholarly journals Analysis of the code relating sequence to conformation in globular proteins. The distribution of residue pairs in turns and kinks in the backbone chain

1974 ◽  
Vol 141 (3) ◽  
pp. 899-904 ◽  
Author(s):  
Barry Robson ◽  
Roger H. Pain
Keyword(s):  
Amino Acids ◽  
Low Frequency ◽  
Globular Proteins ◽  
Proton Donor ◽  
Side Chain ◽  
Donor Side ◽  
Different Types ◽  
Random Structures ◽  
Α Helix

1. The residue pair is considered as the fundamental unit which differentiates α-helix, β-pleated sheet and the various turns and kink structures of the protein backbone. 2. The HPLG alphabet (Robson & Pain, 1974) is used to group pairs of residues, giving 16 possible conformational pairs, all of which are found with differing frequencies in the nine proteins examined. 3. The frequencies of occurrence of the 16 different types of turn or kink are analysed in relation to the constituent amino acids. Those containing the L or G conformation are of low frequency and are grouped for purposes of this analysis. 4. The distribution of amino acids within all the conformational pairs is non-random, with distinct preferences shown by certain residues. 5. All pairs containing an L or G conformation require the presence of a glycine or a proton-donor side chain. 6. The results are discussed in terms of the determination of these ‘random’ structures by local interactions.

The effect of conformational freedom of side chain on low-frequency motions of amino acids in solid-state

2018 ◽  
Vol 1171 ◽  
pp. 87-93 ◽  
Author(s):  
Yin Li ◽  
Li Xu ◽  
Qing Liu ◽  
Wenfei Yang ◽  
Shuning Yang ◽  
...  
Keyword(s):  
Amino Acids ◽  
Solid State ◽  
Low Frequency ◽  
Side Chain ◽  
Conformational Freedom

The Pyoverdins of Pseudomonas syringae and Pseudomonas cichorii

2004 ◽  
Vol 59 (9-10) ◽  
pp. 613-618 ◽  
Author(s):  
Alain Bultreys ◽  
Isabelle Gheysen ◽  
Mathias Schäfer ◽  
Herbert Budzikiewicz ◽  
Bernard Wathelet
Keyword(s):  
Mass Spectrometry ◽  
Amino Acids ◽  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Pseudomonas Syringae ◽  
Structure Elucidation ◽  
Side Chain ◽  
Closely Related Species ◽  
Pseudomonas Cichorii

Abstract The structure elucidation of the cyclic (lactonic) forms of the pyoverdins with a succinamide side chain originally produced by the closely related species Pseudomonas syringae and P. cichorii is reported. Mass spectrometry and nuclear magnetic resonance analyses as well as the determination of the configuration of the amino acids after degradation indicate that these two pyoverdins differ only by the replacement of the first in-chain serine by glycine. The pyoverdins of P. syringae and P. cichorii and the dihydropyoverdin of P. syringae can be used by both species as siderophores.

13. Studies in the Ripening of Cheddar Cheese I. A Method of Following the Course of Ripening of Cheddar Cheese

1930 ◽  
Vol 2 (1) ◽  
pp. 38-67 ◽  
Author(s):  
L. A. Allen
Keyword(s):  
Amino Acids ◽  
Cheddar Cheese ◽  
Water Soluble ◽  
Soluble Nitrogen ◽  
Decomposition Products ◽  
The Past ◽  
Proteolytic Bacteria ◽  
Different Types ◽  
Molecular Complexity

A Study of the chemical changes involved in the ripening of Cheddar cheese becomes largely a study of protein degradation. The result of the breakdown of the casein through the combined effect of rennin, milk enzymes and proteolytic bacteria is to furnish water-soluble decomposition products which increase in amount as the ripening progresses. In consequence a method used by many workers in the past to follow the course of ripening was to determine at intervals the percentage of soluble nitrogen present in the cheese. It must be remembered, however, that the decomposition products which make up this soluble nitrogen factor comprise different compounds such as caseoses, peptones, polypeptides, amino acids and ammonia, which are of decreasing molecular complexity in the order named. All these compounds are soluble in water to varying extents and, therefore, a determination of the soluble nitrogen merely gives an estimate of the sum total of the nitrogen which they represent, and gives no information as to the way in which it is distributed amongst the different types.

Methionine-Specific Staining of Collagen

1982 ◽  
Vol 40 ◽  
pp. 294-295
Author(s):  
E.M. Kuhn ◽  
K.D. Marenus ◽  
M. Beer
Keyword(s):  
Amino Acids ◽  
Collagen Fibers ◽  
Type Iii Collagen ◽  
Type I ◽  
Electron Microscopic ◽  
Good Correspondence ◽  
Specific Staining ◽  
Type Iii ◽  
Different Types ◽  
Sulfur Containing

Fibers composed of different types of collagen cannot be differentiated by conventional electron microscopic stains. We are developing staining procedures aimed at identifying collagen fibers of different types.Pt(Gly-L-Met)Cl binds specifically to sulfur-containing amino acids. Different collagens have methionine (met) residues at somewhat different positions. A good correspondence has been reported between known met positions and Pt(GLM) bands in rat Type I SLS (collagen aggregates in which molecules lie adjacent to each other in exact register). We have confirmed this relationship in Type III collagen SLS (Fig. 1).

Polypeptides Folding: Rules for the Calculation of the Backbone Dihedral Angles φ starting from the Amino Acid Sequence

2020 ◽  
Author(s):  
Michele Larocca
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Theoretical Approach ◽  
Polypeptide Chain ◽  
Hydrophobic Effect ◽  
Side Chain ◽  
Dihedral Angles ◽  
Mechanical Forces ◽  
Specific Chemical

<p>Protein folding is strictly related to the determination of the backbone dihedral angles and depends on the information contained in the amino acid sequence as well as on the hydrophobic effect. To date, the type of information embedded in the amino acid sequence has not yet been revealed. The present study deals with these problematics and aims to furnish a possible explanation of the information contained in the amino acid sequence, showing and reporting rules to calculate the backbone dihedral angles φ. The study is based on the development of mechanical forces once specific chemical interactions are established among the side chain of the residues in a polypeptide chain. It aims to furnish a theoretical approach to predict backbone dihedral angles which, in the future, may be applied to computational developments focused on the prediction of polypeptide structures.</p>

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