Influence of Water on Protein Structure. An Analysis of the Preferences of Amino Acid Residues for the Inside or Outside and for Specific Conformations in a Protein Molecule

1978 ◽  
Vol 11 (1) ◽  
pp. 9-15 ◽  
Author(s):  
David H. Wertz ◽  
Harold A. Scheraga
Keyword(s):  
Protein Structure ◽  
Amino Acid ◽  
Protein Molecule ◽  
Amino Acid Residues ◽  
Influence Of Water

Characterization of the sulfated glycopeptide of chicken pepsinogen

1982 ◽  
Vol 47 (2) ◽  
pp. 709-718 ◽  
Author(s):  
Miroslav Baudyš ◽  
Vladimír Kostka ◽  
Karel Grüner ◽  
Jan Pohl
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Protein Molecule ◽  
Amino Acid Residues ◽  
Terminal Sequence ◽  
Sugar Moiety ◽  
Pepsinogen A ◽  
Identical Amino Acid Sequence ◽  
High Voltage Electrophoresis

S-sulfonated chicken pepsinogen was digested with TPCK-trypsin; large tryptic peptides, separated on Sephadex G-25 fine, were subjected to additional cleavage with α-chymotrypsin. The hold-up fraction of the chymotryptic digest from the Sephadex G-25 column, was resolved by high voltage electrophoresis. The three most acidic zones contained glycopeptides of identical amino acid sequence Val-Ser-Thr-Asn-Glu-Thr-Val-Tyr, yet differed in the composition of the sugar moiety. These glycopeptides, moreover, bear different numbers of sulfate groups which enabled the resolution of the peptides. The most acidic glycopeptide contains 7 glucosamine residues, 3 mannose residues and 5 sulfate groups, the second one 6 glucosamine residues, 3 mannose residues and 4 sulfate groups and the slowest, minority glycopeptide, 5 glucosamine residues, 2 mannose residues and 2 sulfate groups. The entire sugar moiety is attached to one of the chain viaasparagine. In other experiments the glycopeptides were also isolated from the thermolytic digest of chicken pepsin; their C-terminal sequence was shorter by two amino acid residues. The tentative assignment of the glycopeptides to the amino acid sequence of pepsinogen resulted from the analysis of the limited tryptic digest of the whole protein molecule. Chicken pepsinogen is glycosylated at the site of the chain occupied by a phosphoserine residue in hog pepsinogen A.

scholarly journals Isolation and oncogenic potential of a novel human src-like gene.

1986 ◽  
Vol 6 (12) ◽  
pp. 4195-4201 ◽  
Author(s):  
T Kawakami ◽  
C Y Pennington ◽  
K C Robbins
Keyword(s):  
Amino Acid ◽  
Protein Molecule ◽  
Nucleotide Sequence Analysis ◽  
Protein Kinase Activity ◽  
Amino Acid Residues ◽  
Amino Acid Homology ◽  
Oncogenic Potential ◽  
Coding Sequence ◽  
Amino Terminal ◽  
Sarcoma Virus

We have isolated cDNA molecules representing the complete coding sequence of a new human gene which is a member of the src family of oncogenes. Nucleotide sequence analysis revealed that this gene, termed slk, encoded a 537-residue protein which was 86% identical to the chicken proto-oncogene product, p60c-src, over a stretch of 191 amino acids at its carboxy terminus. In contrast, only 6% amino acid homology was observed within the amino-terminal 82 amino acid residues of these two proteins. It was possible to activate slk as a transforming gene by substituting approximately two-thirds of the slk coding sequence for an analogous region of the v-fgr onc gene present in Gardner-Rasheed feline sarcoma virus. The resulting hybrid protein molecule expressed in transformed cells demonstrated protein kinase activity with specificity for tyrosine residues.

scholarly journals Conformational stability of bovine α-crystallin. Evidence for a destabilizing effect of ascorbate

1992 ◽  
Vol 287 (1) ◽  
pp. 107-112 ◽  
Author(s):  
S A Santini ◽  
A Mordente ◽  
E Meucci ◽  
G A D Miggiano ◽  
G E Martorana
Keyword(s):  
Amino Acid ◽  
Conformational Stability ◽  
Gel Filtration ◽  
Protein Molecule ◽  
Oxidative Modification ◽  
Amino Acid Residues ◽  
Alpha Crystallin ◽  
Protein Dissociation ◽  
Covalent Adducts ◽  
Polypeptide Chains

Short-term incubation of bovine alpha-crystallin with ascorbate alters the protein conformational stability. The denaturation curves with urea and guanidinium-chloride show different patterns, suggesting a deviation from a two-state mechanism owing to the presence of one or more intermediates in the unfolding of ascorbate-modified alpha-crystallin. Furthermore, the latter protein profiles are shifted to lower denaturant concentrations indicating a destabilizing action of ascorbate, which is capable of facilitating protein dissociation into subunits as demonstrated by gel filtration with 1.5 M-urea. The decrease in conformational stability cannot be ascribed to any major structural alteration, but rather to localized changes in the protein molecule. In fact, no difference between native and ascorbate-treated alpha-crystallin can be detected by amino acid analysis but perturbation of the tryptophan and tyrosine environment is indicated by alterations in intrinsic fluorescence. Furthermore, turbidity and light-scattering measurements suggest an involvement of the lysine side chains, since aggregability patterns with acetylsalicylic acid are significantly altered. The ascorbate-destabilizing effect on the conformational stability of alpha-crystallin, probably exerted through oxidative modification of amino acid residues and/or the formation of covalent adducts, provokes unfavourable steric interactions between residues along the polypeptide chains, thus favouring aggregation and insolubilization of crystallins which can lead to cataract formation, as also demonstrated by proteolytic digestion patterns which show a lower rate of degradation of the ascorbate-modified alpha-crystallin.

Highly accurate sequence-based prediction of half-sphere exposures of amino acid residues in proteins

2015 ◽  
Vol 32 (6) ◽  
pp. 843-849 ◽  
Author(s):  
Rhys Heffernan ◽  
Abdollah Dehzangi ◽  
James Lyons ◽  
Kuldip Paliwal ◽  
Alok Sharma ◽  
...  
Keyword(s):  
Protein Structure ◽  
Amino Acid ◽  
Structure Prediction ◽  
Protein Structures ◽  
Correlation Coefficients ◽  
Accessible Surface Area ◽  
Solvent Accessible Surface Area ◽  
Supplementary Information ◽  
Amino Acid Residues ◽  
Solvent Exposure

Abstract Motivation: Solvent exposure of amino acid residues of proteins plays an important role in understanding and predicting protein structure, function and interactions. Solvent exposure can be characterized by several measures including solvent accessible surface area (ASA), residue depth (RD) and contact numbers (CN). More recently, an orientation-dependent contact number called half-sphere exposure (HSE) was introduced by separating the contacts within upper and down half spheres defined according to the Cα-Cβ (HSEβ) vector or neighboring Cα-Cα vectors (HSEα). HSEα calculated from protein structures was found to better describe the solvent exposure over ASA, CN and RD in many applications. Thus, a sequence-based prediction is desirable, as most proteins do not have experimentally determined structures. To our best knowledge, there is no method to predict HSEα and only one method to predict HSEβ. Results: This study developed a novel method for predicting both HSEα and HSEβ (SPIDER-HSE) that achieved a consistent performance for 10-fold cross validation and two independent tests. The correlation coefficients between predicted and measured HSEβ (0.73 for upper sphere, 0.69 for down sphere and 0.76 for contact numbers) for the independent test set of 1199 proteins are significantly higher than existing methods. Moreover, predicted HSEα has a higher correlation coefficient (0.46) to the stability change by residue mutants than predicted HSEβ (0.37) and ASA (0.43). The results, together with its easy Cα-atom-based calculation, highlight the potential usefulness of predicted HSEα for protein structure prediction and refinement as well as function prediction. Availability and implementation: The method is available at http://sparks-lab.org. Contact: [email protected] or [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.

scholarly journals Gas-Phase Ion/Ion Chemistry for Structurally Sensitive Probes of Gaseous Protein Ion Structure: Electrostatic and Electrostatic to Covalent Cross-Linking

2021 ◽  
Author(s):  
Melanie Cheung See Kit ◽  
Veronica V. Carvalho ◽  
Jonah Z. Vilseck ◽  
Ian Webb
Keyword(s):  
Protein Structure ◽  
Amino Acid ◽  
Gas Phase ◽  
Structural Changes ◽  
Cross Linking ◽  
Distance Constraint ◽  
Amino Acid Residues ◽  
Ion Chemistry ◽  
Specific Chemical ◽  
Gas Phase Ion

Intramolecular interactions within a protein are key in maintaining protein tertiary structure and understanding how proteins function. Ion mobility-mass spectrometry (IM-MS) has become a widely used approach in structural biology since it provides rapid measurements of collision cross sections (CCS), which inform on the gas-phase conformation of the biomolecule under study. Gas-phase ion/ion reactions target amino acid residues with specific chemical properties and the modified sites can be identified by MS. In this study, electrostatically reactive, gas-phase ion/ion chemistry and IM-MS are combined to characterize the structural changes between ubiquitin electrosprayed from aqueous and denaturing conditions. The electrostatic attachment of sulfo-NHS acetate to ubiquitin via ion/ion reactions and fragmentation by electron-capture dissociation (ECD) provide the identification of the most accessible protonated sites within ubiquitin as the sulfonate group forms an electrostatic complex with accessible protonated side chains. The protonated sites identified by ECD from the different solution conditions are distinct and, in some cases, reflect the disruption of interactions such as salt bridges that maintain the native protein structure. This agrees with previously published literature demonstrating that a high methanol concentration at low pH causes the structure of ubiquitin to change from a native (N) state to a more elongated A state. Results using gas-phase, electrostatic cross-linking reagents also point to similar structural changes and further confirm the role of methanol and acid in favoring a more unfolded conformation. Since cross-linking reagents have a distance constraint for the two reactive sites, the data is valuable in guiding computational structures generated by molecular dynamics. The research presented here describes a promising strategy that can detect subtle changes in the local environment of targeted amino acid residues to inform on changes in the overall protein structure.

Isolation and oncogenic potential of a novel human src-like gene

1986 ◽  
Vol 6 (12) ◽  
pp. 4195-4201
Author(s):  
T Kawakami ◽  
C Y Pennington ◽  
K C Robbins
Keyword(s):  
Amino Acid ◽  
Protein Molecule ◽  
Nucleotide Sequence Analysis ◽  
Protein Kinase Activity ◽  
Amino Acid Residues ◽  
Amino Acid Homology ◽  
Oncogenic Potential ◽  
Coding Sequence ◽  
Amino Terminal ◽  
Sarcoma Virus

We have isolated cDNA molecules representing the complete coding sequence of a new human gene which is a member of the src family of oncogenes. Nucleotide sequence analysis revealed that this gene, termed slk, encoded a 537-residue protein which was 86% identical to the chicken proto-oncogene product, p60c-src, over a stretch of 191 amino acids at its carboxy terminus. In contrast, only 6% amino acid homology was observed within the amino-terminal 82 amino acid residues of these two proteins. It was possible to activate slk as a transforming gene by substituting approximately two-thirds of the slk coding sequence for an analogous region of the v-fgr onc gene present in Gardner-Rasheed feline sarcoma virus. The resulting hybrid protein molecule expressed in transformed cells demonstrated protein kinase activity with specificity for tyrosine residues.

Some comments on proteins and protein structure

1953 ◽  
Vol 141 (902) ◽  
pp. 97-103 ◽  
Keyword(s):  
Protein Structure ◽  
Amino Acid ◽  
Structural Formula ◽  
Protein Chemistry ◽  
Amino Acid Residues ◽  
Outstanding Achievement ◽  
Complete Determination ◽  
Cross Links ◽  
Polypeptide Chains

I have been given the last word in this discussion, and I take advantage of the opportunity with some diffidence. The discussion has ranged widely over the field, but the major issues under dispute have been in the province of the crystallographers. I certainly cannot count myself among them, and am often quite incompetent to judge of the validity of what they say. However, the issues involved are of such importance to protein chemists, and to many biologists as well, that I offer com­ments on some of them. First of all, it is really amazing, to one who has been in the field of protein chemistry for a quarter of a century, that this discussion could be carried on, at this level, in the year 1952. Even five years ago it would have seemed almost incredible that we could have begun so soon to probe so deeply into the finer details of protein structure. The possibility of thinking in these terms has certainly been profoundly influenced by a development which has not found any but an incidental place in to-day’s discussion—the determination of the sequence of amino-acid residues in polypeptide chains (Sanger 1952). The outstanding achievement in this field hitherto is of course the complete determination of the sequence in the two kinds of peptide chain in insulin, by Sanger & Tuppy (1951) and Sanger & Thomp­son (1952). It appears that it remains only to fix the nature of the disulphide cross-links in order to have a complete structural formula for at least one protein.

scholarly journals 3P017 Identification of structure determinant amino acid residues in the A2G80 peptide derived from laminin α2 by molecular dynamics simulation(01A. Protein: Structure,Poster)

2013 ◽  
Vol 53 (supplement1-2) ◽  
pp. S214
Author(s):  
Yuka Fukasawa ◽  
Jun Kumai ◽  
Fumihiko Katagiri ◽  
Yamato Kikkawa ◽  
Kentaro Hozumi ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Protein Structure ◽  
Amino Acid ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Amino Acid Residues ◽  
Laminin Α2
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