The role of stochasticity on compactness of the native state of protein peptide backbone

2010 ◽  
Vol 133 (8) ◽  
pp. 085102
Author(s):  
P. H. Figueirêdo ◽  
M. A. Moret ◽  
S. Coutinho ◽  
E. Nogueira
Keyword(s):  
Native State ◽  
Peptide Backbone

scholarly journals Role of peptide backbone conformation on biological activity of chemotactic peptides.

1991 ◽  
Vol 266 (28) ◽  
pp. 18460-18468
Author(s):  
A.R. Dentino ◽  
P.A. Raj ◽  
K.K. Bhandary ◽  
M.E. Wilson ◽  
M.J. Levine
Keyword(s):  
Biological Activity ◽  
Peptide Backbone ◽  
Backbone Conformation ◽  
Chemotactic Peptides ◽  
Peptide Backbone Conformation

Electrophoresis and Electrofocusing of Phytochrome from Etiolated Avena sativa L.

1989 ◽  
Vol 44 (1-2) ◽  
pp. 12-18 ◽  
Author(s):  
Rudolf Schendel ◽  
Wolfhart Rüdiger
Keyword(s):  
Isoelectric Focusing ◽  
Avena Sativa ◽  
Posttranslational Modification ◽  
Negative Charge ◽  
Native State ◽  
Signal Region ◽  
Unfolded State ◽  
Native Gel ◽  
Peptide Region

Abstract Phytochrome from etiolated oat seedlings (Avena sativa L.) was investigated by “native” gel electrophoresis and by isoelectric focusing. At pH 8 . 8 the Pfr form migrated faster than the Pr form in electrophoresis. We assume a difference in the surface charge rather than a difference in shape for the phytochrome forms. This assumption was confirmed by isoelectric focusing which clearly showed relatively more negative charge in the Pfr form than in the Pr form. The role of the peptide region from residue 323 to 360 is discussed in this connection. It carries 9 negatively charged residues, it is exposed only in the Pfr form and it has already been described as a signal region for rapid protein degradation (PEST sequence, see Rogers et al., Science 234, 364-368, 1986). The experiments on electrofocusing revealed a microheterogeneity of phytochrome which was present in the native state as well as in the completely unfolded state. The most probable reason could be either posttranslational modification or genetic polymorphism of phytochrome in oat.

scholarly journals The role of conformational entropy in the determination of structural-kinetic relationships for helix-coil transitions

2017 ◽  
Author(s):  
Joseph F. Rudzinski ◽  
Tristan Bereau
Keyword(s):  
Simulation Models ◽  
Structural Features ◽  
Coarse Grained ◽  
Kinetic Properties ◽  
Conformational Entropy ◽  
Peptide Backbone ◽  
The Relationship ◽  
Insight Into

Coarse-grained molecular simulation models can provide significant insight into the complex behavior of protein systems, but suffer from an inherently distorted description of dynamical properties. We recently demonstrated that, for a heptapeptide of alanine residues, the structural and kinetic properties of a simulation model are linked in a rather simple way, given a certain level of physics present in the model. In this work, we extend these findings to a longer peptide, for which the representation of configuration space in terms of a full enumeration of sequences of helical/coil states along the peptide backbone is impractical. We verify the structural-kinetic relationships by scanning the parameter space of a simple native-biased model and then employ a distinct transferable model to validate and generalize the conclusions. Our results further demonstrate the validity of the previous findings, while clarifying the role of conformational entropy in the determination of the structural-kinetic relationships. More specifically, while the global, long timescale kinetic properties of a particular class of models with varying energetic parameters but approximately fixed conformational entropy are determined by the overarching structural features of the ensemble, a shift in these kinetic observables occurs for models with a distinct representation of steric interactions. At the same time, the relationship between structure and more local, faster kinetic properties is not affected by varying the conformational entropy of the model.

scholarly journals EL TENDERO TRADICIONAL COLOMBIANO, UN ESTRATEGA AL NATURAL

2014 ◽  
Vol 18 (52) ◽  
pp. 103-118
Author(s):  
Dagoberto Páramo Morales
Keyword(s):  
Ethnographic Methods ◽  
Strategic Decisions ◽  
Native State ◽  
Consumer Perspective ◽  
National Life ◽  
Analytical Tools

RESUMEN Objetivo: Como resultado de diferentes trabajos de investigación de corte cualitativo en busca de encontrar el papel que juega la tienda tradicional colombiana en la vida nacional, en este documento se presentan los principales argumentos que dan sentido al carácter estratégico del tendero en su natural estado de autoextensión de su propia personalidad. Material y método: Los hallazgos se sustentan en la rigurosidad propia de los métodos etnográficos para la recopilación de la información, en las herramientas analíticas de la etnología para contrastar las diferentes realidades, y en los creativos ejercicios de interpretación que proporciona la antropología con todo su arsenal epistemológico. Resultados: A manera de síntesis de largos años de investigación en el contexto colombiano, se señala aquí la naturaleza de las relaciones que el tendero establece con compradores –ocasionales o permanentes- con proveedores y con empleados y familiares dependientes, sobre las cuales toma sus grandes decisiones de carácter estratégico. Conclusiones: Se sintetizan los tipos de tenderos que hasta el momento han sido descubiertos, así como una tipología de tiendas que vistas desde la perspectiva del consumidor denotan la estrategia del tendero para desarrollar su labor. ABSTRACT Objective: As a result of different qualitative researches done in order to search the role of the traditional Colombian store in the national life, here are presented the main arguments that give sense to the strategic nature of the shopkeeper in his native state of selfextension of his own personality. Material and method: The findings are based on the strictness involved in the ethnographic methods for gathering information, on the analytical tools of ethnology to contrast the different realities, and on the creative interpretation exercises provided by the anthropology with its entire epistemological arsenal. Results: As a synthesis of years of research in the Colombian context, it is noted here the nature of the relationships made by the shopkeeper with occasional and permanent buyers, with suppliers, and with employees and dependent relatives, on which the shopkeeper makes his great strategic decisions. Conclusions: the types of shopkeepers that have so far been discovered are synthesized, as well as a typology of stores that from a consumer perspective denotes the shopkeeper strategy to develop his work.

scholarly journals Crystal structure of the fluorescent protein fromDendronephthyasp. in both green and photoconverted red forms

2016 ◽  
Vol 72 (8) ◽  
pp. 922-932 ◽  
Author(s):  
Nadya V. Pletneva ◽  
Sergei Pletnev ◽  
Alexey A. Pakhomov ◽  
Rita V. Chertkova ◽  
Vladimir I. Martynov ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Blue Light ◽  
Considerable Increase ◽  
Fluorescent Protein ◽  
Fluorescent Proteins ◽  
Three Dimensional ◽  
Red Shift ◽  
Peptide Backbone

The fluorescent protein fromDendronephthyasp. (DendFP) is a member of the Kaede-like group of photoconvertible fluorescent proteins with a His62-Tyr63-Gly64 chromophore-forming sequence. Upon irradiation with UV and blue light, the fluorescence of DendFP irreversibly changes from green (506 nm) to red (578 nm). The photoconversion is accompanied by cleavage of the peptide backbone at the Cα—N bond of His62 and the formation of a terminal carboxamide group at the preceding Leu61. The resulting double Cα=Cβbond in His62 extends the conjugation of the chromophore π system to include imidazole, providing the red fluorescence. Here, the three-dimensional structures of native green and photoconverted red forms of DendFP determined at 1.81 and 2.14 Å resolution, respectively, are reported. This is the first structure of photoconverted red DendFP to be reported to date. The structure-based mutagenesis of DendFP revealed an important role of positions 142 and 193: replacement of the original Ser142 and His193 caused a moderate red shift in the fluorescence and a considerable increase in the photoconversion rate. It was demonstrated that hydrogen bonding of the chromophore to the Gln116 and Ser105 cluster is crucial for variation of the photoconversion rate. The single replacement Gln116Asn disrupts the hydrogen bonding of Gln116 to the chromophore, resulting in a 30-fold decrease in the photoconversion rate, which was partially restored by a further Ser105Asn replacement.

scholarly journals Role of Native-State Topology in the Stabilization of Intracellular Antibodies

2001 ◽  
Vol 81 (5) ◽  
pp. 2935-2945 ◽  
Author(s):  
Giovanni Settanni ◽  
Antonino Cattaneo ◽  
Amos Maritan
Keyword(s):  
Native State

scholarly journals Reconstruction of the immunogenic peptide RNase(43-56) by identification and transfer of the critical residues into an unrelated peptide backbone.

1989 ◽  
Vol 170 (1) ◽  
pp. 203-215 ◽  
Author(s):  
R G Lorenz ◽  
A N Tyler ◽  
P M Allen
Keyword(s):  
Amino Acid ◽  
T Cell ◽  
Single Amino Acid ◽  
Amino Acid Residues ◽  
Peptide Backbone ◽  
Chimeric Peptide ◽  
Critical Residues

The involvement of each of the amino acid residues of the I-Ak-restricted T cell determinant RNase(43-56) was examined in detail using a series of peptides containing single amino acid substitutions. Four positions were identified as being essential for the formation of the determinant, Phe-46, Val-47, His-48, and Leu-51. When these four residues were substituted into the backbone of the unrelated peptide HA(130-144), a nonstimulatory peptide was obtained. The inclusion of an additional residue, Val-54, resulted in a chimeric peptide, RN/HA2, which was nearly as active as the native molecule. The peptide RN/HA2 was able to prime in vivo for RNase reactivity, confirming that these five residues contained all of the specificity of the RNase(43-56) determinant. The role of three of these critical residues was examined using both a functional competition assay and an in vivo priming assay. It was ascertained that the Phe-46 was directly involved in contacting the TCR, while the His-48 and Leu-51 were either involved in binding to the I-Ak molecule or in determining the conformation of the peptide. Thus, by critically evaluating the contribution of each of the amino acid residues in a T cell determinant, we were able to generate a chimeric peptide only containing 5 of 15 residues from the RNase(43-56) sequence that was functionally identical to the native RNase(43-56) molecule both in vitro and in vivo.

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