scholarly journals Detecting local residue environment similarity for recognizing near-native structure models

2014 ◽  
Vol 82 (12) ◽  
pp. 3255-3272 ◽  
Author(s):  
Hyungrae Kim ◽  
Daisuke Kihara
Keyword(s):  
Native Structure ◽  
Local Residue

The native structure of the eukaryotic ribosome

1983 ◽  
Vol 41 ◽  
pp. 432-433
Author(s):  
R.A. Milligan ◽  
P.N.T. Unwin
Keyword(s):  
Ribosomal Proteins ◽  
Crystal Form ◽  
Native Structure ◽  
X Ray Diffraction ◽  
Eukaryotic Ribosome ◽  
Vitro Analysis ◽  
In Vitro Analysis ◽  
Resolution Structure ◽  
Stable Unit

A detailed understanding of the mechanism of protein synthesis will ultimately depend on knowledge of the native structure of the ribosome. Towards this end we have investigated the low resolution structure of the eukaryotic ribosome embedded in frozen buffer, making use of a system in which the ribosomes crystallize naturally.The ribosomes in the cells of early chicken embryos form crystalline arrays when the embryos are cooled at 4°C. We have developed methods to isolate the stable unit of these arrays, the ribosome tetramer, and have determined conditions for the growth of two-dimensional crystals in vitro, Analysis of the proteins in the crystals by 2-D gel electrophoresis demonstrates the presence of all ribosomal proteins normally found in polysomes. There are in addition, four proteins which may facilitate crystallization. The crystals are built from two oppositely facing P4 layers and the predominant crystal form, accounting for >80% of the crystals, has the tetragonal space group P4212, X-ray diffraction of crystal pellets demonstrates that crystalline order extends to ~ 60Å.

The Study on Molecular Flexibility Treating and Near-Native Structure Screening in Protein-Protein Docking Approaches

2012 ◽  
Vol 28 (1) ◽  
pp. 15
Author(s):  
Feng YANG ◽  
Libin CAO ◽  
Xinqi GONG ◽  
Shan CHANG ◽  
Weizu CHEN ◽  
...  
Keyword(s):  
Protein Docking ◽  
Native Structure ◽  
Molecular Flexibility

scholarly journals Hide and seek: interplay between influenza viruses and B cells

2020 ◽  
Vol 32 (9) ◽  
pp. 605-611 ◽  
Author(s):  
Masayuki Kuraoka ◽  
Yu Adachi ◽  
Yoshimasa Takahashi
Keyword(s):  
B Cells ◽  
B Cell ◽  
Surface Protein ◽  
Influenza Viruses ◽  
Influenza Vaccines ◽  
Native Structure ◽  
Humoral Immune ◽  
Protective Antibodies ◽  
Major Surface ◽  
And Function

Abstract Influenza virus constantly acquires genetic mutations/reassortment in the major surface protein, hemagglutinin (HA), resulting in the generation of strains with antigenic variations. There are, however, HA epitopes that are conserved across influenza viruses and are targeted by broadly protective antibodies. A goal for the next-generation influenza vaccines is to stimulate B-cell responses against such conserved epitopes in order to provide broad protection against divergent influenza viruses. Broadly protective B cells, however, are not easily activated by HA antigens with native structure, because the virus has multiple strategies to escape from the humoral immune responses directed to the conserved epitopes. One such strategy is to hide the conserved epitopes from the B-cell surveillance by steric hindrance. Technical advancement in the analysis of the human B-cell antigen receptor (BCR) repertoire has dissected the BCRs to HA epitopes that are hidden in the native structure but are targeted by broadly protective antibodies. We describe here the characterization and function of broadly protective antibodies and strategies that enable B cells to seek these hidden epitopes, with potential implications for the development of universal influenza vaccines.

Survival of native structure and biological activity in fibronectin pasteurized in the presence of sucrose

1982 ◽  
Vol 27 (3) ◽  
pp. 286-296 ◽  
Author(s):  
Donald G. Wallace ◽  
Phillip M. Schneider ◽  
Ann M. Meunier ◽  
John L. Lundblad
Keyword(s):  
Biological Activity ◽  
Native Structure

Room temperature freezing and orientational control of surface-immobilized peptides in air

2015 ◽  
Vol 51 (55) ◽  
pp. 11015-11018 ◽  
Author(s):  
Yaoxin Li ◽  
Xiaoxian Zhang ◽  
John Myers ◽  
Nicholas L. Abbott ◽  
Zhan Chen
Keyword(s):  
High Temperatures ◽  
Room Temperature ◽  
Peptide Structure ◽  
Native Structure ◽  
Immobilized Peptide

The “native” structure and orientation of a surface immobilized peptide was successfully controlled in air with a sugar layer. The robust peptide structure could also be retained at high temperatures.

scholarly journals The Functional Quality of Soluble Recombinant Polypeptides Produced in Escherichia coli Is Defined by a Wide Conformational Spectrum

2008 ◽  
Vol 74 (23) ◽  
pp. 7431-7433 ◽  
Author(s):  
Mónica Martínez-Alonso ◽  
Nuria González-Montalbán ◽  
Elena García-Fruitós ◽  
Antonio Villaverde
Keyword(s):  
Escherichia Coli ◽  
Green Fluorescent Protein ◽  
Recombinant Proteins ◽  
Fluorescent Protein ◽  
Native Structure ◽  
Functional Quality ◽  
Soluble Aggregates ◽  
Recombinant Polypeptides ◽  
Green Fluorescent

ABSTRACT We have observed that a soluble recombinant green fluorescent protein produced in Escherichia coli occurs in a wide conformational spectrum. This results in differently fluorescent protein fractions in which morphologically diverse soluble aggregates abound. Therefore, the functional quality of soluble versions of aggregation-prone recombinant proteins is defined statistically rather than by the prevalence of a canonical native structure.

Experiments with a biological material for the closure of incisional hernias

1987 ◽  
Vol 21 (3) ◽  
pp. 195-200 ◽  
Author(s):  
M. Walter ◽  
U. Brenner ◽  
W. Holzmüller ◽  
J. M. Müller
Keyword(s):  
Collagen Type I ◽  
Morphological Properties ◽  
Type I ◽  
Native Structure ◽  
Incisional Hernias ◽  
Small Vessels ◽  
Collagen Implant ◽  
Infiltrating Cells ◽  
High Level ◽  
Special Case

A new preparation process was studied which should allow the implantation of collagen type I in its native structure in reconstructive surgery, in this special case for closure of incisional hernias. As experimental animals we used 30 female Lewis rats. A defect of the anterior abdominal wall measuring 3 cm × 4 cm was closed with our collagen substitute. Biopsies taken after 4, 6 and 8 weeks were examined morphologically. As criteria for revitalization and revascularization we used the type of infiltrating cells, the depth and density of infiltration and the formation of new blood vessels. After 4 weeks the implants were infiltrated by fibroblasts that decreased in density towards the centre. Good revascularization could be seen on the muscle-implant interface. After 6 weeks the density of infiltrating cells had increased markedly even to the centre of the collagen implant. Sporadically small vessels could be seen. Eight weeks after implantation the density of infiltrated cells was at the same high level, and capillary bundles could be seen within the whole implant. We believe that this collagen implant is suitable for the closure of hernias as shown by its physical and morphological properties. In particular it appears to guarantee an earlier and tighter closure of hernias than other materials.

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