A General Solution for the Optimal Superimposition of Protein Structures

2006 ◽  
pp. 352-361
Author(s):  
Qishen Li ◽  
Jian Shu ◽  
Zhaojun Shi ◽  
Dandan Zhang
Keyword(s):  
General Solution ◽  
Protein Structures

The Role of VLBI in the Establishment of Coordinate Systems

1975 ◽  
Vol 26 ◽  
pp. 293-295 ◽  
Author(s):  
I. Zhongolovitch
Keyword(s):  
General Solution ◽  
Future Development ◽  
Rational Approach ◽  
Radio Telescopes ◽  
Coordinate Systems ◽  
Tectonic Plates ◽  
Astronomical Observations ◽  
Optical Instruments ◽  
Fundamental Polyhedron

Considering the future development and general solution of the problem under consideration and also the high precision attainable by astronomical observations, the following procedure may be the most rational approach:1. On the main tectonic plates of the Earth’s crust, powerful movable radio telescopes should be mounted at the same points where standard optical instruments are installed. There should be two stations separated by a distance of about 6 to 8000 kilometers on each plate. Thus, we obtain a fundamental polyhedron embracing the whole Earth with about 10 to 12 apexes, and with its sides represented by VLBI.

Insights into the biochemical and functional characterization of sortase E transpeptidase of Corynebacterium glutamicum

2019 ◽  
Vol 476 (24) ◽  
pp. 3835-3847 ◽  
Author(s):  
Aliyath Susmitha ◽  
Kesavan Madhavan Nampoothiri ◽  
Harsha Bajaj
Keyword(s):  
Protein Engineering ◽  
Cell Attachment ◽  
Functional Characterization ◽  
Protein Structures ◽  
Structural Similarity ◽  
Surface Proteins ◽  
Sortase A ◽  
Peptide Cleavage ◽  
New Findings

Most Gram-positive bacteria contain a membrane-bound transpeptidase known as sortase which covalently incorporates the surface proteins on to the cell wall. The sortase-displayed protein structures are involved in cell attachment, nutrient uptake and aerial hyphae formation. Among the six classes of sortase (A–F), sortase A of S. aureus is the well-characterized housekeeping enzyme considered as an ideal drug target and a valuable biochemical reagent for protein engineering. Similar to SrtA, class E sortase in GC rich bacteria plays a housekeeping role which is not studied extensively. However, C. glutamicum ATCC 13032, an industrially important organism known for amino acid production, carries a single putative sortase (NCgl2838) gene but neither in vitro peptide cleavage activity nor biochemical characterizations have been investigated. Here, we identified that the gene is having a sortase activity and analyzed its structural similarity with Cd-SrtF. The purified enzyme showed a greater affinity toward LAXTG substrate with a calculated KM of 12 ± 1 µM, one of the highest affinities reported for this class of enzyme. Moreover, site-directed mutation studies were carried to ascertain the structure functional relationship of Cg-SrtE and all these are new findings which will enable us to perceive exciting protein engineering applications with this class of enzyme from a non-pathogenic microbe.

Sequence Specific Dihedral Angle Distribution: Application in Protein Structure Prediction and Evaluation

1970 ◽  
Vol 19 (2) ◽  
pp. 217-226
Author(s):  
S. M. Minhaz Ud-Dean ◽  
Mahdi Muhammad Moosa
Keyword(s):  
Protein Structure ◽  
Dihedral Angle ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
Protein Structures ◽  
Angle Distribution ◽  
Ramachandran Plot ◽  
Specific Data ◽  
Specific Distribution ◽  
Structure Evaluation

Protein structure prediction and evaluation is one of the major fields of computational biology. Estimation of dihedral angle can provide information about the acceptability of both theoretically predicted and experimentally determined structures. Here we report on the sequence specific dihedral angle distribution of high resolution protein structures available in PDB and have developed Sasichandran, a tool for sequence specific dihedral angle prediction and structure evaluation. This tool will allow evaluation of a protein structure in pdb format from the sequence specific distribution of Ramachandran angles. Additionally, it will allow retrieval of the most probable Ramachandran angles for a given sequence along with the sequence specific data. Key words: Torsion angle, φ-ψ distribution, sequence specific ramachandran plot, Ramasekharan, protein structure appraisal D.O.I. 10.3329/ptcb.v19i2.5439 Plant Tissue Cult. & Biotech. 19(2): 217-226, 2009 (December)

The limit state of concrete and reinforced concrete rods at complex and longitudinal-transverse bending

2020 ◽  
pp. 60-73
Author(s):  
Yu V Nemirovskii ◽  
S V Tikhonov
Keyword(s):  
General Solution ◽  
Least Squares ◽  
Nonlinear Differential Equations ◽  
Limit State ◽  
Algebraic Equations ◽  
Method Of Least Squares ◽  
Elasticity Limit ◽  
Limit Values ◽  
Symbolic Calculations ◽  
Deformation Diagrams

The work considers rods with a constant cross-section. The deformation law of each layer of the rod is adopted as an approximation by a polynomial of the second order. The method of determining the coefficients of the indicated polynomial and the limit deformations under compression and tension of the material of each layer is described with the presence of three traditional characteristics: modulus of elasticity, limit stresses at compression and tension. On the basis of deformation diagrams of the concrete grades B10, B30, B50 under tension and compression, these coefficients are determined by the method of least squares. The deformation diagrams of these concrete grades are compared on the basis of the approximations obtained by the limit values and the method of least squares, and it is found that these diagrams approximate quite well the real deformation diagrams at deformations close to the limit. The main problem in this work is to determine if the rod is able withstand the applied loads, before intensive cracking processes in concrete. So as a criterion of the conditional limit state this work adopts the maximum permissible deformation value under tension or compression corresponding to the points of transition to a falling branch on the deformation diagram level in one or more layers of the rod. The Kirchhoff-Lyav classical kinematic hypotheses are assumed to be valid for the rod deformation. The cases of statically determinable and statically indeterminable problems of bend of the rod are considered. It is shown that in the case of statically determinable loadings, the general solution of the problem comes to solving a system of three nonlinear algebraic equations which roots can be obtained with the necessary accuracy using the well-developed methods of computational mathematics. The general solution of the problem for statically indeterminable problems is reduced to obtaining a solution to a system of three nonlinear differential equations for three functions - deformation and curvatures. The Bubnov-Galerkin method is used to approximate the solution of this equation on the segment along the length of the rod, and specific examples of its application to the Maple system of symbolic calculations are considered.

Solutions and Stability of Generalized Mixed Type QCA-Functional Equations in Random Normed Spaces

2013 ◽  
Vol 59 (2) ◽  
pp. 299-320
Author(s):  
M. Eshaghi Gordji ◽  
Y.J. Cho ◽  
H. Khodaei ◽  
M. Ghanifard
Keyword(s):  
Functional Equation ◽  
General Solution ◽  
Functional Equations ◽  
Mixed Type ◽  
Additive Functional ◽  
Normed Spaces ◽  
Additive Functional Equation ◽  
Probabilistic Normed Spaces ◽  
Random Normed Spaces ◽  
Generalized Stability

Abstract In this paper, we investigate the general solution and the generalized stability for the quartic, cubic and additive functional equation (briefly, QCA-functional equation) for any k∈ℤ-{0,±1} in Menger probabilistic normed spaces.

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