Alignment of helical membrane protein sequences using AlignMe

Few sequence alignment methods have been designed specifically for integral membrane proteins, even though these important proteins have distinct evolutionary and structural properties that might affect their alignments. Existing approaches typically consider membrane-related information either by using membrane-specific substitution matrices or by assigning distinct penalties for gap creation in transmembrane and non-transmembrane regions. Here, we ask whether favoring matching of predicted transmembrane segments within a standard dynamic programming algorithm can improve the accuracy of pairwise membrane protein sequence alignments. We tested various strategies using a specifically designed program called AlignMe. An updated set of homologous membrane protein structures, called HOMEP2, was used as a reference for optimizing the gap penalties. The best of the membrane-protein optimized approaches were then tested on an independent reference set of membrane protein sequence alignments from the BAliBASE collection. When secondary structure (S) matching was combined with evolutionary information (using a position-specific substitution matrix (P)), in an approach we called AlignMePS, the resultant pairwise alignments were typically among the most accurate over a broad range of sequence similarities when compared to available methods. Matching transmembrane predictions (T), in addition to evolutionary information, and secondary-structure predictions, in an approach called AlignMePST, generally reduces the accuracy of the alignments of closely-related proteins in the BAliBASE set relative to AlignMePS, but may be useful in cases of extremely distantly related proteins for which sequence information is less informative. The open source AlignMe code is available at https://sourceforge.net/projects/alignme​/, and at http://www.forrestlab.org, along with an online server and the HOMEP2 data set

Comparison of two experiments on radiative neutron decay

Over 10 years ago we proposed an experiment on measuring the characteristics of radiative neutron decay in papers [1, 2]. At the same time we had published the theoretical spectrum of radiative gamma quanta, calculated within the framework of the electroweak interactions, on the basis of which we proposed the methodology for the future experiment [3,4]. However, because we were denied beam time on the intensive cold neutron beam at ILL (Grenoble, France) for a number of years, we could only conduct the experiment in 2005 on the newly opened FRMII reactor of Technical University of Muenchen. The main result of this experiment was the discovery of radiative neutron decay and the measurement of its relative intensity B.R.= (3.2+-1.6)10-3 with C.L.=99.7% for radiative gamma quanta with energy over 35 kev [5,6]. Over a year after our first announcement about the results of the conducted experiment, "Nature" [7] published a letter asserting that its authors have also measured the branching ratio of radiative neutron decay B.R.= (3.13+-0.34)10-3 with C.L.=68% and gamma quanta energy from 15 to 340 kev. This article aims to compare these two experiments. It is shown that the use of strong magnetic fields in the NIST (Washington, USA) experiment methodology not only prevents any exact measurement of the branching ratio and identification of radiative neutron decay events, but also makes registration of ordinary neutron decay events impossible.Comment: contribution on conference ISINN-1

Processing methods with imposing of electric field at low- waste division of materials

© Published under licence by IOP Publishing Ltd. Due to everything extending practice of electrochemical processing of firm alloys the important role is got by studying of their electrochemical behavior. Management of the combined process of probably independent change of parameters of a chemical and mechanical component with restrictions of their limiting values

Ways of decrease in the material consumption in case of their separation by the combined methods

© Published under licence by IOP Publishing Ltd. When processing hardly processed materials it is necessary to consider the combined methods. Application of an anode component in the combined process considerably reduces cutting forces from mechanical influence at division of materials that will allow to accelerate process without violation of accuracy and quality of a blanket. Electrochemical processing doesn't damage a processed surface, provides a high class of purity

Economic efficiency and effectiveness of ways of separating materials electro diamond processing

Purveying operations on the division of all types of materials include a hand and machine scission on the equipment of the different setting. In an engineer there is reliable information about the mastered methods, their maximum possibilities and defects. With the increase of stake of expenses there was a problem of research of new types of division of materials on materials, especially it touched scarce and expensive alloys

Processing methods with imposing of electric field at low- waste division of materials

© Published under licence by IOP Publishing Ltd. Due to everything extending practice of electrochemical processing of firm alloys the important role is got by studying of their electrochemical behavior. Management of the combined process of probably independent change of parameters of a chemical and mechanical component with restrictions of their limiting values