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      New Insectotoxin from Tibellus Oblongus Spider Venom Presents Novel Adaptation of ICK Fold

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          Abstract

          The Tibellus oblongus spider is an active predator that does not spin webs and remains poorly investigated in terms of venom composition. Here, we present a new toxin, named Tbo-IT2, predicted by cDNA analysis of venom glands transcriptome. The presence of Tbo-IT2 in the venom was confirmed by proteomic analyses using the LC-MS and MS/MS techniques. The distinctive features of Tbo-IT2 are the low similarity of primary structure with known animal toxins and the unusual motif of 10 cysteine residues distribution. Recombinant Tbo-IT2 (rTbo-IT2), produced in E. coli using the thioredoxin fusion protein strategy, was structurally and functionally studied. rTbo-IT2 showed insecticidal activity on larvae of the housefly Musca domestica (LD 100 200 μg/g) and no activity on the panel of expressed neuronal receptors and ion channels. The spatial structure of the peptide was determined in a water solution by NMR spectroscopy. The Tbo-IT2 structure is a new example of evolutionary adaptation of a well-known inhibitor cystine knot (ICK) fold to 5 disulfide bonds configuration, which determines additional conformational stability and gives opportunities for insectotoxicity and probably some other interesting features.

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          NMRPipe: a multidimensional spectral processing system based on UNIX pipes.

          The NMRPipe system is a UNIX software environment of processing, graphics, and analysis tools designed to meet current routine and research-oriented multidimensional processing requirements, and to anticipate and accommodate future demands and developments. The system is based on UNIX pipes, which allow programs running simultaneously to exchange streams of data under user control. In an NMRPipe processing scheme, a stream of spectral data flows through a pipeline of processing programs, each of which performs one component of the overall scheme, such as Fourier transformation or linear prediction. Complete multidimensional processing schemes are constructed as simple UNIX shell scripts. The processing modules themselves maintain and exploit accurate records of data sizes, detection modes, and calibration information in all dimensions, so that schemes can be constructed without the need to explicitly define or anticipate data sizes or storage details of real and imaginary channels during processing. The asynchronous pipeline scheme provides other substantial advantages, including high flexibility, favorable processing speeds, choice of both all-in-memory and disk-bound processing, easy adaptation to different data formats, simpler software development and maintenance, and the ability to distribute processing tasks on multi-CPU computers and computer networks.
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            A Cross-platform Toolkit for Mass Spectrometry and Proteomics

            Mass-spectrometry-based proteomics has become an important component of biological research. Numerous proteomics methods have been developed to identify and quantify the proteins in biological and clinical samples 1 , identify pathways affected by endogenous and exogenous perturbations 2 , and characterize protein complexes 3 . Despite successes, the interpretation of vast proteomics datasets remains a challenge. There have been several calls for improvements and standardization of proteomics data analysis frameworks, as well as for an application-programming interface for proteomics data access 4,5 . In response, we have developed the ProteoWizard Toolkit, a robust set of open-source, software libraries and applications designed to facilitate proteomics research. The libraries implement the first-ever, non-commercial, unified data access interface for proteomics, bridging field-standard open formats and all common vendor formats. In addition, diverse software classes enable rapid development of vendor-agnostic proteomics software. Additionally, ProteoWizard projects and applications, building upon the core libraries, are becoming standard tools for enabling significant proteomics inquiries.
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              Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions.

              The present paper describes the SSM algorithm of protein structure comparison in three dimensions, which includes an original procedure of matching graphs built on the protein's secondary-structure elements, followed by an iterative three-dimensional alignment of protein backbone Calpha atoms. The SSM results are compared with those obtained from other protein comparison servers, and the advantages and disadvantages of different scores that are used for structure recognition are discussed. A new score, balancing the r.m.s.d. and alignment length Nalign, is proposed. It is found that different servers agree reasonably well on the new score, while showing considerable differences in r.m.s.d. and Nalign.
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                Author and article information

                Journal
                Toxins (Basel)
                Toxins (Basel)
                toxins
                Toxins
                MDPI
                2072-6651
                04 January 2021
                January 2021
                : 13
                : 1
                : 29
                Affiliations
                [1 ]Department of Molecular Neurobiology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 16/10 Miklukho-Maklay Str., 117997 Moscow, Russia; katerina@ 1234561ns.ru (E.M.); mikov.alexander@ 123456gmail.com (A.M.); ay@ 123456land.ru (Y.A.); serg@ 123456ibch.ru (S.K.)
                [2 ]Skolkovo Institute of Science and Technology, 30 Bld. 1, Bolshoy Boulevard, 121205 Moscow, Russia
                [3 ]V.L. Talrose Institute for Energy Problems of Chemical Physics, N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld. 2, 119334 Moscow, Russia; lobas.anka@ 123456gmail.com (A.L.); lisavetasol@ 123456gmail.com (E.S.); mike.gorshkov@ 123456gmail.com (M.G.)
                [4 ]Department of Molecular and Chemical Physics, Moscow Institute of Physics and Technology (National Research University), 9 Institutsky Per., 141700 Dolgoprudny, Russia
                [5 ]Moscow Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 8 Bld. 2, Trubetskaya Str., 119991 Moscow, Russia
                [6 ]Toxicology and Pharmacology, University of Leuven (KU Leuven), Campus Gasthuisberg, O&N2, Herestraat 49, P.O. Box 922, B-3000 Leuven, Belgium; steve.peigneur@ 123456kuleuven.be (S.P.); jan.tytgat@ 123456kuleuven.be (J.T.)
                [7 ]Department of Biological and Medicinal Physics, Moscow Institute of Physics and Technology (National Research University), 9 Institutsky Per., 141700 Dolgoprudny, Russia; kornilov.fd@ 123456phystech.edu (F.K.); lushpa@ 123456phystech.edu (V.L.); konstantin.mineev@ 123456gmail.com (K.M.)
                [8 ]Department of Structural Biology, Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry RAS, 16/10 Miklukho-Maklay Str., 117997 Moscow, Russia
                Author notes
                [* ]Correspondence: july@ 123456mx.ibch.ru ; Tel.: +7-495-336-6540
                Author information
                https://orcid.org/0000-0001-8556-5366
                https://orcid.org/0000-0001-9572-3452
                https://orcid.org/0000-0002-7628-0980
                https://orcid.org/0000-0003-0504-5702
                https://orcid.org/0000-0002-0242-4240
                Article
                toxins-13-00029
                10.3390/toxins13010029
                7824768
                33406803
                c76e9436-19f6-4206-b1a9-6fe7566d2106
                © 2021 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                : 18 November 2020
                : 30 December 2020
                Categories
                Article

                Molecular medicine
                spider venom,transcriptome,proteome,insectotoxin,ick fold,nmr structure
                Molecular medicine
                spider venom, transcriptome, proteome, insectotoxin, ick fold, nmr structure

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