Environmental and structural proteomics

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Foreword

Environmental and structural proteomics This issue of the Proteomics Journal is dedicated to the 3rd International Congress on Analytical Proteomics (ICAP) and is covering two important proteomics areas: Environmental Proteomics and Structural Proteomics. Although different in terms of their concepts, they provide complementary information making it possible for a better understanding of a studied system. Therefore, from a didactic point of view, the purpose is for each one of these areas to be presented separately and discussed briefly, helping the reader realize the interdependence between them. Environmental proteomics is defined as the study of the expression profile of proteins extracted directly from living organisms and some stabilized proteins present in environmental samples [1,2]. More so, the study contains processes such as simple protein mapping (inside an ecosystem at a certain time), comparative and quantitative proteomics, analyses of protein localizations, discovery of post-translational modifications (which might affect protein functionality), investigation of protein–protein interactions and even determination of amino-acid sequences and genotypes [3]. Structural proteomics include the identification of all possible proteins on a genome-wide scale and the determination of their structure–function relationship. Also, they outline the precise three-dimensional structures of the proteins [4]. The joining of proteomics and structure also opens the possibility to investigate the conformational changes caused by post-translational modification and ligand or protein interaction [5]. In this way, the role played by structural proteomics will have an immediate influence on medicinal chemistry and molecular pharmacology, as well as, increase the impact on disciplines such as neurobiology, immunology, molecular medicine, developmental biology among others [6,7]. Additionally, changes in the environment may perturb the conformation of proteins, requiring the combination of structural and proteomic strategies to investigate this phenomenon [8,9]. After defining them, it is easy to understand their interdependence and the necessity to use powerful strategies for both of them to be well carried-out. They start on “omics” standard-technologies which comprise four basic steps: (1) sample preparation; (2) protein denaturation and reduction;

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(3) protein (peptide) separation, enzymatic digestion, and MS analysis; and (4) bioinformatic approaches and protein identification. In fact, all of these strategies and other based on analytical proteomics, which is an emerging field, were the focus of the 3rd ICAP, which was celebrated in the city of São Pedro, São Paulo state, Brazil, from the 28th to the 31st of July, 2013. The first edition of this event was in Costa da Caparica, Portugal in 2009 and its second edition was celebrated in Ourense, Spain, in 2011, both having as chairs Prof. José Luis Capelo and Carlos Lodeiro. In its 3rd edition, the ICAP presented as the main theme Applications and Technologies in Proteomics, and as it is rapidly expanding in Brazil, the proteomics community showed a great interest in the event. Therefore, ca. 120 attendees were present at the congress from different countries (Brazil, Spain, Portugal, Singapore, USA, Germany, Sweden, Russian Federation, Switzerland, United Kingdom, Australia, Uruguay, and France) and different companies dedicated to proteomic and related areas, such as Thermo Scientific/Analítica, Horiba, ABSciex, Perkin-Elmer, Sigma-Aldrich, Waters, Allcrom, US Biosolutions and Drafra Technologies, Royal Society of Chemistry and General Electric were our partners. The scientific schedule, which was divided into lectures, plenary, keynotes, oral presentations, shotguns and poster session, included, apart from world renowned scientists, the Nobel Prize winner, Prof. Kurt Wüthrich, who presented the opening lecture in the 3rd ICAP. Therefore, the current topical issue reports on some papers related to environmental and structural proteomics, since analytical proteomics can help a great deal with such areas. In fact, the readers can find inside this issue a diversity of applications ranging from “Structural and functional characterization of the chaperone Hsp70 from sugarcane” to “Evaluation of metal toxicity in mice M. spretus as bioindicator”, to name a few. The conference chairs express their gratitude to all the participants, as well as, to all the contributors to this special issue. Last but not least, we wish to acknowledge the support of the journal of Proteomics for kindly allowing us to edit this special issue. Dr. J. L. Capelo and Dr. C. Lodeiro would like thank profusely the Brasilian team led by Dr. Marco Arruda and Dr. Carlos

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Ramos as they did an outstanding work in organizing the 3rd International Conference on Analytical Proteomics. The ICAP series of conferences on analytical proteomics was born in 2009 in Caparica-Portugal and has quickly begun to be a worldwide reference for all of us working in this field of research. The IV edition will take place in Caparica-Portugal in 2015 (www.icap-congress.com/2015) and we kindly encourage you to book this event in your agenda (8–10 September 2015). We look forward to meeting you all again there.

REFERENCES [1] Renella G, Ogunseitan O, Giagnoni L, Arenella M. Soil Biol Biochem 2014;69:34. [2] Taylor NL, Tan YF, Jacoby RP, Millar AH. J Proteomics 2009;72: 367. [3] Schneider T, Riedel K. Proteomics 2010;10:785. [4] Liu H-L, Hsu J-P. Proteomics 2005;5:2056. [5] Ryslavá H, Doubnerová V, Kavan D, Vanek O. J Proteomics 2013;92:80. [6] Timperio AM, Egidi MG, Zolla L. J Proteomics 2008;71:391. [7] Höhn A, König J, Grune T. J Proteomics 2013;92:132. [8] Abreu IA, Farinha AP, Negrão S, Gonçalves N, Fonseca C, Rodrigues M, et al. J Proteomics 2013;93:145. [9] Rochette S, Gagnon-Arsenault I, Diss G, Landry CR. J Proteomics 2014;100:25.

Marco Aurélio Zezzi Arruda is a Full Professor at the University of Campinas — Unicamp (Campinas, Brazil), Institute of Chemistry, Department of Analytical Chemistry, head of the Department of Analytical Chemistry, and member of the National Institute of Science and Technology — INCT for Bioanalitics. His current research interests include trans-disciplinary work involving comparative omics of plants (i.e. soybean, sunflower, Arabidopsis thaliana) and human body fluids (i.e. blood serum, urine) to identify possible biomarkers for transgenic species and human diseases, as well as to evaluate reactive oxygen species production, and (metallo) proteins responses under stress in a given system. He is the author or co-author over 150 research articles, 7 book chapters and 5 patents, is on the editorial staff or advisory board of the Analytical and Bioanalytical Chemistry, Metallomics, Journal of Integrated Omics and Brazilian Journal of Analytical Chemistry, and member of the advisory board of the Brazilian Mass Spectrometry Society (BrMASS) and Brazilian Chemistry Association (ABQ).

José Luis Capelo received his PhD in Chemistry in 2002 by the University of Vigo (Spain). In 2002 he moved to the Instituto Superior Técnico de Lisboa (Portugal) as post-doc and in 2004 he was appointed Fellow Researcher at REQUIMTE, laboratory associated to the Chemistry Department of the New University of Lisbon. In 2009 he moved to the Physical Chemistry Department of the University of Vigo at Ourense Campus (Spain), and in 2012 he was appointed Assistant Professor at the Chemistry Department of the New University of Lisbon. Currently he co-leads the Bioscope group (www.bioscopegroup.org). J. L. Capelo has leading research on the following topics: (i) quantification of metal and metals species in environmental and food samples, (ii) new methods to speed protein identification mass spectrometry-based workflows, (iii) accurate bottom-up protein quantification, (iv) bacterial identification through mass spectrometry, (v) fast determination of steroids in human samples, (v) biomarker discovery and (vi) application of sensors and chemosensor to the detection/quantification of metals. J. L. Capelo is authors or co-author of more than 150 manuscripts, 10 book chapters and 2 patents. Dr. Capelo is member of the Portuguese Chemistry Society (SPQ), the Royal Society of Chemistry (RSC) and the ProteoMass Society.

Carlos Lodeiro received his PhD in Chemistry in 1999 from the University of Santiago de Compostela, Spain. Between 1999 and 2008 he worked at the University NOVA of Lisbon (UNL) in Portugal as a European Marie Curie postdoctoral researcher (1999– 2003), Assistant Researcher (2004–2008) and Invited Lecture (2005–2008). From 2009 till 2012 he was IPP (Isidro Parga Pondal) Researcher–lecturer in the Physical Chemistry Department at the University of Vigo, Faculty of Sciences at Ourense Campus (FCOU), Spain. In 2012 he was appointed as Assistant Professor at the Chemistry Department of the New University of Lisbon. Currently he co-leads the Bioscope group (www.bioscopegroup.org). His research interests comprise (i) physical-organic and physical-inorganic chemistry of fluorescence chemosensors, (ii) synthesis of macrocyclic and peptide chemosensors, (iii) functionalized metal nanoparticle synthesis, (iv) syntheses of new MALDI-MS matrices, and (v) supramolecular analytical proteomics. C. Lodeiro is co-author of more than 160 manuscripts and 15 book chapters. C. Lodeiro is member of the Portuguese Chemistry Society (SPQ), the Royal Society of Chemistry (RSC) and the ProteoMass Society.

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Carlos Ramos majored in Biochemistry at the University of Minas Gerais — Brazil in 1991, and received his PhD in Biochemistry in 1996 for work using molecular biology and protein biochemistry at the University of São Paulo (USP) — Brazil. Realizing the importance of folding and stability to the understanding of protein function, he performed postdoctoral work with Prof. Robert Baldwin at Stanford University from 1996 to 1998. He was nominated as a PEW Fellow in 1997, received the Title of Privat-dozent in Biochemistry from the Institute of Chemistry from USP in 2005 and in 2006 received a Fogart International Research Collaboration Award from the NIH. He is the Chair of the Organic Chemistry Department from University of Campinas (UNICAMP) since 2011 and Full Professor since 2013. Dr. Ramos' contributions to science generated 87 publications and are mainly related to the folding/unfolding and misfolding of myoglobin, a model for globular proteins, on the stability of protein domains, on the relationship between structure and function in molecular chaperones from high eukaryotes and on studies focused on protein homeostasis. Presently, he coordinates scientific projects focused on the structure, function and interaction of Hsp90s and disaggregates from human and plants.

Marco A.Z. Arruda José Luis Capelo Carlos Lodeiro Carlos H.I. Ramos

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