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[PMID]: 26101259 [Au] Autor: Topilina NI; Novikova O; Stanger M; Banavali NK; Belfort M [Ad] Endereço: Department of Biological Sciences and RNA Institute, University at Albany, 1400 Washington Avenue, Albany, NY 12222, USA. [Ti] Título: Post-translational environmental switch of RadA activity by extein-intein interactions in protein splicing. [So] Source: Nucleic Acids Res;43(13):6631-48, 2015 Jul 27. [Is] ISSN: 1362-4962 [Cp] País de publicação: England [La] Idioma: eng [Ab] Resumo: Post-translational control based on an environmentally sensitive intervening intein sequence is described. Inteins are invasive genetic elements that self-splice at the protein level from the flanking host protein, the exteins. Here we show in Escherichia coli and in vitro that splicing of the RadA intein located in the ATPase domain of the hyperthermophilic archaeon Pyrococcus horikoshii is strongly regulated by the native exteins, which lock the intein in an inactive state. High temperature or solution conditions can unlock the intein for full activity, as can remote extein point mutations. Notably, this splicing trap occurs through interactions between distant residues in the native exteins and the intein, in three-dimensional space. The exteins might thereby serve as an environmental sensor, releasing the intein for full activity only at optimal growth conditions for the native organism, while sparing ATP consumption under conditions of cold-shock. This partnership between the intein and its exteins, which implies coevolution of the parasitic intein and its host protein may provide a novel means of post-translational control. [Mh] Termos MeSH primário: Proteínas Arqueais/química Proteínas de Ligação a DNA/química Exteínas Inteínas Processamento de Proteína [Mh] Termos MeSH secundário: Proteínas Arqueais/metabolismo Proteínas de Bactérias/química Proteínas de Ligação a DNA/metabolismo Modelos Moleculares Mutação Estrutura Secundária de Proteína Estrutura Terciária de Proteína Pyrococcus horikoshii/genética Recombinases Rec A/química Temperatura Ambiente [Pt] Tipo de publicação: JOURNAL ARTICLE; RESEARCH SUPPORT, U.S. GOV'T, NON-P.H.S. [Nm] Nome de substância: 0 (Archaeal Proteins); 0 (Bacterial Proteins); 0 (DNA-Binding Proteins); 0 (RadA protein, archaeal); 0 (RadA protein, bacteria); EC 2.7.7.- (Rec A Recombinases) [Em] Mês de entrada: 1510 [Cu] Atualização por classe: 170220 [Lr] Data última revisão: 170220 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 150624 [St] Status: MEDLINE [do] DOI: 10.1093/nar/gkv612

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[PMID]: 25281002 [Au] Autor: Pearson CS; Belfort G; Belfort M; Shekhtman A [Ad] Endereço: Howard P. Isermann Department of Chemical and Biological Engineering and The Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA. [Ti] Título: Backbone assignments of mini-RecA intein with short native exteins and an active N-terminal catalytic cysteine. [So] Source: Biomol NMR Assign;9(2):235-8, 2015 Oct. [Is] ISSN: 1874-270X [Cp] País de publicação: Netherlands [La] Idioma: eng [Ab] Resumo: The backbone resonance assignments of an engineered splicing-inactive mini-RecA intein based on triple resonance experiments with [(13)C,(15)N]-labeled protein are reported. The construct contains inactivating mutations specifically designed to retain most catalytic residues, especially those that are potentially metal-coordinating. The assignments are essential for protein structure determination of a precursor with an active N-terminal catalytic cysteine and for investigation of the atomic details of splicing. [Mh] Termos MeSH primário: Cisteína/química Exteínas Inteínas Ressonância Magnética Nuclear Biomolecular Recombinases Rec A/química [Mh] Termos MeSH secundário: Biocatálise Engenharia de Proteínas Espectroscopia de Prótons por Ressonância Magnética [Pt] Tipo de publicação: JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL [Nm] Nome de substância: EC 2.7.7.- (Rec A Recombinases); K848JZ4886 (Cysteine) [Em] Mês de entrada: 1606 [Cu] Atualização por classe: 170220 [Lr] Data última revisão: 170220 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 141005 [St] Status: MEDLINE [do] DOI: 10.1007/s12104-014-9581-z

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[PMID]: 25451033 [Au] Autor: Cheriyan M; Chan SH; Perler F [Ad] Endereço: New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA. [Ti] Título: Traceless splicing enabled by substrate-induced activation of the Nostoc punctiforme Npu DnaE intein after mutation of a catalytic cysteine to serine. [So] Source: J Mol Biol;426(24):4018-29, 2014 Dec 12. [Is] ISSN: 1089-8638 [Cp] País de publicação: England [La] Idioma: eng [Ab] Resumo: Inteins self-catalytically cleave out of precursor proteins while ligating the surrounding extein fragments with a native peptide bond. Much attention has been lavished on these molecular marvels with the hope of understanding and harnessing their chemistry for novel biochemical transformations including coupling peptides from synthetic or biological origins and controlling protein function. Despite an abundance of powerful applications, the use of inteins is still hampered by limitations in our understanding of their specificity (defined as flanking sequences that permit splicing) and the challenge of inserting inteins into target proteins. We examined the frequently used Nostoc punctiforme Npu DnaE intein after the C-extein cysteine nucleophile (Cys+1) was mutated to serine or threonine. Previous studies demonstrated reduced rates and/or splicing yields with the Npu DnaE intein after mutation of Cys+1 to Ser+1. In this study, genetic selection identified extein sequences with Ser+1 that enabled the Npu DnaE intein to splice with only a 5-fold reduction in rate compared to the wild-type Cys+1 intein and without mutation of the intein itself to activate Ser+1 as a nucleophile. Three different proteins spliced efficiently after insertion of the intein flanked by the selected sequences. We then used this selected specificity to achieve traceless splicing in a targeted enzyme at a location predicted by primary sequence similarity to only the selected C-extein sequence. This study highlights the latent catalytic potential of the Npu DnaE intein to splice with an alternative nucleophile and enables broader intein utility by increasing insertion site choices. [Mh] Termos MeSH primário: Proteínas de Bactérias/genética DNA Polimerase III/genética Inteínas/genética Mutação de Sentido Incorreto Nostoc/genética [Mh] Termos MeSH secundário: Aldeído Liases/genética Aldeído Liases/metabolismo Sequência de Aminoácidos Proteínas de Bactérias/metabolismo Western Blotting Domínio Catalítico/genética Cisteína/genética DNA Polimerase III/química DNA Polimerase III/metabolismo Ativação Enzimática Proteínas de Escherichia coli/genética Proteínas de Escherichia coli/metabolismo Exteínas/genética Dados de Sequência Molecular Nostoc/enzimologia Processamento de Proteína Serina/genética Especificidade por Substrato Treonina/genética [Pt] Tipo de publicação: JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T [Nm] Nome de substância: 0 (Bacterial Proteins); 0 (Escherichia coli Proteins); 2ZD004190S (Threonine); 452VLY9402 (Serine); EC 2.7.7.- (DNA Polymerase III); EC 2.7.7.- (DNA polymerase III, alpha subunit); EC 4.1.2.- (Aldehyde-Lyases); EC 4.1.2.14 (phospho-2-keto-3-deoxy-gluconate aldolase); K848JZ4886 (Cysteine) [Em] Mês de entrada: 1504 [Cu] Atualização por classe: 141206 [Lr] Data última revisão: 141206 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 141203 [St] Status: MEDLINE

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MEDLINE

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[PMID]: 24872446 [Au] Autor: Callahan BP; Belfort M [Ad] Endereço: Chemistry Department, State University of New York at Binghamton, Binghamton, NY 13902; and mbelfort@albany.edu callahan@binghamton.edu. [Ti] Título: Branching out of the intein active site in protein splicing. [So] Source: Proc Natl Acad Sci U S A;111(23):8323-4, 2014 Jun 10. [Is] ISSN: 1091-6490 [Cp] País de publicação: United States [La] Idioma: eng [Mh] Termos MeSH primário: Exteínas/genética Inteínas/genética Processamento de Proteína Proteínas/genética [Pt] Tipo de publicação: COMMENT; JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL; RESEARCH SUPPORT, NON-U.S. GOV'T [Nm] Nome de substância: 0 (Proteins) [Em] Mês de entrada: 1409 [Cu] Atualização por classe: 170220 [Lr] Data última revisão: 170220 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 140530 [St] Status: MEDLINE [do] DOI: 10.1073/pnas.1407116111

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[PMID]: 24778214 [Au] Autor: Liu Z; Frutos S; Bick MJ; Vila-Perelló M; Debelouchina GT; Darst SA; Muir TW [Ad] Endereço: Frick Laboratory, Department of Chemistry, Princeton University, Princeton, NJ 08544; and. [Ti] Título: Structure of the branched intermediate in protein splicing. [So] Source: Proc Natl Acad Sci U S A;111(23):8422-7, 2014 Jun 10. [Is] ISSN: 1091-6490 [Cp] País de publicação: United States [La] Idioma: eng [Ab] Resumo: Inteins are autoprocessing domains that cut themselves out of host proteins in a traceless manner. This process, known as protein splicing, involves multiple chemical steps that must be coordinated to ensure fidelity in the process. The committed step in splicing involves attack of a conserved Asn side-chain amide on the adjacent backbone amide, leading to an intein-succinimide product and scission of that peptide bond. This cleavage reaction is stimulated by formation of a branched intermediate in the splicing process. The mechanism by which the Asn side-chain becomes activated as a nucleophile is not understood. Here we solve the crystal structure of an intein trapped in the branched intermediate step in protein splicing. Guided by this structure, we use protein-engineering approaches to show that intein-succinimide formation is critically dependent on a backbone-to-side-chain hydrogen-bond. We propose that this interaction serves to both position the side-chain amide for attack and to activate its nitrogen as a nucleophile. Collectively, these data provide an unprecedented view of an intein poised to carry out the rate-limiting step in protein splicing, shedding light on how a nominally nonnucleophilic group, a primary amide, can become activated in a protein active site. [Mh] Termos MeSH primário: Exteínas/genética Inteínas/genética Processamento de Proteína Proteínas/genética [Mh] Termos MeSH secundário: Amidas/química Amidas/metabolismo Sequência de Aminoácidos Asparagina/química Asparagina/genética Asparagina/metabolismo Domínio Catalítico DNA Girase/química DNA Girase/genética DNA Girase/metabolismo Eletroforese em Gel de Poliacrilamida Ligações de Hidrogênio Cinética Modelos Moleculares Dados de Sequência Molecular Estrutura Molecular Mutação Estrutura Secundária de Proteína Estrutura Terciária de Proteína Proteínas/química Proteínas/metabolismo Espectrometria de Massas por Ionização por Electrospray [Pt] Tipo de publicação: JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL; RESEARCH SUPPORT, U.S. GOV'T, NON-P.H.S. [Nm] Nome de substância: 0 (Amides); 0 (Proteins); 7006-34-0 (Asparagine); EC 5.99.1.3 (DNA Gyrase) [Em] Mês de entrada: 1409 [Cu] Atualização por classe: 170220 [Lr] Data última revisão: 170220 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 140430 [St] Status: MEDLINE [do] DOI: 10.1073/pnas.1402942111

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[PMID]: 24695729 [Au] Autor: Mills KV; Johnson MA; Perler FB [Ad] Endereço: From the Department of Chemistry, College of the Holy Cross, Worcester, Massachusetts 01610. [Ti] Título: Protein splicing: how inteins escape from precursor proteins. [So] Source: J Biol Chem;289(21):14498-505, 2014 May 23. [Is] ISSN: 1083-351X [Cp] País de publicação: United States [La] Idioma: eng [Ab] Resumo: Inteins are nature's escape artists; they facilitate their excision from flanking polypeptides (exteins) concomitant with extein ligation to produce a mature host protein. Splicing requires sequential nucleophilic displacement reactions catalyzed by strategies similar to proteases and asparagine lyases. Inteins require precise reaction coordination rather than rapid turnover or tight substrate binding because they are single turnover enzymes with covalently linked substrates. This has allowed inteins to explore alternative mechanisms with different steps or to use different methods for activation and coordination of the steps. Pressing issues include understanding the underlying details of catalysis and how the splicing steps are controlled. [Mh] Termos MeSH primário: Inteínas/genética Modelos Genéticos Precursores de Proteínas/genética Processamento de Proteína/genética [Mh] Termos MeSH secundário: Aminoácidos/química Aminoácidos/genética Exteínas/genética Estrutura Molecular Precursores de Proteínas/química Proteínas/química Proteínas/genética [Pt] Tipo de publicação: JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T; RESEARCH SUPPORT, U.S. GOV'T, NON-P.H.S.; REVIEW [Nm] Nome de substância: 0 (Amino Acids); 0 (Protein Precursors); 0 (Proteins) [Em] Mês de entrada: 1410 [Cu] Atualização por classe: 150806 [Lr] Data última revisão: 150806 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 140404 [St] Status: MEDLINE [do] DOI: 10.1074/jbc.R113.540310

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[PMID]: 23906287 [Au] Autor: Nicastri MC; Xega K; Li L; Xie J; Wang C; Linhardt RJ; Reitter JN; Mills KV [Ad] Endereço: Department of Chemistry, College of the Holy Cross, Worcester, Massachusetts 01610, United States. [Ti] Título: Internal disulfide bond acts as a switch for intein activity. [So] Source: Biochemistry;52(34):5920-7, 2013 Aug 27. [Is] ISSN: 1520-4995 [Cp] País de publicação: United States [La] Idioma: eng [Ab] Resumo: Inteins are intervening polypeptides that catalyze their own removal from flanking exteins, concomitant to the ligation of the exteins. The intein that interrupts the DP2 (large) subunit of DNA polymerase II from Methanoculleus marisnigri (Mma) can promote protein splicing. However, protein splicing can be prevented or reduced by overexpression under nonreducing conditions because of the formation of a disulfide bond between two internal intein Cys residues. This redox sensitivity leads to differential activity in different strains of E. coli as well as in different cell compartments. The redox-dependent control of in vivo protein splicing in an intein derived from an anaerobe that can occupy multiple environments hints at a possible physiological role for protein splicing. [Mh] Termos MeSH primário: Dissulfetos/farmacologia Inteínas/genética Processamento de Proteína/genética [Mh] Termos MeSH secundário: Cisteína/química DNA Polimerase II/genética Eletroforese em Gel de Poliacrilamida Exteínas/genética Oxirredução Processamento de Proteína/efeitos dos fármacos Espectrometria de Massas em Tandem [Pt] Tipo de publicação: JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL; RESEARCH SUPPORT, NON-U.S. GOV'T; RESEARCH SUPPORT, U.S. GOV'T, NON-P.H.S. [Nm] Nome de substância: 0 (Disulfides); EC 2.7.7.- (DNA Polymerase II); K848JZ4886 (Cysteine) [Em] Mês de entrada: 1310 [Cu] Atualização por classe: 161019 [Lr] Data última revisão: 161019 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 130803 [St] Status: MEDLINE [do] DOI: 10.1021/bi400736c

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[PMID]: 23621664 [Au] Autor: Selgrade DF; Lohmueller JJ; Lienert F; Silver PA [Ad] Endereço: Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA. [Ti] Título: Protein scaffold-activated protein trans-splicing in mammalian cells. [So] Source: J Am Chem Soc;135(20):7713-9, 2013 May 22. [Is] ISSN: 1520-5126 [Cp] País de publicação: United States [La] Idioma: eng [Ab] Resumo: Conditional protein splicing is a powerful biotechnological tool that can be used to rapidly and post-translationally control the activity of a given protein. Here we demonstrate a novel conditional splicing system in which a genetically encoded protein scaffold induces the splicing and activation of an enzyme in mammalian cells. In this system the protein scaffold binds to two inactive split intein/enzyme extein protein fragments leading to intein fragment complementation, splicing, and activation of the firefly luciferase enzyme. We first demonstrate the ability of antiparallel coiled-coils (CCs) to mediate splicing between two intein fragments, effectively creating two new split inteins. We then generate and test two versions of the scaffold-induced splicing system using two pairs of CCs. Finally, we optimize the linker lengths of the proteins in the system and demonstrate 13-fold activation of luciferase by the scaffold compared to the activity of negative controls. Our protein scaffold-triggered conditional splicing system is an effective strategy to control enzyme activity using a protein input, enabling enhanced genetic control over protein splicing and the potential creation of splicing-based protein sensors and autoregulatory systems. [Mh] Termos MeSH primário: Processamento de Proteína Proteínas/metabolismo [Mh] Termos MeSH secundário: Células Cultivadas Ativação Enzimática Exteínas Seres Humanos Inteínas Luciferases/química Luciferases/metabolismo Proteínas/química [Pt] Tipo de publicação: JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T; RESEARCH SUPPORT, U.S. GOV'T, NON-P.H.S. [Nm] Nome de substância: 0 (Proteins); EC 1.13.12.- (Luciferases) [Em] Mês de entrada: 1312 [Cu] Atualização por classe: 161025 [Lr] Data última revisão: 161025 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 130430 [St] Status: MEDLINE [do] DOI: 10.1021/ja401689b

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[PMID]: 23506399 [Au] Autor: Shah NH; Eryilmaz E; Cowburn D; Muir TW [Ad] Endereço: Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, USA. [Ti] Título: Extein residues play an intimate role in the rate-limiting step of protein trans-splicing. [So] Source: J Am Chem Soc;135(15):5839-47, 2013 Apr 17. [Is] ISSN: 1520-5126 [Cp] País de publicação: United States [La] Idioma: eng [Ab] Resumo: Split inteins play an important role in modern protein semisynthesis techniques. These naturally occurring protein splicing domains can be used for in vitro and in vivo protein modification, peptide and protein cyclization, segmental isotopic labeling, and the construction of biosensors. The most well-characterized family of split inteins, the cyanobacterial DnaE inteins, show particular promise, as many of these can splice proteins in less than 1 min. Despite this fact, the activity of these inteins is context-dependent: certain peptide sequences surrounding their ligation junction (called local N- and C-exteins) are strongly preferred, while other sequences cause a dramatic reduction in the splicing kinetics and yield. These sequence constraints limit the utility of inteins, and thus, a more detailed understanding of their participation in protein splicing is needed. Here we present a thorough kinetic analysis of the relationship between C-extein composition and split intein activity. The results of these experiments were used to guide structural and molecular dynamics studies, which revealed that the motions of catalytic residues are constrained by the second C-extein residue, likely forcing them into an active conformation that promotes rapid protein splicing. Together, our structural and functional studies also highlight a key region of the intein structure that can be re-engineered to increase intein promiscuity. [Mh] Termos MeSH primário: Exteínas Simulação de Dinâmica Molecular Proteínas/química Proteínas/genética Trans-Splicing [Mh] Termos MeSH secundário: Domínio Catalítico Cinética Movimento Proteínas/metabolismo Relação Estrutura-Atividade [Pt] Tipo de publicação: JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL [Nm] Nome de substância: 0 (Proteins) [Em] Mês de entrada: 1310 [Cu] Atualização por classe: 170220 [Lr] Data última revisão: 170220 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 130320 [St] Status: MEDLINE [do] DOI: 10.1021/ja401015p

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MEDLINE

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[PMID]: 22560994 [Au] Autor: Oeemig JS; Zhou D; Kajander T; Wlodawer A; Iwaï H [Ad] Endereço: Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, Helsinki FIN-00014, Finland. [Ti] Título: NMR and crystal structures of the Pyrococcus horikoshii RadA intein guide a strategy for engineering a highly efficient and promiscuous intein. [So] Source: J Mol Biol;421(1):85-99, 2012 Aug 03. [Is] ISSN: 1089-8638 [Cp] País de publicação: England [La] Idioma: eng [Ab] Resumo: In protein splicing, an intervening protein sequence (intein) in the host protein excises itself out and ligates two split host protein sequences (exteins) to produce a mature host protein. Inteins require the involvement for the splicing of the first residue of the extein that follows the intein (which is Cys, Ser, or Thr). Other extein residues near the splicing junctions could modulate splicing efficiency even when they are not directly involved in catalysis. Mutual interdependence between this molecular parasite (intein) and its host protein (exteins) is not beneficial for intein spread but could be advantageous for intein survival during evolution. Elucidating extein-intein dependency has increasingly become important since inteins are recognized as useful biotechnological tools for protein ligation. We determined the structures of one of inteins with high splicing efficiency, the RadA intein from Pyrococcus horikoshii (PhoRadA). The solution NMR structure and the crystal structures elucidated the structural basis for its high efficiency and directed our efforts of engineering that led to rational design of a functional minimized RadA intein. The crystal structure of the minimized RadA intein also revealed the precise interactions between N-extein and the intein. We systematically analyzed the effects at the -1 position of N-extein and were able to significantly improve the splicing efficiency of a less robust splicing variant by eliminating the unfavorable extein-intein interactions observed in the structure. This work provides an example of how unveiling structure-function relationships of inteins offer a promising way of improving their properties as better tools for protein engineering. [Mh] Termos MeSH primário: Proteínas Arqueais/química Proteínas de Ligação a DNA/química Inteínas Pyrococcus horikoshii/química [Mh] Termos MeSH secundário: Sequência de Aminoácidos Domínio Catalítico Cristalografia por Raios X Exteínas/genética Inteínas/genética Espectroscopia de Ressonância Magnética Modelos Moleculares Dados de Sequência Molecular Conformação Proteica Engenharia de Proteínas/métodos Processamento de Proteína [Pt] Tipo de publicação: JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., INTRAMURAL; RESEARCH SUPPORT, NON-U.S. GOV'T [Nm] Nome de substância: 0 (Archaeal Proteins); 0 (DNA-Binding Proteins); 0 (RadA protein, archaeal) [Em] Mês de entrada: 1210 [Cu] Atualização por classe: 170220 [Lr] Data última revisão: 170220 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 120508 [St] Status: MEDLINE [do] DOI: 10.1016/j.jmb.2012.04.029

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