Literature DB >> 30598552

Understanding molecular mechanisms in cell signaling through natural and artificial sequence variation.

Neel H Shah1, John Kuriyan2,3,4,5,6.   

Abstract

The functionally tolerated sequence space of proteins can now be explored in an unprecedented way, owing to the expansion of genomic databases and the development of high-throughput methods to interrogate protein function. For signaling proteins, several recent studies have shown how the analysis of sequence variation leverages the available protein-structure information to provide new insights into specificity and allosteric regulation. In this Review, we discuss recent work that illustrates how this emerging approach is providing a deeper understanding of signaling proteins.

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Year:  2018        PMID: 30598552      PMCID: PMC6463301          DOI: 10.1038/s41594-018-0175-9

Source DB:  PubMed          Journal:  Nat Struct Mol Biol        ISSN: 1545-9985            Impact factor:   15.369


  98 in total

1.  Evolutionarily conserved networks of residues mediate allosteric communication in proteins.

Authors:  Gürol M Süel; Steve W Lockless; Mark A Wall; Rama Ranganathan
Journal:  Nat Struct Biol       Date:  2003-01

2.  Specificity is complex and time consuming: mutual exclusivity in tyrosine kinase-mediated signaling.

Authors:  Lisa O'Rourke; John E Ladbury
Journal:  Acc Chem Res       Date:  2003-06       Impact factor: 22.384

3.  Simultaneous identification of specifically interacting paralogs and interprotein contacts by direct coupling analysis.

Authors:  Thomas Gueudré; Carlo Baldassi; Marco Zamparo; Martin Weigt; Andrea Pagnani
Journal:  Proc Natl Acad Sci U S A       Date:  2016-10-11       Impact factor: 11.205

Review 4.  Emerging methods in protein co-evolution.

Authors:  David de Juan; Florencio Pazos; Alfonso Valencia
Journal:  Nat Rev Genet       Date:  2013-03-05       Impact factor: 53.242

5.  Protein sectors: evolutionary units of three-dimensional structure.

Authors:  Najeeb Halabi; Olivier Rivoire; Stanislas Leibler; Rama Ranganathan
Journal:  Cell       Date:  2009-08-21       Impact factor: 41.582

Review 6.  The Ras protein superfamily: evolutionary tree and role of conserved amino acids.

Authors:  Ana Maria Rojas; Gloria Fuentes; Antonio Rausell; Alfonso Valencia
Journal:  J Cell Biol       Date:  2012-01-23       Impact factor: 10.539

7.  System-Wide Modulation of HECT E3 Ligases with Selective Ubiquitin Variant Probes.

Authors:  Wei Zhang; Kuen-Phon Wu; Maria A Sartori; Hari B Kamadurai; Alban Ordureau; Chong Jiang; Peter Y Mercredi; Ryan Murchie; Jicheng Hu; Avinash Persaud; Manjeet Mukherjee; Nan Li; Anne Doye; John R Walker; Yi Sheng; Zhenyue Hao; Yanjun Li; Kevin R Brown; Emmanuel Lemichez; Junjie Chen; Yufeng Tong; J Wade Harper; Jason Moffat; Daniela Rotin; Brenda A Schulman; Sachdev S Sidhu
Journal:  Mol Cell       Date:  2016-03-03       Impact factor: 17.970

8.  High-resolution comparative modeling with RosettaCM.

Authors:  Yifan Song; Frank DiMaio; Ray Yu-Ruei Wang; David Kim; Chris Miles; Tj Brunette; James Thompson; David Baker
Journal:  Structure       Date:  2013-09-12       Impact factor: 5.006

9.  Kinome-wide decoding of network-attacking mutations rewiring cancer signaling.

Authors:  Pau Creixell; Erwin M Schoof; Craig D Simpson; James Longden; Chad J Miller; Hua Jane Lou; Lara Perryman; Thomas R Cox; Nevena Zivanovic; Antonio Palmeri; Agata Wesolowska-Andersen; Manuela Helmer-Citterich; Jesper Ferkinghoff-Borg; Hiroaki Itamochi; Bernd Bodenmiller; Janine T Erler; Benjamin E Turk; Rune Linding
Journal:  Cell       Date:  2015-09-17       Impact factor: 41.582

Review 10.  The Src module: an ancient scaffold in the evolution of cytoplasmic tyrosine kinases.

Authors:  Neel H Shah; Jeanine F Amacher; Laura M Nocka; John Kuriyan
Journal:  Crit Rev Biochem Mol Biol       Date:  2018-09-05       Impact factor: 8.250

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  8 in total

1.  Defining the landscape of ATP-competitive inhibitor resistance residues in protein kinases.

Authors:  D Hernandez; M Do Carmo; L Brenan; N S Persky; O Cohen; S Kitajima; U Nayar; A Walker; S Pantel; Y Lee; J Cordova; M Sathappa; C Zhu; T K Hayes; P Ram; P Pancholi; T S Mikkelsen; D A Barbie; X Yang; R Haq; F Piccioni; D E Root; C M Johannessen
Journal:  Nat Struct Mol Biol       Date:  2020-01-10       Impact factor: 15.369

Review 2.  Intrinsic dynamics is evolutionarily optimized to enable allosteric behavior.

Authors:  Yan Zhang; Pemra Doruker; Burak Kaynak; She Zhang; James Krieger; Hongchun Li; Ivet Bahar
Journal:  Curr Opin Struct Biol       Date:  2019-11-27       Impact factor: 6.809

Review 3.  Phosphoproteomics Meets Chemical Genetics: Approaches for Global Mapping and Deciphering the Phosphoproteome.

Authors:  Jan Jurcik; Barbara Sivakova; Ingrid Cipakova; Tomas Selicky; Erika Stupenova; Matus Jurcik; Michaela Osadska; Peter Barath; Lubos Cipak
Journal:  Int J Mol Sci       Date:  2020-10-15       Impact factor: 5.923

Review 4.  Into the Tissues: Extracellular Matrix and Its Artificial Substitutes: Cell Signalling Mechanisms.

Authors:  Aleksandra Bandzerewicz; Agnieszka Gadomska-Gajadhur
Journal:  Cells       Date:  2022-03-07       Impact factor: 6.600

5.  Leri: A web-server for identifying protein functional networks from evolutionary couplings.

Authors:  Ngaam J Cheung; Arun T John Peter; Benoit Kornmann
Journal:  Comput Struct Biotechnol J       Date:  2021-06-06       Impact factor: 7.271

6.  Selecting for Altered Substrate Specificity Reveals the Evolutionary Flexibility of ATP-Binding Cassette Transporters.

Authors:  Sriram Srikant; Rachelle Gaudet; Andrew W Murray
Journal:  Curr Biol       Date:  2020-03-26       Impact factor: 10.834

7.  Unraveling allosteric landscapes of allosterome with ASD.

Authors:  Xinyi Liu; Shaoyong Lu; Kun Song; Qiancheng Shen; Duan Ni; Qian Li; Xinheng He; Hao Zhang; Qi Wang; Yingyi Chen; Xinyi Li; Jing Wu; Chunquan Sheng; Guoqiang Chen; Yaqin Liu; Xuefeng Lu; Jian Zhang
Journal:  Nucleic Acids Res       Date:  2020-01-08       Impact factor: 16.971

8.  A functionally divergent intrinsically disordered region underlying the conservation of stochastic signaling.

Authors:  Ian S Hsu; Bob Strome; Emma Lash; Nicole Robbins; Leah E Cowen; Alan M Moses
Journal:  PLoS Genet       Date:  2021-09-10       Impact factor: 5.917

  8 in total

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