4.8 Article

Structural mapping of PEAK pseudokinase interactions identifies 14-3-3 as a molecular switch for PEAK3 signaling

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemistry & Molecular Biology

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

Mihaly Varadi et al.

Summary: AlphaFold DB is an openly accessible database with high-accuracy protein-structure predictions, powered by DeepMind's AlphaFold v2.0. It provides programmatic access to a vast number of predicted structures and is expanding to cover more sequences.

NUCLEIC ACIDS RESEARCH (2022)

Article Biochemistry & Molecular Biology

Database resources of the national center for biotechnology information

Eric W. Sayers et al.

Summary: The National Center for Biotechnology Information (NCBI) produces a variety of online information resources for biology, including databases for nucleic acid sequences and life science journal citations. It provides search and retrieval operations for most of these data from 35 distinct databases, with E-utilities serving as the programming interface. Several resources received significant updates in the past year.

NUCLEIC ACIDS RESEARCH (2022)

Article Biochemistry & Molecular Biology

The Eukaryotic Linear Motif resource: 2022 release

Manjeet Kumar et al.

Summary: The Eukaryotic Linear Motif (ELM) resource remains a crucial source of information for motif-mediated protein-protein interactions, with the current update adding new motif classes focused on various cellular processes. The resource continues to face challenges in keeping up-to-date due to the increasing number of SLiM-mediated interactions being discovered.

NUCLEIC ACIDS RESEARCH (2022)

Article Biochemistry & Molecular Biology

Distinct PEAK3 interactors and outputs expand the signaling potential of the PEAK pseudokinase family

Jianmei Hou et al.

Summary: This article investigates the regulation and role of pseudokinase scaffolds PEAK1 and PEAK2 in cell signaling. The study finds that PEAK3, the third family member, also plays a crucial role in promoting cell proliferation, migration, and invasion by interacting with various proteins.

SCIENCE SIGNALING (2022)

Article Biochemical Research Methods

ColabFold: making protein folding accessible to all

Milot Mirdita et al.

Summary: ColabFold combines fast homology search and optimized model utilization to offer accelerated prediction of protein structures and complexes, with a processing speed that is 40-60 times faster. It serves as a free and accessible platform for protein folding, capable of predicting close to 1,000 structures per day.

NATURE METHODS (2022)

Article Cell Biology

PEAK1 Y635 phosphorylation regulates cell migration through association with Tensin3 and integrins

Alba Zuidema et al.

Summary: Integrins mediate cell adhesion and growth factor receptor signal transduction through interactions with PEAK1, Tensin3, and Shc1.

JOURNAL OF CELL BIOLOGY (2022)

Article Biochemistry & Molecular Biology

UCSF ChimeraX: Structure visualization for researchers, educators, and developers

Eric F. Pettersen et al.

Summary: UCSF ChimeraX is a powerful visualization program with enhanced performance and graphics, offering new tools and analysis features, support for various areas like virtual reality, and improved ease of use, along with an app store for researchers to contribute new tools.

PROTEIN SCIENCE (2021)

Article Biochemistry & Molecular Biology

B-Raf autoinhibition in the presence and absence of 14-3-3

Mingzhen Zhang et al.

Summary: In the presence of 14-3-3, the interaction with B-Raf stabilizes the RBD-CRD-KD interaction, interfering with the KD dimerization. The release of RBD-CRD promotes KD fluctuations and reorientation for dimerization, suggesting a mechanism where one KD monomer is donated by 14-3-3-free B-Raf KD and the other by 14-3-3-bound KD.

STRUCTURE (2021)

Article Oncology

SHED-Dependent Oncogenic Signaling of the PEAK3 Pseudo-Kinase

Youcef Ounoughene et al.

Summary: The human kinome includes about 50 pseudo-kinases with unclear function, but they play important roles in cancer similar to active kinases. PEAK1, PEAK2, and PEAK3 pseudo-kinases are key components in the protein tyrosine kinase pathway, signaling via a SHED module, potentially promoting tumorigenesis.

CANCERS (2021)

Article Multidisciplinary Sciences

Highly accurate protein structure prediction with AlphaFold

John Jumper et al.

Summary: Proteins are essential for life, and accurate prediction of their structures is a crucial research problem. Current experimental methods are time-consuming, highlighting the need for accurate computational approaches to address the gap in structural coverage. Despite recent progress, existing methods fall short of atomic accuracy in protein structure prediction.

NATURE (2021)

Article Multidisciplinary Sciences

Highly accurate protein structure prediction for the human proteome

Kathryn Tunyasuvunakool et al.

Summary: Using the AlphaFold method, the structural coverage of the proteome has been significantly expanded, covering 98.5% of human proteins with 58% of residues having confident predictions and 36% having very high confidence. Introducing new metrics to interpret the dataset and identify disordered regions, this study aims to provide high-quality predictions for generating biological hypotheses.

NATURE (2021)

Review Biochemistry & Molecular Biology

The PEAK family of pseudokinases, their role in cell signalling and cancer

Onisha Patel et al.

FEBS JOURNAL (2020)

Article Neurosciences

Binding of the Human 14-3-3 Isoforms to Distinct Sites in the Leucine-Rich Repeat Kinase 2

Jascha T. Manschwetus et al.

FRONTIERS IN NEUROSCIENCE (2020)

Article Biochemistry & Molecular Biology

Dimerization Induced by C-Terminal 14-3-3 Binding Is Sufficient for BRAF Kinase Activation

Nicholas P. D. Liau et al.

BIOCHEMISTRY (2020)

Article Multidisciplinary Sciences

AXL confers cell migration and invasion by hijacking a PEAK1-regulated focal adhesion protein network

Afnan Abu-Thuraia et al.

NATURE COMMUNICATIONS (2020)

Article Multidisciplinary Sciences

Mechanism of IRSp53 inhibition by 14-3-3

David J. Kast et al.

NATURE COMMUNICATIONS (2019)

Article Multidisciplinary Sciences

PEAK3/C19orf35 pseudokinase, a new NFK3 kinase family member, inhibits CrkII through dimerization

Mitchell L. Lopez et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Multidisciplinary Sciences

Architecture of autoinhibited and active BRAF-MEK1-14-3-3 complexes

Eunyoung Park et al.

NATURE (2019)

Article Biochemistry & Molecular Biology

Improvements to the APBS biomolecular solvation software suite

Elizabeth Jurrus et al.

PROTEIN SCIENCE (2018)

Article Cell Biology

The pseudokinases SgK269 and SgK223: A novel oncogenic alliance in human cancer

Rachelle L. O'Rourke et al.

CELL ADHESION & MIGRATION (2018)

Article Biochemistry & Molecular Biology

An Open Library of Human Kinase Domain Constructs for Automated Bacterial Expression

Steven K. Albanese et al.

BIOCHEMISTRY (2018)

Article Biochemistry & Molecular Biology

Crk adaptor proteins mediate actin-dependent T cell migration and mechanosensing induced by the integrin LFA-1

Nathan H. Roy et al.

SCIENCE SIGNALING (2018)

Correction Biochemistry & Molecular Biology

Dimerization of the Pragmin Pseudo-Kinase Regulates Protein Tyrosine Phosphorylation (vol 26, pg 545, 2018 )

Celine Lecointre et al.

STRUCTURE (2018)

Article Multidisciplinary Sciences

Structure of SgK223 pseudokinase reveals novel mechanisms of homotypic and heterotypic association

Onisha Patel et al.

NATURE COMMUNICATIONS (2017)

Article Biochemistry & Molecular Biology

The Molecular Mechanisms Underlying the Hijack of Host Proteins by the 1918 Spanish Influenza Virus

Qingliang Shen et al.

ACS CHEMICAL BIOLOGY (2017)

Article Biochemistry & Molecular Biology

Homo- and Heterotypic Association Regulates Signaling by the SgK269/PEAK1 and SgK223 Pseudokinases

Ling Liu et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2016)

Article Multidisciplinary Sciences

Novel Role of Src in Priming Pyk2 Phosphorylation

Ming Zhao et al.

PLOS ONE (2016)

Article Biochemistry & Molecular Biology

The pseudokinase SgK223 promotes invasion of pancreatic ductal epithelial cells through JAK1/Stat3 signaling

Carole M. Tactacan et al.

MOLECULAR CANCER (2015)

Article Multidisciplinary Sciences

Grb2 monomer-dimer equilibrium determines normal versus oncogenic function

Zamal Ahmed et al.

NATURE COMMUNICATIONS (2015)

Article Biochemical Research Methods

How good are my data and what is the resolution?

Philip R. Evans et al.

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY (2013)

Article Multidisciplinary Sciences

Temporal regulation of EGF signalling networks by the scaffold protein Shc1

Yong Zheng et al.

NATURE (2013)

Article Multidisciplinary Sciences

Computational Model of Gab1/2-Dependent VEGFR2 Pathway to Akt Activation

Wan Hua Tan et al.

PLOS ONE (2013)

Article Biochemical Research Methods

Towards automated crystallographic structure refinement with phenix.refine

Pavel V. Afonine et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2012)

Review Biochemistry & Molecular Biology

The language of SH2 domain interactions defines phosphotyrosine-mediated signal transduction

Bernard A. Liu et al.

FEBS LETTERS (2012)

Article Biochemistry & Molecular Biology

Domain organization differences explain Bcr-Abl's preference for CrkL over CrkII

Wojciech Jankowski et al.

NATURE CHEMICAL BIOLOGY (2012)

Article Biochemical Research Methods

Overview of the CCP4 suite and current developments

Martyn D. Winn et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2011)

Article Multidisciplinary Sciences

Mammalian Pragmin regulates Src family kinases via the Glu-Pro-Ile-Tyr-Ala (EPIYA) motif that is exploited by bacterial effectors

Fatemeh Safari et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Review Cell Biology

14-3-3 Proteins: Diverse functions in cell proliferation and cancer progression

Alyson K. Freeman et al.

SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY (2011)

Article Biochemical Research Methods

MolProbity: all-atom structure validation for macromolecular crystallography

Vincent B. Chen et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2010)

Article Biochemical Research Methods

XDS

Wolfgang Kabsch

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY (2010)

Article Biochemistry & Molecular Biology

Regulation of IRSp53-Dependent Filopodial Dynamics by Antagonism between 14-3-3 Binding and SH3-Mediated Localization

Jeffrey M. Robens et al.

MOLECULAR AND CELLULAR BIOLOGY (2010)

Article Multidisciplinary Sciences

Pseudopodium-enriched atypical kinase 1 regulates the cytoskeleton and cancer progession

Yingchun Wang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Oncology

PEAK1, a Novel Kinase Target in the Fight Against Cancer

Jonathan A. Kelber et al.

ONCOTARGET (2010)

Review Pharmacology & Pharmacy

Grb2 signaling in cell motility and cancer

Alessio Giubellino et al.

EXPERT OPINION ON THERAPEUTIC TARGETS (2008)

Editorial Material Biochemistry & Molecular Biology

Cooperativity and biological complexity

Adrian Whitty

NATURE CHEMICAL BIOLOGY (2008)

Article Biochemistry & Molecular Biology

PROMALS3D web server for accurate multiple protein sequence and structure alignments

Jimin Pei et al.

NUCLEIC ACIDS RESEARCH (2008)

Article Chemistry, Multidisciplinary

Phaser crystallographic software

Airlie J. McCoy et al.

JOURNAL OF APPLIED CRYSTALLOGRAPHY (2007)

Article Biochemistry & Molecular Biology

Pragmin, a novel effector of Rnd2 GTPase, stimulates RhoA activity

H Tanaka et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2006)

Article Biochemical Research Methods

Crystallization of the SH2-binding site of p130Cas in complex with Lck, a Src-family kinase

F Nasertorabi et al.

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS (2005)

Article Biochemical Research Methods

Coot:: model-building tools for molecular graphics

P Emsley et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2004)

Article Biochemistry & Molecular Biology

WebLogo: A sequence logo generator

GE Crooks et al.

GENOME RESEARCH (2004)

Article Biochemistry & Molecular Biology

CrkL directs ASAP1 to peripheral focal adhesions

A Oda et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2003)

Article Biochemistry & Molecular Biology

Regulation of c-SRC activity and function by the adapter protein CAS

MR Burnham et al.

MOLECULAR AND CELLULAR BIOLOGY (2000)

Article Multidisciplinary Sciences

The Arf GTPase-activating protein ASAP1 regulates the actin cytoskeleton

PA Randazzo et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2000)