4.6 Article

Structural dynamics shape the fitness window of alanine:glyoxylate aminotransferase

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

Crosstalk between Long-Term Sublethal Oxidative Stress and Detrimental Inflammation as Potential Drivers for Age-Related Retinal Degeneration

Lara Macchioni et al.

Summary: Age-related retinal degenerations, such as AMD, are linked to the loss of RPE cells and photoreceptors, involving oxidative stress and inflammatory responses. Long-term oxidative insult can induce senescence in RPE cells, affecting antioxidant response and mitochondrial functionality.

ANTIOXIDANTS (2021)

Review Chemistry, Multidisciplinary

Fuzziness and Frustration in the Energy Landscape of Protein Folding, Function, and Assembly

Stefano Gianni et al.

Summary: Proteins and their complexes can be described as ensembles that populate an energy landscape, where the diversity arises from the conflicts between interactions shaping the energy landscape. Within this framework, alternative sets of suboptimal contacts can encode specificity without achieving a single structural optimum. The interplay between frustration and fuzziness offers insights into the structural and dynamical continuum of protein assemblies.

ACCOUNTS OF CHEMICAL RESEARCH (2021)

Article Chemistry, Physical

Frustration in Fuzzy Protein Complexes Leads to Interaction Versatility

Maria Freiberger et al.

Summary: The study reveals that complexes of disordered proteins exhibit a high degree of local frustration, especially at the binding interface, leading to multiple bound substates with distinct frustration patterns, differently populated in complexes with different partners. This explains how specificity of disordered proteins can be achieved without a single common bound conformation and how the conflict between different interactions can be used to control the binding to multiple partners.

JOURNAL OF PHYSICAL CHEMISTRY B (2021)

Article Biochemistry & Molecular Biology

Diet and Adaptive Evolution of Alanine-Glyoxylate Aminotransferase Mitochondrial Targeting in Birds

Bing-Jun Wang et al.

MOLECULAR BIOLOGY AND EVOLUTION (2020)

Article Multidisciplinary Sciences

Flexibility of intrinsically disordered degrons in AUX/IAA proteins reinforces auxin co-receptor assemblies

Michael Niemeyer et al.

NATURE COMMUNICATIONS (2020)

Article Multidisciplinary Sciences

Mutations in disordered proteins as early indicators of nucleic acid changes triggering speciation

Sergio Forcelloni et al.

SCIENTIFIC REPORTS (2020)

Article Multidisciplinary Sciences

Folding Free Energy Landscape of Ordered and Intrinsically Disordered Proteins

Song-Ho Chong et al.

SCIENTIFIC REPORTS (2019)

Article Multidisciplinary Sciences

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling

Steven E. Guard et al.

JOVE-JOURNAL OF VISUALIZED EXPERIMENTS (2019)

Article Biochemistry & Molecular Biology

The PRIDE database and related tools and resources in 2019: improving support for quantification data

Yasset Perez-Riverol et al.

NUCLEIC ACIDS RESEARCH (2019)

Review Physics, Multidisciplinary

Intrinsically Disordered Proteins and Their Mysterious (Meta)Physics

Vladimir N. Uversky

FRONTIERS IN PHYSICS (2019)

Article Biochemistry & Molecular Biology

Ensembl 2018

Daniel R. Zerbino et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Biochemistry & Molecular Biology

UCSF ChimeraX: Meeting modern challenges in visualization and analysis

Thomas D. Goddard et al.

PROTEIN SCIENCE (2018)

Article Biochemistry & Molecular Biology

SWISS-MODEL: homology modelling of protein structures and complexes

Andrew Waterhouse et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Biochemistry & Molecular Biology

Analyses of N-linked glycans of PrPSc revealed predominantly 2,6-linked sialic acid residues

Elizaveta Katorcha et al.

FEBS JOURNAL (2017)

Article Biochemical Research Methods

ModelFinder: fast model selection for accurate phylogenetic estimates

Subha Kalyaanamoorthy et al.

NATURE METHODS (2017)

Article Genetics & Heredity

The contribution of protein intrinsic disorder to understand the role of genetic variants uncovered by autism spectrum disorders exome studies

Jaqueline Bohrer Schuch et al.

AMERICAN JOURNAL OF MEDICAL GENETICS PART B-NEUROPSYCHIATRIC GENETICS (2016)

Review Biochemistry & Molecular Biology

The contribution of intrinsically disordered regions to protein function, cellular complexity, and human disease

M. Madan Babu

BIOCHEMICAL SOCIETY TRANSACTIONS (2016)

Article Biochemistry & Molecular Biology

Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics

R. Gonzalo Parra et al.

NUCLEIC ACIDS RESEARCH (2016)

Review Biochemistry & Molecular Biology

Liver peroxisomal alanine:glyoxylate aminotransferase and the effects of mutations associated with Primary Hyperoxaluria Type I: An overview

Elisa Oppici et al.

BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS (2015)

Article Biochemistry & Molecular Biology

Widespread Macromolecular Interaction Perturbations in Human Genetic Disorders

Nidhi Sahni et al.

Review Biochemistry & Molecular Biology

Functional roles of transiently and intrinsically disordered regions within proteins

Vladimir N. Uversky

FEBS JOURNAL (2015)

Article Multidisciplinary Sciences

Peptidic degron in EID1 is recognized by an SCF E3 ligase complex containing the orphan F-box protein FBXO21

Cuiyan Zhang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Article Biochemistry & Molecular Biology

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

Lam-Tung Nguyen et al.

MOLECULAR BIOLOGY AND EVOLUTION (2015)

Article Biochemistry & Molecular Biology

The lower limits for protein stability and foldability in primary hyperoxaluria type I

Noel Mesa-Torres et al.

BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS (2014)

Article Chemistry, Physical

Building Water Models: A Different Approach

Saeed Izadi et al.

JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2014)

Article Biochemical Research Methods

Proteomic analysis of cerebrospinal fluid extracellular vesicles: A comprehensive dataset

Davide Chiasserini et al.

JOURNAL OF PROTEOMICS (2014)

Review Biochemistry & Molecular Biology

Advantages of proteins being disordered

Zhirong Liu et al.

PROTEIN SCIENCE (2014)

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)

Review Biotechnology & Applied Microbiology

Protein Homeostasis Defects of Alanine-Glyoxylate Aminotransferase: New Therapeutic Strategies in Primary Hyperoxaluria Type I

Angel L. Pey et al.

BIOMED RESEARCH INTERNATIONAL (2013)

Article Biochemistry & Molecular Biology

The N-terminal extension is essential for the formation of the active dimeric structure of liver peroxisomal alanine:glyoxylate aminotransferase

Riccardo Montioli et al.

INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY (2012)

Article Biochemistry & Molecular Biology

Multiple Adaptive Losses of Alanine-Glyoxylate Aminotransferase Mitochondrial Targeting in Fruit-Eating Bats

Yang Liu et al.

MOLECULAR BIOLOGY AND EVOLUTION (2012)

Article Biochemistry & Molecular Biology

The Influence of Rate Heterogeneity among Sites on the Time Dependence of Molecular Rates

Julien Soubrier et al.

MOLECULAR BIOLOGY AND EVOLUTION (2012)

Editorial Material Biochemistry & Molecular Biology

Disease mutations in disordered regions-exception to the rule?

Vladimir Vacic et al.

MOLECULAR BIOSYSTEMS (2012)

Article Biochemical Research Methods

REFMAC5 for the refinement of macromolecular crystal structures

Garib N. Murshudov et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2011)

Review Biochemistry & Molecular Biology

Human liver peroxisomal alanine:glyoxylate aminotransferase: Characterization of the two allelic forms and their pathogenic variants

Barbara Cellini et al.

BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS (2011)

Article Biochemical Research Methods

SAINT: probabilistic scoring of affinity purification-mass spectrometry data

Hyungwon Choi et al.

NATURE METHODS (2011)

Article Biochemical Research Methods

Molecular replacement with MOLREP

Alexei Vagin et al.

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY (2010)

Article Biochemical Research Methods

XDS

Wolfgang Kabsch

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY (2010)

Article Biochemical Research Methods

PHENIX: a comprehensive Python-based system for macromolecular structure solution

Paul D. Adams et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2010)

Article Biochemical Research Methods

Structural implications of a G170R mutation of alanine:glyoxylate aminotransferase that is associated with peroxisome-to-mitochondrion mistargeting

Snezana Djordjevic et al.

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS (2010)

Article Multidisciplinary Sciences

Molecular defects of the glycine 41 variants of alanine glyoxylate aminotransferase associated with primary hyperoxaluria type I

Barbara Cellini et al.

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

Article Biochemical Research Methods

Jalview Version 2-a multiple sequence alignment editor and analysis workbench

Andrew M. Waterhouse et al.

BIOINFORMATICS (2009)

Review Chemistry, Multidisciplinary

CHARMM: The Biomolecular Simulation Program

B. R. Brooks et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2009)

Article Biochemistry & Molecular Biology

In Vivo and in Vitro Examination of Stability of Primary Hyperoxaluria-associated Human Alanine: Glyoxylate Aminotransferase

Erin D. Hopper et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2008)

Article Chemistry, Multidisciplinary

Thermodynamics and kinetics of aggregation for the GNNQQNY peptide

Birgit Strodel et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2007)

Article Chemistry, Physical

Canonical sampling through velocity rescaling

Giovanni Bussi et al.

JOURNAL OF CHEMICAL PHYSICS (2007)

Review Biochemistry & Molecular Biology

Primary hyperoxaluria type 1: AGT mistargeting highlights the fundamental differences between the peroxisomal and mitochondrial protein import pathways

Christopher J. Danpure

BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH (2006)

Article Biochemistry & Molecular Biology

Differential enzyme targeting as an evolutionary adaptation to herbivory in Carnivora

GM Birdsey et al.

MOLECULAR BIOLOGY AND EVOLUTION (2004)

Article Multidisciplinary Sciences

Water in protein structure prediction

GA Papoian et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)

Article Biochemical Research Methods

Coot:: model-building tools for molecular graphics

P Emsley et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2004)