4.7 Article

Engineering the Active Site Lid Dynamics to Improve the Catalytic Efficiency of Yeast Cytosine Deaminase

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

Functional roles of enzyme dynamics in accelerating active site chemistry: Emerging techniques and changing concepts

Shuaihua Gao et al.

Summary: With the growing acceptance of the importance of protein conformational ensembles in enzyme catalysis and regulation, research in protein dynamics is now focused on understanding the atomic properties and mechanisms behind protein dynamical networks. This includes the networks that communicate with the protein/water interface. Advances in experimental tools and biophysical methods have allowed for real-time visualization of dynamics in thermal activation pathways.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2022)

Article Chemistry, Physical

Substrate Tunnel Engineering Aided by X-ray Crystallography and Functional Dynamics Swaps the Function of MIO-Enzymes

Zsofia Bata et al.

Summary: The study reveals that a small opening of the inner loop is sufficient for ligand egress in both eukaryotic aromatic amino acid ammonia-lyases and aminomutases, and the ligand-binding tunnels in these enzymes are analogous. Additionally, engineering of these binding tunnels can convert an (R)-aminomutase to a highly selective (S)-beta-lyase, establishing a novel enzyme function.

ACS CATALYSIS (2021)

Article Multidisciplinary Sciences

Engineering the protein dynamics of an ancestral luciferase

Andrea Schenkmayerova et al.

Summary: This study presents a protein-engineering framework based on InDel mutagenesis and fragment transplantation, leading to improved catalysis and longer glow-type bioluminescence of the ancestral luciferase. The research tracks the role of dynamics in evolution, revealing the importance of protein dynamics in functional innovation.

NATURE COMMUNICATIONS (2021)

Review Chemistry, Physical

Enzyme Dynamics: Looking Beyond a Single Structure

Pratul K. Agarwal et al.

CHEMCATCHEM (2020)

Review Chemistry, Multidisciplinary

Harnessing Conformational Plasticity to Generate Designer Enzymes

Rory M. Crean et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2020)

Article Chemistry, Multidisciplinary

Hydrogen-Deuterium Exchange within Adenosine Deaminase, a TIM Barrel Hydrolase, Identifies Networks for Thermal Activation of Catalysis

Shuaihua Gao et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2020)

Article Chemistry, Multidisciplinary

Remarkable Rigidity of the Single α-Helical Domain of Myosin-VI As Revealed by NMR Spectroscopy

C. Ashley Barnes et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2019)

Article Biochemical Research Methods

Protein-Programmed Accumulation of Yeast Cytosine Deaminase in Cancer Cells in Response to Mock-Hypoxia

Tiana D. Warren et al.

ACS SYNTHETIC BIOLOGY (2019)

Article Biochemistry & Molecular Biology

A Biophysical Perspective on Enzyme Catalysis

Pratul K. Agarwal

BIOCHEMISTRY (2019)

Review Chemistry, Multidisciplinary

Role of conformational dynamics in the evolution of novel enzyme function

Miguel A. Maria-Solano et al.

CHEMICAL COMMUNICATIONS (2018)

Article Biochemistry & Molecular Biology

Laboratory evolution of protein conformational dynamics

Eleanor C. Campbell et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2018)

Article Multidisciplinary Sciences

Rescue of conformational dynamics in enzyme catalysis by directed evolution

Renee Otten et al.

NATURE COMMUNICATIONS (2018)

Article Multidisciplinary Sciences

Entropy in molecular recognition by proteins

Jose A. Caro et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)

Review Pharmacology & Pharmacy

Progress and problems with the use of suicide genes for targeted cancer therapy

Zahra Karjoo et al.

ADVANCED DRUG DELIVERY REVIEWS (2016)

Review Chemistry, Multidisciplinary

The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery

Elena Papaleo et al.

CHEMICAL REVIEWS (2016)

Review Chemistry, Multidisciplinary

Solution NMR Spectroscopy for the Study of Enzyme Allostery

George P. Lisi et al.

CHEMICAL REVIEWS (2016)

Article Biochemistry & Molecular Biology

The role of protein dynamics in the evolution of new enzyme function

Eleanor Campbell et al.

NATURE CHEMICAL BIOLOGY (2016)

Review Biophysics

Protein dynamics and function from solution state NMR spectroscopy

Michael Kovermann et al.

QUARTERLY REVIEWS OF BIOPHYSICS (2016)

Review Chemistry, Multidisciplinary

Enzyme Dynamics from NMR Spectroscopy

Arthur G. Palmer

ACCOUNTS OF CHEMICAL RESEARCH (2015)

Article Multidisciplinary Sciences

How amide hydrogens exchange in native proteins

Filip Persson et al.

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

Article Multidisciplinary Sciences

Direct observation of hierarchical protein dynamics

Jozef R. Lewandowski et al.

SCIENCE (2015)

Article Biochemistry & Molecular Biology

Protein dynamics and motions in relation to their functions: several case studies and the underlying mechanisms

Li-Quan Yang et al.

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2014)

Article Biochemical Research Methods

Automating crystallographic structure solution and refinement of protein-ligand complexes

Nathaniel Echols et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2014)

Article Biochemistry & Molecular Biology

Divergent evolution of protein conformational dynamics in dihydrofolate reductase

Gira Bhabha et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2013)

Article Biochemistry & Molecular Biology

Emerging Implications of Nonmammalian Cytosine Deaminases on Cancer Therapeutics

Vinod Kumar Yata et al.

APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY (2012)

Article Biochemistry & Molecular Biology

Role of Glutamate 64 in the Activation of the Prodrug 5-Fluorocytosine by Yeast Cytosine Deaminase

Jifeng Wang et al.

BIOCHEMISTRY (2012)

Article Multidisciplinary Sciences

Protein activity regulation by conformational entropy

Shiou-Ru Tzeng et al.

NATURE (2012)

Article Biochemistry & Molecular Biology

Evidence for dynamics in proteins as a mechanism for ligand dissociation

Mary J. Carroll et al.

NATURE CHEMICAL BIOLOGY (2012)

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

Features and development of Coot

P. Emsley et al.

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 Multidisciplinary Sciences

Conformational sampling, catalysis, and evolution of the bacterial phosphotriesterase

C. J. Jackson et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Article Biochemistry & Molecular Biology

Yeast cytosine deaminase mutants with increased thermostability impart sensitivity to 5-fluorocytosine

Tiffany S. Stolworthy et al.

JOURNAL OF MOLECULAR BIOLOGY (2008)

Article Biochemistry & Molecular Biology

Long single alpha-helical tail domains bridge the gap between structure and function of myosin VI

Benjamin J. Spink et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2008)

Article Chemistry, Multidisciplinary

Multimodal image-guided enzyme/prodrug cancer therapy

Cong Li et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)

Article Chemistry, Physical

A molecular dynamics exploration of the catalytic mechanism of yeast cytosine deaminase

LS Yao et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2005)

Article Chemistry, Multidisciplinary

Catalytic mechanism of yeast cytosine deaminase: An ONIOM computational study

S Sklenak et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2004)

Article Biochemistry & Molecular Biology

Crystal structure of yeast cytosine deaminase - Insights into enzyme mechanism and evolution

TP Ko et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2003)

Review Chemistry, Physical

Hydrogen exchange in peptides and proteins using NMR-spectroscopy

CE Dempsey

PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY (2001)