The Structure of a Thermophilic Kinase Shapes Fitness upon Random Circular Permutation (Q35956927)

11 August 2017

The Structure of a Thermophilic Kinase Shapes Fitness upon Random Circular Permutation (English)

1 reference

11 August 2017

0 references

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26976658 AND SRC:MED&resulttype=core&format=json

1 June 2020

Joshua T Atkinson

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26976658 AND SRC:MED&resulttype=core&format=json

1 June 2020

Thomas H Segall-Shapiro

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26976658 AND SRC:MED&resulttype=core&format=json

1 June 2020

author name string

Alicia M Jones

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26976658 AND SRC:MED&resulttype=core&format=json

1 June 2020

Emily E Thomas

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26976658 AND SRC:MED&resulttype=core&format=json

1 June 2020

Shirley Liu

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26976658 AND SRC:MED&resulttype=core&format=json

1 June 2020

Jonathan J Silberg

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26976658 AND SRC:MED&resulttype=core&format=json

1 June 2020

publication date

14 March 2016

1 reference

11 August 2017

ACS Synthetic Biology

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26976658 AND SRC:MED&resulttype=core&format=json

1 June 2020

volume

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26976658 AND SRC:MED&resulttype=core&format=json

1 June 2020

issue

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26976658 AND SRC:MED&resulttype=core&format=json

1 June 2020

page(s)

415-425

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26976658 AND SRC:MED&resulttype=core&format=json

Design of protein switches based on an ensemble model of allostery

1 June 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

How structural and physicochemical determinants shape sequence constraints in a functional enzyme

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Detection of circular permutations within protein structures using CE-CP

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Adenylate kinase from Streptococcus pneumoniae is essential for growth through its catalytic activity.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

A 'resource allocator' for transcription based on a highly fragmented T7 RNA polymerase.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Modulation of frustration in folding by sequence permutation.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

A comprehensive, high-resolution map of a gene's fitness landscape

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Improved biocatalysts from a synthetic circular permutation library of the flavin-dependent oxidoreductase old yellow enzyme

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

PFunkel: efficient, expansive, user-defined mutagenesis.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

CPred: a web server for predicting viable circular permutations in proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Circular permutation in the Ω-loop of TEM-1 β-lactamase results in improved activity and altered substrate specificity

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

The interface of protein structure, protein biophysics, and molecular evolution

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Deciphering the preference and predicting the viability of circular permutations in proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

A transposase strategy for creating libraries of circularly permuted proteins.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Mesophilic and hyperthermophilic adenylate kinases differ in their tolerance to random fragmentation.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Circular permutation: a different way to engineer enzyme structure and function

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Circular permutation of Bacillus circulans xylanase: a kinetic and structural study

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Rational modulation of conformational fluctuations in adenylate kinase reveals a local unfolding mechanism for allostery and functional adaptation in proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Automated design of synthetic ribosome binding sites to control protein expression

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

The folding, stability and conformational dynamics of beta-barrel fluorescent proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Structure and biochemical characterization of an adenylate kinase originating from the psychrophilic organismMarinibacillus marinus

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Structural and Thermodynamic Analysis of a Conformationally Strained Circular Permutant of Barnase †

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

CPSARST: an efficient circular permutation search tool applied to the detection of novel protein structural relationships

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Intrinsic motions along an enzymatic reaction trajectory

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Clustal W and Clustal X version 2.0

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Relative tolerance of mesostable and thermostable protein homologs to extensive mutation

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Duplication, divergence and formation of novel protein topologies

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Roles of static and dynamic domains in stability and catalysis of adenylate kinase

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Evolution of Circular Permutations in Multidomain Proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Engineering and characterization of a superfolder green fluorescent protein

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Identification and characterization of key substructures involved in the early folding events of a (beta/alpha)8-barrel protein as studied by experimental and computational methods.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Improving the Catalytic Activity of Candida antarctica Lipase B by Circular Permutation

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Directed evolution of protein switches and their application to the creation of ligand-binding proteins.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Mathematical expressions useful in the construction, description and evaluation of protein libraries.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Thermodynamic prediction of protein neutrality

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

ASAView: database and tool for solvent accessibility representation in proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

MUSCLE: multiple sequence alignment with high accuracy and high throughput

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Thermotoga neapolitana adenylate kinase is highly active at 30 degrees C

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

A novel view of domain flexibility in E. coli adenylate kinase based on structural mode-coupling (15)N NMR relaxation.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Circularly permuted proteins in the protein structure database

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Circular permutation and receptor insertion within green fluorescent proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Circularly permuted variants of the green fluorescent protein

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Random circular permutation of DsbA reveals segments that are essential for protein folding and stability

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Crystal structures of Bacillus stearothermophilus adenylate kinase with bound Ap5A, Mg2 Ap5A, and Mn2 Ap5A reveal an intermediate lid position and six coordinate octahedral geometry for bound Mg2 and Mn2

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Contact order, transition state placement and the refolding rates of single domain proteins.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Structure, Catalysis and Supramolecular Assembly of Adenylate Kinase from Maize

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Circularly permuted beta-lactamase from Staphylococcus aureus PC1

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Random circular permutation of genes and expressed polypeptide chains: application of the method to the catalytic chains of aspartate transcarbamoylase

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

VMD: visual molecular dynamics

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Native-like in vivo folding of a circularly permuted jellyroll protein shown by crystal structure analysis

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 A resolution. A model for a catalytic transition state

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Molecular characterization of cDNA encoding for adenylate kinase of rice (Oryza sativa L.)

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Evolutionary conservation in protein folding kinetics

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Circular permutations of natural protein sequences: structural evidence

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

High‐resolution structures of adenylate kinase from yeast ligated with inhibitor Ap5A, showing the pathway of phosphoryl transfer

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Dynamics in Thermotoga neapolitana adenylate kinase: 15N relaxation and hydrogen-deuterium exchange studies of a hyperthermophilic enzyme highly active at 30 degrees C.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Circular permutation and deletion studies of myoglobin indicate that the correct position of its N-terminus is required for native stability and solubility but not for native-like heme binding and folding.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Linkage between dynamics and catalysis in a thermophilic-mesophilic enzyme pair

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Structures and analysis of highly homologous psychrophilic, mesophilic, and thermophilic adenylate kinases

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

24 September 2018

Creation of a zymogen

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Complete change of the protein folding transition state upon circular permutation.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Circularly permuted dihydrofolate reductase of E. coli has functional activity and a destabilized tertiary structure.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

P1,P5-Di(adenosine-5′)pentaphosphate, a Potent Multisubstrate Inhibitor of Adenylate Kinase

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Evolution of new protein topologies through multistep gene rearrangements

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5122316

Sequence and positional requirements for DNA sites in a mu transpososome

24 September 2018

1 reference

12 December 2020

Systematic circular permutation of an entire protein reveals essential folding elements

1 reference

12 December 2020

Adenylate kinases from thermosensitive Escherichia coli strains

1 reference

12 December 2020

Circular permutation of T4 lysozyme

1 reference

12 December 2020

10.1021/ACSSYNBIO.5B00305

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26976658 AND SRC:MED&resulttype=core&format=json

1 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26976658 AND SRC:MED&resulttype=core&format=json

1 June 2020

PubMed publication ID

26976658

1 reference