Basis for substrate recognition and distinction by matrix metalloproteinases (Q34407655)

2 August 2017

Basis for substrate recognition and distinction by matrix metalloproteinases (English)

1 reference

2 August 2017

9

1 reference

2 August 2017

Marat Kazanov

7

0 references

Alex Strongin

object named as

Alex Strongin

12

0 references

Yoshinobu Igarashi

6

object named as

Yoshinobu Igarashi

1 reference

2 August 2017

Boris I Ratnikov

1

1 reference

2 August 2017

Piotr Cieplak

2

1 reference

2 August 2017

Kosi Gramatikoff

3

1 reference

2 August 2017

James Pierce

4

1 reference

2 August 2017

Alexey Eroshkin

5

1 reference

2 August 2017

Qing Sun

8

1 reference

2 August 2017

Andrei Osterman

10

1 reference

2 August 2017

Boguslaw Stec

11

1 reference

2 August 2017

Jeffrey W Smith

13

1 reference

2 August 2017

language of work or name

English

0 references

publication date

22 September 2014

1 reference

Proceedings of the National Academy of Sciences of the United States of America

2 August 2017

1 reference

2 August 2017

111

1 reference

2 August 2017

E4148-55

1 reference

2 August 2017

40

1 reference

FFAS-3D: improving fold recognition by including optimized structural features and template re-ranking

2 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Antibody-directed coupling of endoglin and MMP-14 is a key mechanism for endoglin shedding and deregulation of TGF-β signaling

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Matrix metalloproteinase-2 (MMP-2) generates soluble HLA-G1 by cell surface proteolytic shedding.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Catalytic site identification--a web server to identify catalytic site structural matches throughout PDB.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Engineering of TEV protease variants by yeast ER sequestration screening (YESS) of combinatorial libraries

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Protein structure based prediction of catalytic residues

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Commercial proteases: present and future

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Protein TAILS: when termini tell tales of proteolysis and function

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Disentangling evolutionary signals: conservation, specificity determining positions and coevolution. Implication for catalytic residue prediction

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Single-molecule tracking of collagenase on native type I collagen fibrils reveals degradation mechanism

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Detection of MMP-2 and MMP-9 activity in vivo with a triple-helical peptide optical probe

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Global kinetic analysis of proteolysis via quantitative targeted proteomics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

The interface between catalytic and hemopexin domains in matrix metalloproteinase-1 conceals a collagen binding exosite.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Identifying and quantifying proteolytic events and the natural N terminome by terminal amine isotopic labeling of substrates

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Structural determinants of limited proteolysis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Internal organization of large protein families: relationship between the sequence, structure, and function-based clustering

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Proteases as therapeutics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Recognition and Specificity Determinants of the Human Cbx Chromodomains

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Multiplex N-terminome analysis of MMP-2 and MMP-9 substrate degradomes by iTRAQ-TAILS quantitative proteomics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

SeSAW: balancing sequence and structural information in protein functional mapping

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Combining structure and sequence information allows automated prediction of substrate specificities within enzyme families

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Engineering next generation proteases

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Identification of specific hemopexin-like domain residues that facilitate matrix metalloproteinase collagenolytic activity.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Structural and functional bases for allosteric control of MMP activities: can it pave the path for selective inhibition?

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Using evolutionary information to find specificity-determining and co-evolving residues.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

High throughput substrate phage display for protease profiling

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Coevolution in defining the functional specificity

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Protein meta-functional signatures from combining sequence, structure, evolution, and amino acid property information

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

MMP-12 catalytic domain recognizes triple helical peptide models of collagen V with exosites and high activity

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Highly active and selective endopeptidases with programmed substrate specificities

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Differentiation of secreted and membrane-type matrix metalloproteinase activities based on substitutions and interruptions of triple-helical sequences

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Sequence comparison by sequence harmony identifies subtype-specific functional sites

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

The roles of substrate thermal stability and P2 and P1' subsite identity on matrix metalloproteinase triple-helical peptidase activity and collagen specificity

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Control of ErbB signaling through metalloprotease mediated ectodomain shedding of EGF-like factors

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

WebProAnalyst: an interactive tool for analysis of quantitative structure-activity relationships in protein families

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Collagenase unwinds triple-helical collagen prior to peptide bond hydrolysis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

The interplay of fold recognition and experimental structure determination in structural genomics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

WebLogo: A Sequence Logo Generator

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

MUSCLE: multiple sequence alignment with high accuracy and high throughput

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Amino acids determining enzyme-substrate specificity in prokaryotic and eukaryotic protein kinases

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

A residue in the S2 subsite controls substrate selectivity of matrix metalloproteinase-2 and matrix metalloproteinase-9.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Matrix metalloproteinase processing of monocyte chemoattractant proteins generates CC chemokine receptor antagonists with anti-inflammatory properties in vivo

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Inflammation dampened by gelatinase A cleavage of monocyte chemoattractant protein-3

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Identification of the (183)RWTNNFREY(191) region as a critical segment of matrix metalloproteinase 1 for the expression of collagenolytic activity

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Co-evolution of proteins with their interaction partners

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Protein structure prediction in the postgenomic era.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Broad antitumor and antiangiogenic activities of AG3340, a potent and selective MMP inhibitor undergoing advanced oncology clinical trials

6 July 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

6 July 2018

https://api.crossref.org/works/10.1073%2FPNAS.1406134111

Matrix metalloproteinases: structures, evolution, and diversification

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Identification of a region in the integrin beta3 subunit that confers ligand binding specificity

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

The coevolution of gene family trees

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Substrate phage: selection of protease substrates by monovalent phage display

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Modification of the amino acid specificity of tyrosyl-tRNA synthetase by protein engineering

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Modification of the substrate specificity of an acyl-acyl carrier protein thioesterase by protein engineering

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

High-resolution epitope mapping of hGH-receptor interactions by alanine-scanning mutagenesis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4210027

Sequences and topology: from genome structure to protein structure.

6 July 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1406134111

Protein Secondary Structure Prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1406134111

InterPro protein classification.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1406134111

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1406134111

Using orthologous and paralogous proteins to identify specificity-determining residues in bacterial transcription factors.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1406134111

Pivotal molecular determinants of peptidic and collagen triple helicase activities reside in the S3' subsite of matrix metalloproteinase 8 (MMP-8): the role of hydrogen bonding potential of ASN188 and TYR189 and the connecting cis bond

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1406134111

Platelet shedding of CD40L is regulated by matrix metalloproteinase-9 in abdominal sepsis

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1406134111

Substrate hydrolysis by matrix metalloproteinase-9.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1406134111

Low molecular weight inhibitors in corneal ulceration

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1406134111

Using MCL to extract clusters from networks.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1406134111

Visualizing large hierarchical clusters in hyperbolic space

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25246591

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Mutational investigation of the specificity determining region of the Src SH2 domain

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25246591

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.1406134111

1 reference

2 August 2017

0 references

1 reference

2 August 2017

1 reference