(Q42876442)

9 November 2017

Specificity of a protein-protein interface: local dynamics direct substrate recognition of effector caspases (English)

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9 November 2017

5

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9 November 2017

Susanne von Grafenstein

series ordinal

2

object named as

Susanne von Grafenstein

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9 November 2017

4

Hannes G Wallnoefer

1 reference

9 November 2017

Julian E Fuchs

1

1 reference

9 November 2017

Roland G Huber

series ordinal

3

1 reference

9 November 2017

language of work or name

English

0 references

publication date

19 October 2013

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9 November 2017

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9 November 2017

82

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9 November 2017

4

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9 November 2017

546-555

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describes a project that uses

9 November 2017

PyMOL

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&rettype=xml&id=PMC4282588

cites work

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Global identification of peptidase specificity by multiplex substrate profiling

27 May 2018

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Allosteric modulation of caspase 3 through mutagenesis

27 May 2018

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Exploring protein dynamics space: the dynasome as the missing link between protein structure and function

27 May 2018

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FLIM-FRET Imaging of Caspase-3 Activity in Live Cells Using Pair of Red Fluorescent Proteins.

27 May 2018

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MEROPS: the database of proteolytic enzymes, their substrates and inhibitors

27 May 2018

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Exploiting differences in caspase-2 and -3 S₂ subsites for selectivity: structure-based design, solid-phase synthesis and in vitro activity of novel substrate-based caspase-2 inhibitors

27 May 2018

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27 May 2018

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Dynamics of preferential substrate recognition in HIV-1 protease: redefining the substrate envelope

27 May 2018

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Caspase-1 promiscuity is counterbalanced by rapid inactivation of processed enzyme

27 May 2018

1 reference

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A bifunctional allosteric site in the dimer interface of procaspase-3

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Caspase substrates and cellular remodeling

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Current strategies for probing substrate specificity of proteases

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

NMR resonance assignments of thrombin reveal the conformational and dynamic effects of ligation.

27 May 2018

1 reference

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Prediction of protease substrates using sequence and structure features

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Stabilizing of a globular protein by a highly complex water network: a molecular dynamics simulation study on factor Xa.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Improved side-chain torsion potentials for the Amber ff99SB protein force field

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Cascleave: towards more accurate prediction of caspase substrate cleavage sites

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Caspase substrates: easily caught in deep waters?

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

The role of dynamic conformational ensembles in biomolecular recognition

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Proteome-wide substrate analysis indicates substrate exclusion as a mechanism to generate caspase-7 versus caspase-3 specificity

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Conformational similarity in the activation of caspase-3 and -7 revealed by the unliganded and inhibited structures of caspase-7

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Protein dynamics and conformational disorder in molecular recognition

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Human caspases: activation, specificity, and regulation

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Caspase-3 binds diverse P4 residues in peptides as revealed by crystallography and structural modeling

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Protonate3D: assignment of ionization states and hydrogen coordinates to macromolecular structures

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Structural basis for executioner caspase recognition of P5 position in substrates

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Executioner caspase-3 and caspase-7 are functionally distinct proteases

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Proteome-derived, database-searchable peptide libraries for identifying protease cleavage sites

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Dynamic personalities of proteins

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Plasticity of S2-S4 specificity pockets of executioner caspase-7 revealed by structural and kinetic analysis

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Conformational entropy in molecular recognition by proteins

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Structural and functional definition of the specificity of a novel caspase-3 inhibitor, Ac-DNLD-CHO.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

The CASBAH: a searchable database of caspase substrates

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

SVM-based prediction of caspase substrate cleavage sites

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Role of loop bundle hydrogen bonds in the maturation and activity of (Pro)caspase-3.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Small-molecule activation of procaspase-3 to caspase-3 as a personalized anticancer strategy

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Caspases 3 and 7: key mediators of mitochondrial events of apoptosis

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Caspases: pharmacological manipulation of cell death

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Specificity of trypsin and chymotrypsin: loop-motion-controlled dynamic correlation as a determinant

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

The many faces of protease-protein inhibitor interaction

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

The protein structures that shape caspase activity, specificity, activation and inhibition

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

A novel method for evaluation and screening of caspase inhibitory peptides by the amino acid positional fitness score

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Conformational restrictions in the active site of unliganded human caspase-3

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Molecular dynamics studies of caspase-3.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Serine protease mechanism and specificity

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Crystal structure of a procaspase-7 zymogen: mechanisms of activation and substrate binding

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

The biochemistry of apoptosis

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Internally quenched fluorescent peptide substrates disclose the subsite preferences of human caspases 1, 3, 6, 7 and 8

27 May 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

27 May 2018

https://api.crossref.org/works/10.1002%2FPROT.24417

The structures of caspases-1, -3, -7 and -8 reveal the basis for substrate and inhibitor selectivity

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Folding funnels, binding funnels, and protein function

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

27 May 2018

Caspases: enemies within

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Evolutionary divergence of substrate specificity within the chymotrypsin-like serine protease fold

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

A combinatorial approach defines specificities of members of the caspase family and granzyme B. Functional relationships established for key mediators of apoptosis

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Decreased apoptosis in the brain and premature lethality in CPP32-deficient mice

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

The three-dimensional structure of apopain/CPP32, a key mediator of apoptosis

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Principles of protein-protein recognition from structure to thermodynamics

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Structural basis of substrate specificity in the serine proteases

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Kinetic and structural characterization of mutations of glycine 216 in alpha-lytic protease: a new target for engineering substrate specificity

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Converting trypsin to chymotrypsin: the role of surface loops

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Towards a better understanding of the specificity of protein-protein interaction.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Backbone flexibility controls the activity and specificity of a protein-protein interface: specificity in snake venom metalloproteases

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Reconciling the lock-and-key and dynamic views of canonical serine protease inhibitor action

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Evaluation of recombinant caspase specificity by competitive substrates.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Caspase-7 expanded function and intrinsic expression level underlies strain-specific brain phenotype of caspase-3-null mice.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Molecular dynamics simulations of structural changes during procaspase 3 activation

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Functional Linkage Between the Active Site of α-Lytic Protease and Distant Regions of Structure: Scanning Alanine Mutagenesis of a Surface Loop Affects Activity and Substrate Specificity

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282588

Comparison of simple potential functions for simulating liquid water

16 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1002%2FPROT.24417

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1002%2FPROT.24417

Folding pathways for initiator and effector procaspases from computer simulations

21 January 2018

1 reference

12 December 2020

Substrate specificities of caspase family proteases

1 reference

12 December 2020

Convergent dynamics in the protease enzymatic superfamily

1 reference

12 December 2020

Altered flexibility in the substrate-binding site of related native and engineered high-alkaline Bacillus subtilisins

1 reference

12 December 2020

Identifiers

DOI

10.1002/PROT.24417

1 reference

9 November 2017

1 reference

9 November 2017

PubMed publication ID

24085488

1 reference