Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

Protein structure to function: insights from computation.

D Ringe1, Y Wei, K R Boino

  • 1Rosenstiel Basic Medical Sciences Research Center and Department of Chemistry, Brandeis University, Waltham, Massachusetts 02454, USA.

Cellular and Molecular Life Sciences : CMLS
|March 5, 2004
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Preservation of forelimb function by UPF1 gene therapy in a rat model of TDP-43-induced motor paralysis.

Gene therapy·2014
Same author

Latrepirdine stimulates autophagy and reduces accumulation of α-synuclein in cells and in mouse brain.

Molecular psychiatry·2012
Same author

Latrepirdine improves cognition and arrests progression of neuropathology in an Alzheimer's mouse model.

Molecular psychiatry·2012
Same author

Targeted elimination of leukemia stem cells; a new therapeutic approach in hemato-oncology.

Current drug targets·2009
Same author

Risk factors for gestational diabetes mellitus in Chinese women: a prospective study of 16,286 pregnant women in China.

Diabetic medicine : a journal of the British Diabetic Association·2009
Same author

In vitro and in vivo delivery of novel anticancer fusion protein MULT1E/FasTI via adenoviral vectors.

Cancer gene therapy·2009
Same journal

The BmCPV-derived viral small peptide vsp1S4(-) suppresses viral replication by triggering apoptosis via the ROS-JNK signalling pathway.

Cellular and molecular life sciences : CMLS·2026
Same journal

UBE2L6 promotes invasion and metastasis of triple-negative breast cancer by enhancing autophagy through STK38 ISGylation.

Cellular and molecular life sciences : CMLS·2026
Same journal

Inhibition of ferroptosis via SLC25A39-NRF2 axis drives Osimertinib resistance in lung adenocarcinoma.

Cellular and molecular life sciences : CMLS·2026
Same journal

PHLDA1 knockdown exacerbates emphysema in COPD by attenuating proliferation of alveolar type II cells via modulating GLI1 nuclear translocation.

Cellular and molecular life sciences : CMLS·2026
Same journal

Single-Cell dissection of fibrodysplasia ossificans progressiva identifies SPP1 as a mediator of macrophage-fibroadipogenic progenitors crosstalk.

Cellular and molecular life sciences : CMLS·2026
Same journal

Ablation of the renal tubular gluconeogenic enzyme PCK1 drives AKI-to-CKD transition by negatively regulating the TGF-β/Smad3 signaling pathway.

Cellular and molecular life sciences : CMLS·2026
See all related articles

THEMATICS, a computational method, identifies enzyme active sites by predicting residue properties from protein structures. It successfully located catalytic and recognition sites in serine proteases, aiding specificity studies.

Area of Science:

  • Computational biology
  • Enzymology
  • Structural bioinformatics

Background:

  • Functional genomics relies heavily on computational methods.
  • Identifying enzyme active sites is crucial for understanding protein function and designing inhibitors.
  • Existing methods may not fully capture the nuances of enzyme-protein interactions.

Purpose of the Study:

  • To introduce THEMATICS, a novel computational method for identifying enzyme active sites.
  • To demonstrate THEMATICS's ability to predict catalytic and recognition residues.
  • To explore enzyme specificity through the identification of recognition sites.

Main Methods:

  • THEMATICS utilizes the 3D structure of a protein as input.
  • It predicts chemical and electrostatic properties of amino acid residues.

Related Experiment Videos

  • The method analyzes these properties to identify catalytic and recognition sites within enzymes.

    • Main Results:

    • THEMATICS accurately identified catalytic residues in serine proteases Kex2 and subtilisin.
    • The method successfully pinpointed recognition sites (S1 and S2) in the specific enzyme Kex2.
    • No comparable recognition sites were identified for the non-specific enzyme subtilisin, highlighting THEMATICS's specificity.

    Conclusions:

    • THEMATICS is an effective computational tool for identifying active sites in enzymes.
    • The method's ability to find recognition sites offers insights into enzyme specificity.
    • This approach can facilitate the design of targeted enzyme inhibitors.