Logo Medical Science Monitor

Call: +1.631.470.9640
Mon - Fri 10:00 am - 02:00 pm EST

Contact Us

Logo Medical Science Monitor Logo Medical Science Monitor Logo Medical Science Monitor

07 August 2002

Structural criteria of biologically active RGD-sites for analysis of protein cellular function – a bioinformatics study

Ivan Y. Torshin

Med Sci Monit 2002; 8(8): BR301-312 :: ID: 13590

Abstract

Background: Cell adhesion involves interactions of integrins and extracellular proteins, often facilitated by the RGD motif. Only presence of the RGD in a sequence of a protein may be not sufficient for the biological activity (binding to an integrin) and additional biochemical and/or structural studies are essential.
Material/Methods: Structural criteria that would allow identification biologically active RGD-sites on the base of a spatial structure may assist analysis of function of a protein in the cell. For the first time, computational analysis of RGD-sites in a large non-redundant set of protein structures was done.
Results: Out of 3819 protein chains sequences of about 100 contained RGDs. Analysis of the structures of the RGD-’native’ proteins has allowed establishing main determinants of the biologically
active conformations of the RGD sites: surface accessibility of the whole RGD-sequence and the secondary structure. The criteria, applied to the remaining proteins of the set, identify 23 proteins (~25%) with potentially active RGD-sites. The results strongly suggest that RGD has
a high propensity for being involved in protein-protein interactions and this may explain occurrence of RGDs in intracellular proteins.
Results of the analysis suggest (in some cases, confirm) novel integrin-related activities for 7 membrane/extracellular proteins, as well as confirm RGD-facilitated cell attachment for 5 viral
proteins.
Conclusions: Only presence of RGD in a sequence is not sufficient to propose biological activity of this site. The results also suggest that the method can be used on large scale: for example, for identifying
potential integrin-interacting proteins in an animal genome.

Keywords: Amino Acid Sequence, Computational Biology, Disintegrins - chemistry, Integrins - metabolism, Models, Molecular, Molecular Sequence Data, Oligopeptides - chemistry, Oligopeptides - genetics, Protein Conformation, Proteins - chemistry, Proteins - genetics, Receptors, Immunologic - chemistry

Add Comment 0 Comments

497 4

Editorial

01 June 2023 : Editorial  

Editorial: Infectious Disease Surveillance Using Artificial Intelligence (AI) and its Role in Epidemic and Pandemic Preparedness

Dinah V. Parums
Science Editor, Medical Science Monitor, International Scientific Information, Inc., Melville, NY, USA

DOI: 10.12659/MSM.941209

Med Sci Monit 2023; 29:e941209

0:00

In Press

08 Jun 2023 : Clinical Research  

Risk Factors for New Vertebral Compression Fracture After Percutaneous Vertebral Augmentation: A Retrospect...

Med Sci Monit In Press; DOI: 10.12659/MSM.940134  

08 Jun 2023 : Clinical Research  

A Nomogram for Identifying HR+/Her2- Breast Cancer Patients with Positive Sentinel Lymph Nodes and Omitted ...

Med Sci Monit In Press; DOI: 10.12659/MSM.940124  

08 Jun 2023 : Clinical Research  

Burden of COVID-19 on Mental Health of Resident Doctors in Poland

Med Sci Monit In Press; DOI: 10.12659/MSM.940208  

08 Jun 2023 : Clinical Research  

Risk Prediction for Rapidly Progressive Interstitial Lung Disease in Anti-MDA5-Positive Dermatomyositis: Th...

Med Sci Monit In Press; DOI: 10.12659/MSM.940251  

Most Viewed Current Articles

13 Nov 2021 : Clinical Research  

Acceptance of COVID-19 Vaccination and Its Associated Factors Among Cancer Patients Attending the Oncology ...

DOI :10.12659/MSM.932788

Med Sci Monit 2021; 27:e932788

0:00

30 Dec 2021 : Clinical Research  

Retrospective Study of Outcomes and Hospitalization Rates of Patients in Italy with a Confirmed Diagnosis o...

DOI :10.12659/MSM.935379

Med Sci Monit 2021; 27:e935379

08 Mar 2022 : Review article  

A Review of the Potential Roles of Antioxidant and Anti-Inflammatory Pharmacological Approaches for the Man...

DOI :10.12659/MSM.936292

Med Sci Monit 2022; 28:e936292

01 Jan 2022 : Editorial  

Editorial: Current Status of Oral Antiviral Drug Treatments for SARS-CoV-2 Infection in Non-Hospitalized Pa...

DOI :10.12659/MSM.935952

Med Sci Monit 2022; 28:e935952

Your Privacy

We use cookies to ensure the functionality of our website, to personalize content and advertising, to provide social media features, and to analyze our traffic. If you allow us to do so, we also inform our social media, advertising and analysis partners about your use of our website, You can decise for yourself which categories you you want to deny or allow. Please note that based on your settings not all functionalities of the site are available. View our privacy policy.

Medical Science Monitor eISSN: 1643-3750
Medical Science Monitor eISSN: 1643-3750