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Comparative analysis of human matrix metalloproteinases: Emerging therapeutic targets in diseases.

Jaiswal A, Chhabra A, Malhotra U, Kohli S, Rani V - Bioinformation (2011)

Bottom Line: This initial screening can help to reduce time and cost of testing and experimentation in laboratory.Thus, a plausible grouping of disease responsive MMPs that might be considered as promising clinical targets may be done.This study can be used as a fundamental approach to characterize, analyze and screen large protein families for the identification of signature patterns.

View Article: PubMed Central - PubMed

Affiliation: Department of Biotechnology, Jaypee Institute of Information Technology, A-10, Sector-62, NOIDA- 201307, Uttar Pradesh, India.

ABSTRACT
The identification of specific target proteins for any diseased condition involves extensive characterization of the potentially involved proteins. Members of a protein family demonstrating comparable features may show certain unusual features when implicated in a pathological condition. Advancements in the field of computational biology and the use of various bioinformatics tools for analysis can aid researchers to comprehend their system of work in primary stages of research. This initial screening can help to reduce time and cost of testing and experimentation in laboratory. Human matrix metalloproteinase (MMP) family of endopeptidases is one such family of 23 members responsible for the remodeling of extracellular matrix (ECM) by degradation of the ECM proteins. Though their role has been implicated in various pathological conditions such as arthritis, atherosclerosis, cancer, liver fibrosis, cardio-vascular and neurodegenerative disorders, little is known about the specific involvement of members of the large MMP family in diseases. A comparative in silico characterization of the MMP protein family has been carried out to analyze their physico-chemical, secondary structural and functional properties. Based on the observed patterns of occurrence of atypical features, we hypothesize that cysteine rich and highly thermostable MMPs might be key players in diseased conditions. Thus, a plausible grouping of disease responsive MMPs that might be considered as promising clinical targets may be done. This study can be used as a fundamental approach to characterize, analyze and screen large protein families for the identification of signature patterns.

No MeSH data available.


Related in: MedlinePlus

Analysis of secondary structural features through SOPMA. Thecomputation of 23 human MMPs showed a pre-dominance of random coils,followed by α-helices, extended strands and β-turns in 20 MMPs, whileextended strands exceeded α-helices in MMP-9, 11 and 19. The figure showsan average plot of the data of all 23 human MMPs.
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Figure 4: Analysis of secondary structural features through SOPMA. Thecomputation of 23 human MMPs showed a pre-dominance of random coils,followed by α-helices, extended strands and β-turns in 20 MMPs, whileextended strands exceeded α-helices in MMP-9, 11 and 19. The figure showsan average plot of the data of all 23 human MMPs.

Mentions: Secondary structural analysis indicates a pre-dominance of random coils,followed by α-helices, extended strands and β-turns in 20 MMPs while theextended strands exceed α-helices in MMP-9, 11 and 19 (Figure 4) (see Table 4). This is useful to predict three dimensionalstructures of proteins and can help in approximation of some aspects of proteinfunction and their classification into families [15].


Comparative analysis of human matrix metalloproteinases: Emerging therapeutic targets in diseases.

Jaiswal A, Chhabra A, Malhotra U, Kohli S, Rani V - Bioinformation (2011)

Analysis of secondary structural features through SOPMA. Thecomputation of 23 human MMPs showed a pre-dominance of random coils,followed by α-helices, extended strands and β-turns in 20 MMPs, whileextended strands exceeded α-helices in MMP-9, 11 and 19. The figure showsan average plot of the data of all 23 human MMPs.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3064848&req=5

Figure 4: Analysis of secondary structural features through SOPMA. Thecomputation of 23 human MMPs showed a pre-dominance of random coils,followed by α-helices, extended strands and β-turns in 20 MMPs, whileextended strands exceeded α-helices in MMP-9, 11 and 19. The figure showsan average plot of the data of all 23 human MMPs.
Mentions: Secondary structural analysis indicates a pre-dominance of random coils,followed by α-helices, extended strands and β-turns in 20 MMPs while theextended strands exceed α-helices in MMP-9, 11 and 19 (Figure 4) (see Table 4). This is useful to predict three dimensionalstructures of proteins and can help in approximation of some aspects of proteinfunction and their classification into families [15].

Bottom Line: This initial screening can help to reduce time and cost of testing and experimentation in laboratory.Thus, a plausible grouping of disease responsive MMPs that might be considered as promising clinical targets may be done.This study can be used as a fundamental approach to characterize, analyze and screen large protein families for the identification of signature patterns.

View Article: PubMed Central - PubMed

Affiliation: Department of Biotechnology, Jaypee Institute of Information Technology, A-10, Sector-62, NOIDA- 201307, Uttar Pradesh, India.

ABSTRACT
The identification of specific target proteins for any diseased condition involves extensive characterization of the potentially involved proteins. Members of a protein family demonstrating comparable features may show certain unusual features when implicated in a pathological condition. Advancements in the field of computational biology and the use of various bioinformatics tools for analysis can aid researchers to comprehend their system of work in primary stages of research. This initial screening can help to reduce time and cost of testing and experimentation in laboratory. Human matrix metalloproteinase (MMP) family of endopeptidases is one such family of 23 members responsible for the remodeling of extracellular matrix (ECM) by degradation of the ECM proteins. Though their role has been implicated in various pathological conditions such as arthritis, atherosclerosis, cancer, liver fibrosis, cardio-vascular and neurodegenerative disorders, little is known about the specific involvement of members of the large MMP family in diseases. A comparative in silico characterization of the MMP protein family has been carried out to analyze their physico-chemical, secondary structural and functional properties. Based on the observed patterns of occurrence of atypical features, we hypothesize that cysteine rich and highly thermostable MMPs might be key players in diseased conditions. Thus, a plausible grouping of disease responsive MMPs that might be considered as promising clinical targets may be done. This study can be used as a fundamental approach to characterize, analyze and screen large protein families for the identification of signature patterns.

No MeSH data available.


Related in: MedlinePlus