Find a protein using PDB explorer, describe you protein including disease state or real world application it has.

* Find a protein using PDB explorer, describe you protein including disease state or real world application it has.

When looking to perform research on proteins, one finds that there are many entry level sites available for free on the web.  I have linked a couple of the sites below.  I have chosen to find and report HIV protease.  This is a key enzyme contributing to the overall virulence factor of HIV/AIDS.  I recently, March 4th do be exact presented a PowerPoint presentation.  The presentation happened to be on targeting proteins, more specifically enzymes in the treatment of HIV.  I have placed a link to the presentation below.  I hope that this presentation can answer the question of how a protein can related to a disease and more importantly, how can targeting that proteins function impact the virulence of the disease.   

Specifically, when the new virus buds off from the host cell, it achieves maturation
by HIV protease cleaving the longs budding strands into fragments of smaller size. These smaller fragments are the functional strands which are packaged into other viral components in order to create a new virus.
into smaller functional fragments by HIV proteases


PowerPoint presentation on HIV/AIDS, March 4th, 2010.

HIV/AIDS ENZYME TREATMENT

Protein Database Site:

MCSG Goverment Site

Additional Protein Site:

www.RCSB.org
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Protein of interest:

HIV Protease (Quaternary Structure)

HIV Protease

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HIV Protease from the RCSB site pasted below:

Fragment-Based Screen against HIV Protease
Perryman, A.P.,   Zhang, Q.,   Soutter, H.H.,   Rosenfeld, R.,   McRee, D.E.,   Olson, A.J.,   Elder, J.E.,   Stout, C.D.
(2010) Chem.Biol.Drug Des. 75: 257-268

  

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  Molecular Description

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  Classification:	Hydrolase
  Structure Weight:	23077.79

  Molecule:	Protease
  Polymer:	1	Type:	polypeptide(L)	Length:	99
  Chains:	A, B
  EC#:	3.4.23.16

  
  
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  Source

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  Polymer: 1
  Scientific Name:	Human immunodeficiency virus 1		Expression System:	Escherichia coli

   
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  Related PDB Entries

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  Id	Details
  2AZ8	HIV-1 PROTEASE NL4-3 IN COMPLEX WITH INHIBITOR, TL-3, WILD TYPE
  2AZ9	HIV-1 PROTEASE NL4-3 IN COMPLEX WITH INHIBITOR, TL-3, 1X MUTANT
  2AZB	HIV-1 PROTEASE NL4-3 IN COMPLEX WITH INHIBITOR, TL-3, 3X MUTANT
  2AZC	HIV-1 PROTEASE NL4-3 IN COMPLEX WITH INHIBITOR, TL-3, 6X MUTANT
  3KF1	HIV Protease (PR) dimer without inhibitor; acetate in exo site
  3KFN	HIV Protease (PR) with inhibitor TL-3 and fragment hit 4D9 by soaking
  3KFP	HIV Protease (PR) with inhibitor TL-3 bound, and DMSOs in exo site
  3KFR	HIV Protease (PR) dimer with inhibitor TL-3 bound and fragment 1F1 in the outside/top of flap
  3KFS	HIV Protease (PR) dimer with inhibitor TL-3 bound and fragment 2F4 in the outside/top of flap

  
  
  The above information is a sample of the type of information one can find while visiting a a protein database site.  The information can be kind of overwhelming, but this is the nature of current molecular research today.  It will probably only get more detailed from here, in the future.

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General Information about Protease inhibitors Pasted Below from Wikipedia:

Protease inhibitor (pharmacology)

From Wikipedia, the free encyclopedia:

Protease inhibitors (PIs) are a class of drugs used to treat or prevent infection by viruses, including HIV and Hepatitis C. PIs prevent viral replication by inhibiting the activity of HIV-1 protease, an enzyme used by the viruses to cleave nascent proteins for final assembly of new virons.
Protease inhibitors have been developed or are presently undergoing testing for treating various viruses:

• HIV/AIDS: antiretroviral protease inhibitors (saquinavir, ritonavir, indinavir, nelfinavir, amprenavir^[1] etc.)
• Hepatitis C: experimental agents: BILN 2061 (All clinical trials of BILN 2061 have been suspended due to cardiac issues), VX 950 (trade name Telaprevir), or SCH 503034^[2]

 Given the specificity of the target of these drugs there is the risk, as in antibiotics, of the development of drug-resistant mutated viruses. To reduce this risk it is common to use several different drugs together that are each aimed at different targets.

About Wikepedia and Pasting:

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When you paste from Wikipedia, please note that the information can be just plain wrong.  But it contains some much information that is both accessible and easy to use.  When you paste a paragraph, often the links paste with it, giving you the links back to the site.  This is self serving and can be a distraction to your site, due to the fact that you navigate away from your site, but it can be a great way of presenting NON-FACT CHECKED INFORMATION easily and without a ton of effort on your part.

ENJOY READING THE REMAINDER OF THE BLOG ENTRIES BELOW.

MCB
Signing Off :-)
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