Joseph Tilitsky: Joseph tilitsky/sandbox1 moved to Molecular Playground/DnaK

<applet load='2kho' size='400' color='white' frame='true' align='right' caption='The E. coli Hsp70, DnaK, in the ADP-bound form [[2kho]]'/>

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].

Molecular Playground banner: DnaK, a central hub in maintaining proteostasis in E. coli

<scene name='60/609794/Adp-dnak_1/4'>DnaK in the extended conformation</scene>

The E. coli Hsp70, DnaK, is a protein chaperone whose function is to bind exposed hydrohpobic residues of unfolded proteins. This binding event prevents aggregation and rescues the nascent chain from kinetic traps along the folding pathway. Hsp70 protein chaperones switch between an <scene name='60/609794/Atp-dnak/1'>ATP-bound</scene>, low-substrate affinity form and an <scene name='60/609794/Adp-dnak_1/4'>ADP-bound</scene>, high substrate affinity form during their allosteric cycle.[http://www.ncbi.nlm.nih.gov/pubmed/23123194?dopt=Abstract] [http://www.ncbi.nlm.nih.gov/pubmed/19439666?dopt=Abstract] Hsp70 protein chaperones are ubiquitously found in almost all known organisms and cell types and represent a potential target for anti-cancer and neurodegenerative therapies.[http://www.ncbi.nlm.nih.gov/pubmed/21403392]

===Structure===

DnaK is a 638 residue protein of approximately 70 kDa. The protein can be thought to be made up of two domains, the N-terminal nucleotide-binding domain (<scene name='60/609794/Nbd/4'>NBD</scene>) (residues 1-388), the C-terminal substrate-binding domain (<scene name='60/609794/Sbd/2'>SBD</scene>) (residues 393-638), which are divided by the <scene name='60/609794/Linker/1'>interdomain linker</scene> (residues 389-392, shown in purple). The NBD is further divided into four subdomains: <scene name='60/609794/Subdomain_ia/2'>IA</scene> (residues 1-37, 112-184, 363-383, shown in red), <scene name='60/609794/Subdomain_ib/2'>IB</scene> (residues 38-111, shown in green), <scene name='60/609794/Subdomain_iia/2'>IIA</scene> (residues 185-227, 310-362, shown in gold), and <scene name='60/609794/Subdomain_iib/2'>IIB</scene> (residues 228-309, shown in purple). The SBD of DnaK consists of a <scene name='60/609794/Beta_basket/1'>beta-basket</scene> (residues 393-507), an <scene name='60/609794/Helical_lid/1'>alpha-helical lid</scene> (residues 508-605), and a disordered C-terminal tail (not shown due to lack of available crystal structure).[http://www.ncbi.nlm.nih.gov/pubmed/22576356]

===Function===

DnaK binds stretches (7-8 residues in length) of exposed hydrophobic residues of its client proteins, in the beta-basket of the SBD, in order to prevent their aggregation.[http://www.ncbi.nlm.nih.gov/pubmed/14740253] Upon ATP binding, the NBD subdomains rotate relative to each other and induce a conformational change in the NBD (compare the <scene name='60/609794/Subdomain_iib/1'>ADP-bound</scene> NBD to the <scene name='60/609794/Nbd-atp/2'>ATP-bound</scene> form.[http://www.ncbi.nlm.nih.gov/pubmed/21482798] When ATP binds the NBD, the interdomain linker communicates the allosteric signal to the SBD that induces a conformational change in the SBD, causing the alpha-helical lid to dock onto the NBD. Compare the <scene name='60/609794/Sbd_open/2'>open</scene> form of the SBD (when the NBD binds ATP) and the <scene name='60/609794/Helical_lid/1'>closed</scene> form of the SBD (when the NBD binds ADP).[http://www.ncbi.nlm.nih.gov/pubmed/17434124?dopt=Abstract] The SBD has low substrate affinity in the 'open' conformation, but high substrate affinity in the 'closed' conformation.[http://www.ncbi.nlm.nih.gov/pubmed/24012426] Upon ATP hydrolysis, the NBD reverts to the ADP-bound state, undocking the alpha-helical lid from the NBD and regenerating the 'closed' conformation of the SBD. Alternating cycles of binding and release allow DnaK to unfold kinetically trapped intermediates and allow the client protein to refold to its native state.[http://www.ncbi.nlm.nih.gov/pubmed/20953191] Recently, a third 'allosterically active' state of DnaK has been discovered. In this state, the two domains remain undocked, with the SBD retaining high substrate affinity, but the interdomain linker is bound to the NBD. This state occurs when both ATP and substrate are bound simultaneously and has not yet been crystallized.[http://www.ncbi.nlm.nih.gov/pubmed/23217711]

===Drug Target===

Since Hsp70s are critically positioned in the proteostasis system of many organisms, including humans, they represent a tempting target for anti-cancer and neurodegenerative disease therapies. Recent efforts to develop a competitive inhibitor for Hsp70s, using DnaK as a model system, have met with only marginal success.[http://www.ncbi.nlm.nih.gov/pubmed/24312699] Recently, interactions between Hsp70s and its co-chaperones have been targeted for drug development, but with no leads currently in clinical trials.[http://www.ncbi.nlm.nih.gov/pubmed/22920901]

===3D structures of Hsp70===

Other Hsp70 entries on Proteopedia [http://proteopedia.org/wiki/index.php/Category:Hsp70]

===See Also===

The Wikipedia page on Hsp70 is useful for a general background.[http://en.wikipedia.org/wiki/Hsp70]

This informational video demonstrates the successful folding of a protein in E. coli:
https://www.youtube.com/watch?v=yQ3QUDj1Mv8

The Gierasch lab, in collaboration with the Powers lab at Scripps, has developed a computational model of the proteostasis network in E. coli called FoldEco.[http://www.ncbi.nlm.nih.gov/pubmed/22509487] A web version of FoldEco can be found here:
http://foldeco.scripps.edu

===References===

1. Kityk, R. et al. Mol Cell 2012

2. Bertelsen EB. et al. Proc Natl Acad Sci USA 2009

3. Broer L. et al. J Alzherimers Dis 2011

4. Zuiderweg ER. et al. Top Curr Chem 2013

5. Wegele H. et al. Rev Physiol Biochem Pharmacol 2004

6. Zhuravleva A. et al. Proc Natl Acad Sci USA 2011

7. Swain JF. et al. Mol Cell 2007

8. Mayer MP. Trends Biochem Sci 2013

9. Sharma SK. et al. Nat Chem Bio 2010

10. Zhuravleva A. et al. Cell 2012

11. Li X. et al. ACS Med Chem Lett 2013

12. Assimon VA. et al. Curr Pharm Des 2013

15. Powers ET. et al. Cell Rep 2012

2014-11-22T23:23:20Z

Joseph Tilitsky:

<applet load='5dfr' size='400' color='white' frame='true' align='right' caption='Dihydrofolate Reductase (DHFR) complex with Cl ions [[5dfr]]'/>

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].

Molecular Playground banner: DnaK, a central hub in maintaining proteostasis in E. coli

<scene name='60/609794/Adp-dnak_1/3'>DnaK in the extended conformation</scene>

The E. coli Hsp70, DnaK, is a crucial protein chaperone whose function is to reduce bind exposed hydrohpobic residues of unfolded proteins, which prevents aggregation and rescues the nascent chain from kinetic traps along the folding pathway. Hsp70 protein chaperones switch between an <scene name='60/609794/Atp-dnak/1'>ATP-bound</scene>, low-substrate affinity form and an <scene name='60/609794/Adp-dnak_1/3'>ADP-bound</scene>, high substrate affinity form during their allosteric cycle.[http://www.ncbi.nlm.nih.gov/pubmed/23123194?dopt=Abstract] [http://www.ncbi.nlm.nih.gov/pubmed/19439666?dopt=Abstract] Hsp70 protein chaperones are ubiquitously found in almost all known organisms and cell types and represent a potential target for anti-cancer and neurodegenerative therapies.[http://www.ncbi.nlm.nih.gov/pubmed/21403392]

===Structure===

DnaK is a 638 residue protein of approximately 70 kDa. The protein can be thought to be made up of two domains, the N-terminal nucleotide-binding domain (<scene name='60/609794/Nbd/4'>NBD</scene>) (residues 1-388), the C-terminal substrate-binding domain (<scene name='60/609794/Sbd/1'>SBD</scene>) (residues 393-638), which are divided by the <scene name='60/609794/Linker/1'>interdomain linker</scene> (residues 389-392, shown in purple). The NBD is further divided into four subdomains: <scene name='60/609794/Subdomain_ia/1'>IA</scene> (residues 1-37, 112-184, 363-383, shown in red), <scene name='60/609794/Subdomain_ib/1'>IB</scene> (residues 38-111, shown in green), <scene name='60/609794/Subdomain_iia/1'>IIA</scene> (residues 185-227, 310-362, shown in gold), and <scene name='60/609794/Subdomain_iib/1'>IIB</scene> (residues 228-309, shown in purple). The SBD of DnaK consists of a <scene name='60/609794/Beta_basket/1'>beta-basket</scene> (residues 393-507), an <scene name='60/609794/Helical_lid/1'>alpha-helical lid</scene> (residues 508-605), and a disordered C-terminal tail (not shown due to lack of available crystal structure).[http://www.ncbi.nlm.nih.gov/pubmed/22576356]

===Function===

DnaK binds stretches (7-8 residues in length) of exposed hydrophobic residues of its client proteins in order to prevent their aggregation.[http://www.ncbi.nlm.nih.gov/pubmed/14740253] Upon ATP binding, the NBD subdomains rotate relative to each other and induce a conformational change in the NBD (compare the <scene name='60/609794/Subdomain_iib/1'>ADP-bound</scene> NBD to the <scene name='60/609794/Nbd-atp/1'>ATP-bound</scene> form (shown with ATP bound). When ATP binds the NBD, the interdomain linker communicates the allosteric signal to the SBD that induces a conformational change in the SBD, causing the alpha-helical lid to dock onto the NBD. Compare the <scene name='60/609794/Sbd_open/2'>open</scene> form of the SBD (when the NBD binds ATP) and the <scene name='60/609794/Helical_lid/1'>closed</scene> form of the SBD (when the NBD binds ADP).[http://www.ncbi.nlm.nih.gov/pubmed/17434124?dopt=Abstract] The SBD has low substrate affinity in the 'open' conformation, but high substrate affinity in the 'closed' conformation.[http://www.ncbi.nlm.nih.gov/pubmed/24012426] Alternating cycles of binding and release allow DnaK to unfold kinetically trapped intermediates and allow the client protein to refold to its native state.[http://www.ncbi.nlm.nih.gov/pubmed/20953191] Recently, a third 'allosterically active' state of DnaK has been discovered. In this state, the two domains remain undocked, with the SBD retaining high substrate affinity, but the interdomain linker is bound to the NBD. This state occurs when both ATP and substrate are bound simultaneously and has not yet been crystallized.[http://www.ncbi.nlm.nih.gov/pubmed/23217711]

===Drug Target===

Since DnaK is critically positioned in the proteostasis system of many organisms, including humans, it represents a tempting target for anti-cancer and neurodegenerative disease therapies. Recent efforts to develop a competitive inhibitor for DnaK, and Hsp70s in general, have met with only marginal success.[http://www.ncbi.nlm.nih.gov/pubmed/24312699] Recently, interactions between Hsp70s and its co-chaperones have been targeted for drug development, but with no leads currently in clinical trials.[http://www.ncbi.nlm.nih.gov/pubmed/22920901]

===3D structures of Hsp70===

Other Hsp70 entries on Proteopedia [http://proteopedia.org/wiki/index.php/Category:Hsp70]

===See Also===

The Wikipedia page on Hsp70 is useful for a general background.[http://en.wikipedia.org/wiki/Hsp70]

This informational video demonstrates the successful folding of a protein in E. coli:
https://www.youtube.com/watch?v=yQ3QUDj1Mv8

The Gierasch lab, in collaboration with the Powers lab at Scripps, has developed a computational model of the proteostasis network in E. coli called FoldEco.[http://www.ncbi.nlm.nih.gov/pubmed/22509487] A web version of FoldEco can be found here:
http://foldeco.scripps.edu

===References===

1. Kityk, R. et al. Mol Cell 2012

2. Bertelsen EB. et al. Proc Natl Acad Sci USA 2009

3. Broer L. et al. J Alzherimers Dis 2011

4. Zuiderweg ER. et al. Top Curr Chem 2013

5. Wegele H. et al. Rev Physiol Biochem Pharmacol 2004

6. Swain JF. et al. Mol Cell 2007

7. Mayer MP. Trends Biochem Sci 2013

8. Sharma SK. et al. Nat Chem Bio 2010

9. Zhuravleva A. et al. Cell 2012

10. Li X. et al. ACS Med Chem Lett 2013

11. Assimon VA. et al. Curr Pharm Des 2013

14. Powers ET. et al. Cell Rep 2012