Structural Biology Lab

Studying relation between structure of a biomolecule and its biological function!

 

Atta Ahmad (PhD)

N306 Howell Science Complex,                                                                                                                 ” We have a funded position for graduate student for 2017-18

Department of Biology, Mail Stop 551                                                                                                                             Please contact us for OPEN Positions”

East Carolina University,

Greenville, NC, 27858

Ph: 252-737-4777

Email: ahmada at ecu.edu

 

Research

           My lab is interested in studying protein structure, function and its relation to human diseases. For some time DNA  RNA  Proteins appeared to be the central dogma of life but due to Nobel prize winning work of Christian Anfinsen (1972) and theoreticians like Cyrus Levinthal (Levinthal’s paradox 1969) the importance of protein folding code came to light and central dogma thus extended to DNA  RNA  Polypeptides Functional Proteins. In other words, the forces or code responsible for maintaining protein in its proper 3D-structure and thus efficient function gained impetus in the last part of 20th century. The profound influence of this concept would soon be evident as mis-folded proteins (or toxic-folded) were found responsible for inclusion body problems in biotechnology projects and mis-fold triggered ordered protein aggregates “amyloid” were implicated in Prion, Alzheimer's and Parkinson's diseases. The amyloid has since been found involved in more than 50 human diseases. In addition, protein folding studies resulted in the discovery of a group of enzymes and proteins called “chaperones” that are responsible for helping maintain protein structure and function. We focus specifically on following areas:

 

(if you don’t see the picture please click here)

1) Protein structure and function: We have been investigating the folding landscape of various proteins using chemical and thermal agents. In the process we have identified new folding intermediates of proteins and have contributed to the concept of mis-folding leading to amyloid formation especially using insulin as a model protein. Our articles published in this area have been cited more than 700 times.

 

2) Metal toxicity: We have shown calcium induces amyloid type aggregation of peptides Aβ40, Aβ42. Our studies further support the known implication of calcium in Alzheimer's diseases through Aβ40 and Aβ42. Further, we have shown copper induces structural modifications in protein α-synuclein (implicated in Parkinson’s) again leading to its amyloid type aggregation. Both metal ions exhibit this property at their physiological concentration and therefore, these studies have immediate application in understanding the important aspects that could further aid in the chelation therapy proposed for Alzheimer’s and Parkinson's.

 

3) Hsp70 family Chaperone: Chaperones are groups of enzymes and proteins that help other proteins attain structure essential for their function of which Hsp70 is an important family. If a protein fails to fold Hsp70 tags it for degradation (CHIP/ubiquitin pathway) and thus control the rate of ‘under-regulation/over-regulation’ of proteins or “proteostasis.” It is not known how chaperones are hijacked into uncontrolled over production of protein in the case of cancer or are not invoked during the mis-folded accumulation of proteins inside the cells. Since these proteins have not been investigated in detail the interactions between themselves and with substrate proteins is also not well characterized. Our efforts, in addition to addressing to each of these, also extends to screening chemical libraries to discover efficient modulators of chaperone systems for their immediate application as therapeutics to human disease systems mentioned above.

 

Techniques: Biochemical, Biophysical, Molecular biology, (refer to our publication for details)

 

New Positions:

“We have a funded position for graduate student 2017-18” We are always looking for interested graduate and undergraduate students, please feel free to contact us.

 

 

Current Members

 

Lor Kong                    BS ECU, Biology

 

Teaching

 

BIOL 5870 -           Molecular Biology of the Gene

BIOL 6030/4650 -   Biology of Cancer

BIOL 4891/6244 -   Biochemistry Lab

BIOL 6504/6514 -  Research Problems in Biology

BIOL 7000 -          Dissertation/thesis

 

           

Previous members

David F Jahad              Master’s Student

Hamza Karimi             Research Associate

Christopher Lovick      Research student

Caleb Stratton                  Master’s Student

Paola Perez-May                      Undergraduate student

Aston C Fuller                         Undergraduate student

JoColl Burgess                 Undergraduate student

 

      

 

Publications    [pubmed list]

(* Indicates corresponding author; #ECU students; $ECU faculty)

 

At ECU:

21. Ahmad A*, Jahad DF#, Karimi H# (2018) A modified protocol for transformation step in the commercially available Agilent Quick change site-directed mutagenesis kit (communicated)

 

22. Zuiderweg ERP*, Taylor IR, Ahmad A, Nordhues BA, Bhullar A and Gestwicki JE* (2018) The disorderly conduct of Hsc70 and its interaction with the Alzheimer’s related Tau protein

J Biol Chem. 293(27):10796-10809

 

23. Ahmad A*, Farwell M$, Muzaffar M$. (2017) Identifying Molecular Chaperones As Therapeutic Targets For Cancer - A Mini Review. Biochemistry and Pharmacology (Los Angel) 6:224

 

24. Morozova K, Clement CC, Kaushik S, Stiller B, Arias E, Ahmad A, Rauch JN, Chatterjee V, Melis C, Scharf B, Gestwicki JE, Cuervo AM, Zuiderweg ER, Santambrogio L. (2016) Hsc-70 Structural and Biological Interaction with Phosphatidylserine in Endosomal Microautophagy. J Biol Chem. 291, 18096-106

 

25. Ahmad A*, Muzaffar M (2016) Molecular Chaperones and Co-chaperones as Therapeutic Targets for Cancer. J Mol Pharm Org Process Res. 4:e124 [doi: 10.4172/2329-9053.1000e124]

 

26. Ahmad A*, Stratton CM#, Scemama JL$, Muzaffar M$(2016) Effect of Ca2+ on Aß40 fibrillation is characteristically different. Int J Biol Macromol. 89, 297-304

 

27. Ahmad A*, Zuiderweg ERP DnaK/DnaJ complex in ATP state (in preparation)

28. Ahmad A* Understanding the process of Aβ40/Aβ42 aggregation (in preparation)

29. Ahmad A* Biophysical characterization of structural contribution of BSA towards its amyloid (in preparation)

 

Before ECU

1. Li X, Srinivasan S, Connarn J, Ahmad A, Young Z, Kabza A, Zuiderweg E, Sun D, Gestwicki JE. (2013) Analogs of the Allosteric Heat Shock Protein 70 (Hsp70) Inhibitor MKT-077 as Anti-Cancer Agents. ACS Med Chem Lett 4, 1042-47

 

2. Cesa LC, Patury S, Komiyama T, Ahmad A, Zuiderweg ER and Gestwicki JE. (2013) Inhibitors of Difficult Protein-Protein Interactions Identified by High-Throughput Screening of Multiprotein Complexes. ACS Chem 8, 1988-97

 

3. Zuiderweg ERP, Bertelsen EB, Rousaki A, Mayer MP, Gestwicki JE and Ahmad A (2013) Allostery in the Hsp70 chaperone proteins. Top Curr Chem 328, 99-153

 

4. Ahmad A*, Burns CS, Fink AL and Uversky VN (2012) Peculiarities of copper binding to a-synuclein. Journal of Biomol Struct Dyn 29, 825-842

 

5. Zuiderweg ERP and Ahmad A (2012) Evaluation of competing J domain: Hsp70 Complex Models in light of methods used. Proc Natl Acad Sci USA 109, E735

 

6. Ahmad A, Bhattacharya A, McDonald RA, Cordes M, Ellington B, Bertelsen EB and Zuiderweg ERP (2011) The Hsp70 chaperone/DnaJ co-chaperone complex employs an unusual dynamical interface. Proc Natl Acad Sci USA 108, 18966-18971

 

7. Muzaffar M and Ahmad A* (2011) The Mechanism of Enhanced Insulin Amyloid Fibril Formation by NaCl Is Better Explained by a Conformational Change Model. PLoS ONE 6(11): e27906

 

8. Ahmad A* (2010) DnaK/DnaJ/GrpE of Hsp70 system have differing effects on alpha-synuclein fibrillation involved in Parkinson's disease. Int J Biol Macromol. 46, 275-279.

 

9. Ahmad A*, Muzaffar M and Ingram VM (2009) Ca2+, within the physiological concentrations, selectively accelerates Aβ42 fibril formation and not Aβ40 in vitro. Biochim. Biophys. Acta. 1794, 1536-1547.

 

10. Munishkina LA, Ahmad A, Fink AL and Uversky VN (2008) Guiding protein aggregation by molecular crowding. Biochemistry 47, 8993-9006.

 

11. Hood EE, Love R, Lane J, Bray J, Clough R, Pappu K, Drees C, Hood KR, Yoon S, Ahmad A, Howard JA (2007) Subcellular targeting is a key condition for high-level accumulation of cellulase protein in transgenic maize seed. Plant Biotechnol J. 5, 709-19.

 

12. Hong DP, Ahmad A and Fink AL (2006) Fibrillation of human insulin A and B chain. Biochemistry 45, 9342-9353.

 

13. Ahmad A, Uversky VN, Hong D and Fink AL (2005) Early events in insulin monomer fibrillation J Biol. Chem. 280, 42669-42675.

 

14. Ahmad A, Millet IS, Doniach S, Uversky VN and Fink AL (2004) Stimulation of insulin fibrillation by urea-induced intermediates. J Biol. Chem. 279, 14999-13.

 

15. Ahmad A, Millet IS, Doniach S, Uversky VN and Fink AL (2003) Partially Folded Intermediates in Insulin Fibrillation. Biochemistry 42, 11404-11416.

 

16. Akhtar MS, Ahmad A, and Bhakuni V (2002) Guanidinium chloride and urea induced unfolding of dimeric enzyme glucose oxidase. Biochemistry 41, 3819-3827.

 

17. Akhtar MS, Ahmad A and Bhakuni V (2002) Divalent cation induced changes in structural properties of the dimeric enzyme glucose oxidase: Dual effect of dimer dissociation with loss of cooperative interactions in enzyme monomer. Biochemistry 41, 7142-7149.

 

18. Ahmad A, Akhtar MS and Bhakuni V (2001) Monovalent Cation Induced Conformational Change in Glucose Oxidase Leading to Stabilization of Enzyme. Biochemistry 40, 1945-1955.

 

19. Ahmad A, Madhusudanan KP and Bhakuni V (2000) Trichloroacetic Acid and Trifluoroacetic Acid Induced Unfolding of Cytochrome c: Stabilization of a Native like Folded Intermediate. Biochim. Biophys. Acta. 1480, 201-210.

 

20. Ali V, Prakash K, Kulkarni S, Ahmad A, Madhusudanan KP and Bhakuni V (1999) 8-Anilino-1-Napthalenesulfonic Acid Induces Folding of Acid Unfolded Cytochrome c to Molten Globule State as a Result of Electrostatic Interactions. Biochemistry 38, 13635-13642.

 

Funding

 

Role: PI

Grant/project –$60,000

Title: "Proposal for upgrading Biochemistry lab, HPLC system."

Agency: ITCS (Information Technology and computing services) ECU

Status: Awarded – 07/07/2018

 

Role: PI

Grant/project –$25,000

Title: "Proposal for upgrading Biochemistry lab, Multi-well plate reader."

Agency: ITCS (Information Technology and computing services) ECU

Status: Awarded – 01/12/2018

 

Role: Co-PI

Grant/project - $5000

Title: “Exploring PD-1, PD-L1 interactions with Hsp70 for mechanistic insight and drug target identification in triple negative breast cancer”

Agency: ECU graduate research program – Status: Awarded 8/7/2015 – 7/1/2016

 

Role: PI

Grant/project – $45,000

Title: "Utilizing Chaperones for intervention in cancer as therapeutic and biomarker targets."

Agency: Golfers Against Cancer, Greensboro, NC Chapter - Status: Awarded 5/1/2015 - 4/30/2016

 

 

Role: PI

Grant/project – F033032, $45,000

Title: "Examining role of chaperones in protein quality control and its relation with diabetes."

Agency: MDRC Michigan - Status: Awarded – 2/10/2013-11/30/2013

Funding

Links


01. [Uniprot]                                        02. [Peptide Cutter]                        03. [Peptide Finder]         

04. [Align sequences]                      05. [Zipper DB]                              06. [Protein Extinction MW calculator]

07. [Pubmed] [Google Scholar]                 08. [DNA to Protein]                        09. [PDB]

10. [BlackBoard]                                   11. [ECU Biology Dept