Seyedarabi, Arefeh
 Assistant Professor of Biochemistry and Structural Biology
 Tel: +98-21 66956974
 E-mail: a.seyedarabi@ut.ac.ir		       

 

                    
Research Interests
 
Research in this laboratory focuses on the structure and function of proteins in health and disease using the necessary techniques and tools including protein biochemical and biophysical characterisation, structural determination and bioinformatics analyses. The main structural technique used is X-ray crystallography to solve novel structures both in their Apo or Halo forms. The research areas in this laboratory mainly takes inspiration from nature and also the valuable knowledge of Traditional Iranian Medicine (TIM) or Persian Medicine which is geographically most accessible and readily at hand. Main research interests of the laboratory lies in the field of neurodegenerative diseases, hemoglobin biology and also drug design. The use of TIM recommended flower extracts and the available knowledge of their active constituents is used in research projects in the prevention of amyloid formation aimed at neurodegenerative diseases, in particular Alzheimer's  and Parkinson's diseases, with the aim to develop nasal drugs. Other research areas include the effect of different concentrations of ozone in autohemotherapy on blood proteins including haemoglobin and albumin, with the intention to emphasise on personalising the appropriate and safe concentration of ozone to be used on patients 
 

Personal Record            
                                
Name: Arefeh Seyedarabi                               
Appointment: Assistant Professor of Biochemistry and Structural Biology
Office Address: Institute of Biochemistry and Biophysics,  
University of Tehran P.O.Box 13145-1384 Tehran, Iran    
Telephone No.: +98-21 66956974 
Fax: 0098 21 66404680           
E-Mail: a.seyedarabi@ut.ac.ir
Web Site:www.ibb.ut.ac.ir/~seyedarabi
 
 
Education
 
March 2012-present: Assistant Professor of Biochemistry, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
Research area:
Structure-function studies of proteins involved in health and disease using various biochemical and biophysical techniques.
 
Jan 2011-2012: Senior Research Associate, Institute of Structural and Molecular Biology, University College London (Funded by British Heart Foundation) 
My second postdoctoral research associate position was with Dr Snezana Djordjevic working on the structural and functional analyses of neuropilin-1 and neuropilin-2 interactions with VEGF which involved thermodynamic and kinetics experiments, X-ray crystallography, cell-free and cell-based assays as well as in vivo studies.
 
May 2007- 2010: Postdoctoral Research Assistant, School of Biological and Chemical Sciences, Queen Mary University of London (in collaboration with University of Kent, UK  and Funded by BBSRC)
My postdoctoral research assistant position was with Professor Richard Pickersgill studying the substrate recognition and reaction mechanism of methyltransferases from the cobalamin (Vitamin B12) biosynthetic pathway (in collaboration with Professor Martin Warren, University of Kent). I was able to solve the structures of the following methyltransferases; CobF, CobM and CobL (C- terminal domain) in complex with S-adenosyl homocysteine (the demethylated form of the methyl donor S- adenosyl methionine). I have a first author publication (in Acta Cryst F) and will have more publications pending on the results obtained from this study.
 
Oct. 2003- 2007: PhD in Structure-function studies of proteins involved in infection, School of Biological and Chemical Sciences, Queen Mary University of London (in collaboration with University of Tokyo, Tokyo, Japan)
The focus of my study was on proteins belonging to the human pathogenic bacteria Listeria 
monocytogenes and in particular Shigella flexneri (in collaboration with Professor Chihiro Sasakawa, University of Tokyo) and also the plant pathogenic bacteria Bacillus subtilis. I solved the structure of the dimeric form of Shigella flexneri IpaH9.8 E3 ubiquitin ligase and showed for the first time that its human substrate is U2AF35. In the study of Bacillus subtilis, I solved a number of structures involving Michaelis complexes of pectate lyase bound to different polygalacturonates to unravel the reaction mechanism of the enzyme as well as carrying out ITC experiments to unravel the binding affinity and stoichiometry of hexagalacturonate and pectate lyase. I have first author publications in FEBS Letters and Biochemistry from the studies on Shigella flexneri IpaH9.8 and Bacillus subtilis pectate lyase, respectively.
 
Sept. 2000-June 2003: First Class Honours BSc degree in Genetics and Microbiology,School of Biological Sciences, Queen Mary University of London (obtained the Westfield Trust Prize for Outstanding Academic Achievement)

 
Laboratory/computer based Skills: 
 
  • Molecular Biology -all necessary skills to make constructs (including bicistronic constructs) and also site-directed mutagenesis. I have made many constructs to date using pGEM-T Easy, pET and pGex vectors. 
  • Protein biochemistry –covering protein over-production, purification, SDS-PAGE and native-PAGE analyses, affinity chromatography, ion exchange chromatography and gel filtration chromatography. I have experience in over-producing and purifying numerous difficult proteins by varying induction temperature, duration of induction and E. coli cell strains as well as investigating different buffer environments for proteins such as pH and salt concentration. I also have experience in over-producing soluble human protein in E. coli through gene sequence adaptation.
  • Protein characterisation (functional, biophysical and structural) -use of bioinformatic tools (e.g. from Expasy and EBI websites), limited proteolysis, pull-down assays, ubiquitination assays, western blot analysis, gel filtration, co-expression, circular dichroism (CD), dynamic light scattering (DLS), isothermal titration calorimetry (ITC), Surface Plasmon Resonanace (Biacore), crystallisation screening, and X-ray crystallography (at various synchrotron sources; previously at SRS and presently at Diamond, ESRF and BSRF). 
  • Structure determination- I have experience preparing and freezing crystals, taking crystals to synchrotron sources, collecting datasets, solving and analysing structures using programs such as iMosflm, CCP4 based programs, CNS, Phenix, Coot and PyMoL. I have on many occasions collected native datasets as well as Single wavelength Anomalous Dispersion (SAD) or Multi-wavelength Anomalous Dispersion (MAD) datasets from Selenium labeled proteins and heavy metal soaked crystals.
  • Bioinformatics analyses- use of necessary tools and software to analyse DNA/ protein sequences and protein structures, including those provided in Expasy, Ebi, NCBI webpages, as well as Phyre2, MEGA6, iToL, PhyoT, Chimera, LigPlot and PyMoL. 
 

  1. Zahra Moeini, Zahra Seraj, Toktam Zohoorian Abootorabi, Mohammadreza Ashrafi-Kooshk, Gholamhossein Riazi, Ali Akbar Saboury and Arefeh Seyedarabi*, ‘Unravelling the Novel Effects of Three Volatile Compounds in Preventing Fibril Formation of Disease Related Tau and α-Synuclein Proteins- Towards Identifying Candidate Aromatic Substances for Treating Neurodegenerative Diseases', Frontiers in Pharmacology, section ethnopharmacology, 13: 793727, 2022 https://doi.org/10.3389/fphar.2022.793727 (*Corresponding author)
  2. Fatemeh Toosi-Moghadam, Mehdi Khoobi, Ali Akbar Saboury, Zahra Allahdad, Anahita Khammari, Arefeh Seyedarabi, Leila Karami, Atiyeh Ghasemi, Luciano Saso, ‘Binding of α-lipoic acid to human serum albumin: spectroscopic and molecular modeling studies', Monatshefte für Chemie-Chemical Monthly, 152 (15): 1589-1602, 2021
  3. Fouad Mehraban, Saeed Rayati, Vahid Mirzaaghaei and Arefeh Seyedarabi*, 'Highlighting the importance of water alkalinity using phosphate buffer diluted with deionized, double distilled and tap water, in lowering oxidation effects on human hemoglobin, at high ozone concentrations analysed in vitro', Frontiers in Molecular Biosciences, section Molecular Diagnostics and Therapeutics, 7: 543960, 2020 (*Corresponding author)
  4. Zahra Seraj, Shahin Ahmadian, Matthew R. Groves and Arefeh Seyedarabi*, 'The aroma of TEMED as an activation and stabilizing signal for the antibacterial enzyme HEWL', PLoS ONE, 15(5): e0232953, 2020 https://doi.org/10.1371/journal.pone.0232953. (*Corresponding author)
  5. Zahra Seraj and Arefeh Seyedarabi*, 'The role of cinnamaldehyde and phenyl ethyl alcohol as two types of precipitants affecting protein hydration levels',  International Journal of Biological Macromolecules, 146, 705-715, 2020 (*Corresponding author)
  6. Zahra Seraj, Matthew R. Groves and Arefeh Seyedarabi*, 'Cinnamaldehyde and Phenyl Ethyl Alcohol promote the entrapment of intermediate species of HEWL, as revealed by structural, kinetics and thermal stability studies', Scientific Reports, 9: 18615, 2019 (*Corresponding author)
  7. Fouad Mehraban, Arefeh Seyedarabi*, Shahin Ahmadian, Vahid Mirzaaghaei and Ali Akbar Moosavi-Movahedi, 'Personalizing the safe, appropriate and effective concentration(s) of ozone for type II diabetic patients in autohemotherapy through blood hemoglobin analysis', Journal of translational medicine, 17 (1), 227, 2019 (*Corresponding author)
  8. Seyedarabi, A.*, Ariaeenejad, S., Moosavi-Movahedi, A.A., Rayati, S., Poursasan, N., Asiaie, N., Seraj, Z., Mehraban, F., Seyedarabi, S.E., 'Novel X-ray sequences and crystal structures of Persian and Starry sturgeon methemoglobins: Highlighting the role of heme pocket waters in causing autoxidation', Biochim Biophys Acta Proteins Proteom, 1867: 586-594, 2019 (*Corresponding author)
  9. Fatemeh Kazemi, Adeleh Divsalar, Ali Akbar Saboury, Arefeh Seyedarabi, 'Propolis nanoparticles prevent structural changes in human hemoglobin during glycation and fructation', Colloids and Surfaces B: Biointerfaces, 177; 188-195, 2019
  10. Z. Seraj and A. Seyedarabi*, 'The Importance of the Effect of Aroma or Smell in Human Health', Science Cultivation, 8 (1), 2018 (Article in Persian but abstract available in English) (*Corresponding author)
  11. F. Mehraban and A. Seyedarabi*, Z. Seraj, S. Ahmadian, N. Poursasan, S. Rayati, A. A. Moosavi-Movahedi, 'Molecular insights into the effect of ozone on human hemoglobin in autohemotherapy: Highlighting the importance of the presence of blood antioxidants during ozonation', International Journal of Biological Macromolecules, 119, 1276-1285, 2018 (*Corresponding author)
  12. Z. Seraj and A. Seyedarabi*, A. A. Saboury, M. Habibi-Rezaei, S. Ahmadian and A. Ghasemi, 'Unraveling the novel effects of aroma from small molecules in preventing hen egg white lysozyme amyloid fibril formation', PLOS ONE, https://doi.org/10.1371/journal.pone.0189754, 2018 (*Corresponding author)
  13. M. Fekri Noodeh, A. Divsalar, A. Seyedarabi, A. A. Saboury, 'Antiproliferative and interaction studies of a synthesized palladium(II) complex with human hemoglobin', Journal of Molecular Liquids, 249, 265-271, 2018
  14. F. Kashanian, M. Habibi-Rezaei, A.R. Bagherpour, A. Seyedarabi and A.A. Moosavi-Movahedi, 'Magnetic Nanoparticles as double-edged sword: Concentration-dependent ordering or disordering effects on lysozyme', Royal Society of Chemistry Advances, 7, 54813-54822, 2017
  15. Derakhshandeh H, Izadi Z, Lotfabadi A, Alaei L, Saboury AA, Dinarvand R, Divsalar A, Seyedarabi A, Barzegari E and Evini M, 'Colon cancer and specific ways to deliver drugs to the large intestine', Anti-cancer agents in medicinal chemistry, 17(10), 1317-1327, 2017
  16. Baharara J, Ramezani T, Divsalar A, Mousavi M and Seyedarabi A, 'Induction of apoptosis by green synthsesized gold nanoparticles through activation of caspase-3 and 9 in human cervical cancer cells', Avicenna J Med Biotechnol, 8 (2): 75-83, 2016
  17. Koohshekan B, Divsalar A, Saiedifar M, Saboury AA, Ghalandari B, Gholamian A and Seyedarabi A, 'Protective effects of aspirin on the function of bovine liver catalase: A spectroscopy and molecular docking study', Journal of Molecular Liquids, 218: 8-15, 2016
  18. Bohlooli M, Moosavi-Movahedi AA, Taghavi F, Saboury AA, Maghami P, Seyedarabi A, Moosavi Movahedi F, Ahmad F, Shockravi A, Habibi-Rezaei M, 'Inhibition of fluorescent advanced glycation end products (AGEs) of human serum albumin upon incubation with 3-ß-hydroxybutyrate', Mol Biol Rep, 41 (6): 3705-13, 2014
  19. Divsalar A, Razmi M, Saboury AA, Seyedarabi A, 'The design and characterisation of a novel beta-casein-vehicle loaded with platinum anticancer drug for drug delivery', Anticancer Agents Med Chem, 14 (6): 892-900, 2014
  20. Ahmadzade Kermani H, Shockravi A, Moosavi-Movahedi Z, Khalafi-Nezhad A, Behrouz S, Tsai Fu-Yuan, Hakimelahi G H, Seyedarabi A and Moosavi-Movahedi AA, 'A surfactant-heme-sulfonyl imidazole system as a nano-artificial enzyme', J IRAN CHEM SOC, 10: 961-968, 2013
  21. Arefeh Seyedarabi, Lili Cheng, Ian Zachary and Snezana Djordjevic, ‘Production of soluble human vascular endothelial growth factor VEGF-A165-heparin binding domain in Escherichia coli', PLOS ONE, 8 (2), e55690, 2013
  22. Azadeh Hekmat, Ali A. Saboury, Adeleh Divsalar, Arefeh Seyedarabi, ‘Structural effects of TiO2 nanoparticles and doxorubicin on DNA and their antiproliferative roles on T47D and MCF7 cells', Anti Cancer Agents in Medicinal Chemistry, 13 (6): 932-51, 2013
  23. Bohlooli M, Moosavi-Movahedi AA, Taghavi F, Habibi-Rezaei M, Seyedarabi A, Saboury AA, Ahmad F, 'Thermodynamics of molten globule state of human serum albumin by 3-ß-hydroxybutyrate as a ketone body', Int J Biol Macromol, 54: 258-63, 2013
  24. Evelyne Deery, Susanne Schroeder, Andrew D. Lawrence, Samantha L. Taylor, Arefeh Seyedarabi, Jitka Waterman, Keith S. Wilson, David Brown, Michael A. Geeves, Mark J. Howard, Richard W. Pickersgill and Martin J. Warren, 'An enzyme-trap approach allows isolation of intermediates in cobalamin biosynthesis', Nat Chem Biol, 8(11), 933-940, 2012
  25. Adeleh Divsalar, Ali A. Saboury, Zohre Zare, Mohammad E. Kefayati, Arefeh Seyedarabi, ‘Characterization and side effect analysis of a newly designed nanoemulsion targeting human serum albumin for drug delivery', Colloids and Surface B: Biointerfaces, 98, 80-84, 2012
  26. Adeleh Divsalar, Sajedeh E. Damavandi, Ali A. Saboury, Arefeh Seyedarabi and Ali A. Moosavi-Movahedi, ‘Calorimetric and Spectroscopic investigations .f ß-lactoglobulin upon interaction with copper ion', Journal of dairy research, 79, 209-215, 2012
  27. Arefeh Seyedarabi, A method for labeling polyacrylamide gels, Nature Protocol Exchange, doi:10.1038/protex.2011.222, published online 24 March 2011
  28. Arefeh Seyedarabi, Thomas Hutchison, Teng T. To, Evelyn Deery, Amanda Brindley, Martin J. Warren and Richard W. Pickersgill, 'Cloning, purification and preliminary crystallographic analysis of cobalamin methyltransferases from Rhodobacter capsulatus', Acta Cryst F, F66, 1652-1656, 2010
  29. Arefeh Seyedarabi*, James A. Sullivan, Chihiro Sasakawa and Richard W. Pickersgill*, ‘A disulfide driven domain swap switches off the activity of Shigella IpaH9.8 E3 ligase', FEBS letters, 584 (19), 4163-4168, 2010 (*Joint Corresponding author with my PhD supervisor)
  30. Arefeh Seyedarabi, ‘The orchestrators of Shigella flexneri infection', Crystallography Reviews, 16 (2), 145-165, 2010
  31. Arefeh Seyedarabi, Teng T. To, Salyha Ali, Syeed Hussain, Markus Fries, Robert Madsen, Mads H. Clausen, Susana Teixteira, Keith Brocklehurst and Richard W. Pickersgill, ‘Structural and thermodynamic insights into substrate specificity and the anti ß-elimination mechanism of pectate lyase', Biochemistry, 49 (3), 539-546, 2010
  32. Dana Heldt, Stefanie Frank, Arefeh Seyedarabi, Dimitrios Ladakis, Joshua B. Parsons, Martin J. Warren, Richard W. Pickersgill, ‘Structure of a trimeric bacterial microcompartment shell protein, EtuB, associated with ethanol utilisation in Clostridium kluyveri', Biochemical Journal, 423, 199-207, 2009
  33. Amy Ooi, Syeed Hussain, Arefeh Seyedarabi, and Richard W. Pickersgill, ‘Structure of internalin C from Listeria monocytogenes', Acta Cryst D, D62, 1287-1293, 2006
  34. Jun Okuda, Takahito Toyotome, Naoyuki Kataoka, Mutsuhito Ohno, Hiroyuki Abe, Yoshiro Shimura, Arefeh Seyedarabi, Richard W. Pickersgill, Chihiro Sasakawa, ‘Shigella effector IpaH9.8 binds to a splicing factor U2AF35 to modulate host immune responses', Biochemical and Biophysical Research Communications, 333, 531-539, 2005
 
 
 

 
Posters

 

  • Naji, A. Seyedarabi, A. A. Saboury, A. A. Meratan, 'Novel characteristaion and crystallisation studies on the role of phenyl etheyl alcohol in preventing protein aggregation', 9th User meeting of the Iranian Light Source Facility, May 2017, Qazvin, Iran
  • Naji, A. Seyedarabi, A. A. Saboury, A. A. Meratan, 'The effect of Rosa damascene on lysozyme aggregation as a model system for neurodegenerative diseases', 14th Iranian Biophysical Chemistry Conference, 2016, Zabol, Iran
  • Seyedarabi, T. Hutchinson, M. J. Warren and R. W. Pickersgill, ‘The Methyltransferases of cobalamin (vitamin B12) biosynthesis', poster presented at the Young Crystallographers Satellite meeting and the main British Crystallographic Association Spring meeting, April 2009, Loughborough University (was awarded the David Blow poster prize)
  • Seyedarabi and R. W. Pickersgill, ‘Pectate lyase, a key enzyme in phytopathogenesis', poster presented at the Biological Structures group Winter meeting on ‘Structural Biology of Pathogens', 18th December 2006, University of Birmingham
  • Seyedarabi, S. Hussain, M, Fries, K. Brocklehurst and R. W. Pickersgill, ‘Mechanism of Bacillus subtilis pectate lyase', poster presented at the Biological Structures Group Winter meeting on ‘Structural enzymology', 19th December 2005, University of Bristol
  • Seyedarabi, Chihiro Sasakawa and R.W. Pickersgill, ‘Protein-protein interaction essential for Shigella flexneri infection', poster presentation, 12th-14th April 2005, Loughborough University
  • Seyedarabi and R.W. Pickersgill, ‘Characterisation of protein-protein interactions in Shigella infection: IpaH9.8 interferes with U2AF35-dependent pre-mRNA splicing', poster presented at 2nd year PhD Poster presentation session, February 2005, Queen Mary University of London
 
Talks (selected)
  • ‘Macromolecular X-ray crystallography to solve important biological problems', 25th March 2021, International virtual symposium on the importance of biophysics in solving biological problems, Biophysics week, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
  • ‘Simple ideas turned into scientific importance', 5th March 2020, Diamond Light Source Seminar Series, Diamond Light Source, Oxfordshire, UK
  • 'Structural and functional insights into HEWL fibrillation hotspots using small molecules in their aroma form', 2nd international and 4th National IASBS Symposium in Biological Sciences on Structural biology and molecular basis of diseases, January  2019, Zanjan, Iran
  • 'DRUG DESIGN IN IRAN- The need for Structural Biology Techniques', 10th Users Meeting of the Iranian Light Source Facility, May 2018, Qazvin, Iran
  • ' Macromolecular Crystallography projects in Iran: the first two structures deposited in the protein data bank', 9th User meeting of the Iranian Light Source Facility, May 2017, Qazvin, Iran
  • 'Fundamentals of cryopreservation in protein crystallography', Symposium on Cryobiology, Royan Institute, August 2016, Tehran, Iran (talk presented by PhD student Mr Fouad Mehraban)
  • 'Towards a bright future for Macromolecular Crystallography in Iran, 8th User meeting of the Iranian Light Source Facility, April 2016, Qazvin, Iran
  • 'Diabetes and Vitamin B12 deficiency- a vital human dietary biomolecule with interesting complexities', Symposium on Diabetes and biomolecular Science, November 2015, Institute of Biochemistry and Biophysics, University of Tehran, Iran
  • 'Crystal structure determination of hemoglobin from two sturgeon species of fish, Acipenser persicus and Acipenser stellatus', 13th Conference on Biological Chemistry (CBC), 2015, Ardabil, Iran
  • ‘Structure-function studies of three types of enzymes involved in disease; a pectate lyase, an E3 ubiquitin ligase and three methyltransferases', International Conference on Biophysical Chemistry (ICBC), May 2012, Ardabil, Iran
  • ‘Structural, Functional and Thermodynamic Analyses of Neuropilin-VEGF Heparin Interactions', Institute of Structural & Molecular Biology Retreat meeting, June 2011, Robinson College, Cambridge, UK
  • ‘Vitamin B12 and the seven methyltransferase domains', Tetrapyrrole Discussion Group meeting, 8th April 2010, Royal College of Pathologists, London, UK
  • ‘Structural and functional studies of IpaH9.8 from Shigella flexneri', Winter Biological Structures Group Meeting, December 2009, Royal Free Hospital, London, UK
  • ‘Domain swapping in S. flexneri IpaH9.8', Young Crystallographers Satellite meeting, April 2009, Loughborough University, Loughborough, UK
  • ‘Structural studies of the methyltransferases involved in cobalamin (vitamin B12) biosynthesis', Tetrapyrrole Discussion Group meeting, 1st April 2008, The Novartis Foundation, London, UK
  • ‘Pectate lyase- structural and thermodynamic studies', 18th December 2007, Collaborative meeting on the bacterial Type II secretion system, Lyon, France
  • ‘A recipe for binding and catalysis by pectate lyase', 16th April 2007, The Young Crystallographers Satellite meeting, University of Kent, Canterbury, UK
  • ‘Structural studies of proteins involved in bacterial diseases', July 2004, Collaborative meeting and presentation at the University of Tokyo, Japan
  • ‘Structural studies of proteins from pathogenic bacteria', Summer 2004, short presentation at Bristol Protein Crystallography Summer School, Bristol, UK

 
Professional memberships:
  • Advisor for International Affairs of University of Tehran, representative for the Institute of Biochemistry and Biophysics from 2019-2021
  • Ordinary member of the Iran Society of Biophysical Chemistry (ISOBC) from 2012-present
  • Ordinary member of the British Crystallographic Association (BCA) from 2002-2010
  • Committee member of the Young Crystallographers Group (YCG) representing the Biological Structural Group (2007-2009); I have also chaired a session at the Young Crystallographers satellite meeting, 2009, Loughborough University and represented YCG at numerous BCA Biological Structural Group committee meetings
  • Ordinary member of the Tetrapyrrole Discussion Group (TPDG) from 2007-2010
 

Courses/workshops/training seminars attended:

  • ‘How to write successful grants' and ‘Opportunities in Interdisciplinary research' workshops, 2009, Educational and Staff Development, QMUL
  • Fellowship Days, 2008 and 2009, Educational and Staff Development, QMUL
  • BBSRC New generation conference and workshop, 2008, Newcastle
  • ‘Introduction to Leadership and Managing Teams' workshops by Dr Fiona Stephen, September 2008, Educational and Staff Development, QMUL
  • Business Plan Competition workshop, 2007, Educational and Staff Development, QMUL
  • Intellectual property workshop, December 2007, QMUL
  • ‘Protein characterisation seminar', 31st January 2006, Diamond House, Oxfordshire
  • CCP4 study weekend, 6th-7th January 2006, ‘Crystallography of complexes', University of Leeds
  • CCP4 study weekend, January 2005, ‘Data Collection and Analysis', Reading University
  • Bristol Protein Crystallography Summer School, 2004, Bristol

 

 
 
 
 

 
Honors and awards
  • Award for outstanding talk on 'Crystal structure determination of hemoglobin from two sturgeon species of fish, Acipenser persicus and Acipenser stellatus', 13th Conference on Biological Chemistry (CBC), 2015, Ardabil, Iran
  • Certificate on ‘Biacore Basic Training', July 2011, GE Healthcare
  • Certificate on ‘Introduction to Leadership and Managing Teams', July 2009, Institute of Leadership and Management (course organized by Educational and Staff development, Queen Mary University of London)
  • David Blow poster prize for poster entitled ‘The Methyltransferases of cobalamin (vitamin B12) biosynthesis', British Crystallographic Association Spring meeting, April 2009, Loughborough University
  • Bursary to attend the BBSRC New Generation conference, 2008, Newcastle
  • Runner up in ‘pitch your idea' Business plan competition for the idea of an innovative compact gel documentation system. Received £500 Prize and certificate for my Business plan idea and pitch which was conducted in Dragon's Den style, 2007, Educational and Staff development, Queen Mary University of London. Following this success I now have an invention which I intend to have a patent filed for in the near future
  • Arnold Beevers Bursary to attend the British Crystallographic Association Spring meeting, 2005, Loughborough University
  • Bursary to attend the Bristol Protein Crystallography Summer School, 2004, Bristol
  • Westfield Trust prize for Outstanding Academic Achievement, 2003, Queen Mary University of London

Completed MSc/ PhD student supervision and theses titles:
 
MSc students:
 
* Miss Arefeh Naji
Thesis Title: Investigating the effect of Phenylethyl alcohol and Cinnamaldehyde on lysozyme
aggregation
 
* Mrs Hosna Hoseini
Thesis Title: Optimization of engineering parameters of artificial blood production based on
glutaraldehyde and hemoglobin systems
 
* Miss Zahra Moeeni
Thesis title: Molecular studies on the effects of Cinnamaldehyde, Phenylethyl alcohol and
Tetramethylethylenediamine (in their aroma form) on tau protein aggregation
 
* Miss Maedeh Mahlooji 
Thesis title: Studying the effects of Cinnamaldehyde and Phenylethyl alcohol on Changing the Blood
pH and Structure of Hemoglobin in Whole Blood Samples Ozonated at High Concentrations
 
* Miss Afsaneh Roshanfekr
Thesis title: Experimental and bioinformatic analyses of the antioxidant effects of volatile and
aromatic extracts (Cinnamaldehyde and phenyl ethyl alcohol) in aroma and in solution and common
spices (Cinnamon, Rose, Saffron and Cardamom) in aroma form on SKCGS peptide of Tau protein
 
* Mr Masoud Rasulian
Thesis title: Investigating the anti-fibrillation effects of aroma from cinnamon, saffron and rose
flower on tau protein, in comparison to HEWL as a model protein 
 
* Mr Ramin Naderi
Thesis title: Investigating the effect of different concentrations of ozone in heme oxidation and
hemoglobin oligomerisation using molecular tools and analysing available structures with signs n
 
PhD students:
 
* Mr Fouad Mehraban
Thesis Title: Molecular studies on the effect of ozone and its safety in autohemotherapy (ozone
therapy) on human hemoglobin
 
* Miss Zahra Seraj
Thesis Title: Investigating the anti-amyloidogenic effects of small aromatic or linear molecules,
in the aroma form, on the structure and function of lysozyme as a model protein
 
Students currently working on their projects in the lab:
 
MSc students:
* Miss Zahra Hassaninejad
* Mr Youness Feizollah Shooshtari
 
PhD students:
* Mrs Afrooz Anbaraki
* Miss Zahra Dindar
* Miss Mahzad Irandoust
 
Student "research placements":
 
Miss Zahra Seraj:
* Two months Sesame fellowship at the XALOC beamline in ALBA synchrotron, Spain
* Six months student placement in drug design lab of Mathew Groves at Groningen University,
Holland
 
Courses: 
 
1. Structure and Function of Proteins (compulsory course for MSc level students)
 
Course Objectives:
 Promotion of student's knowledge in the field of structure and function of proteins, and its relation to the organism's functions. 
 
Course contents:
 • Chemical properties, isomerism, CORN law and polarity of amino acids as the basic units determining the structure and function of proteins
 • The study of protein structure (from primary to quaternary structures), types of bonds and chemical connections between amino acids, post-translational modifications including glycosylation, ubiquitination, citrullination and the techniques required to investigate and determine the structure of proteins including CD, NMR, X-ray Crystallography and Cryo-EM
 • The structure and function of various proteins including fibrous proteins, enzymes, antibodies, transporter proteins, membrane proteins, regulatory proteins and motor proteins
 • The mechanisms of protein folding including Levinthal's Paradox, different models of protein folding and the importance of chaperones 
• Structural motifs and common folds in the structure of proteins including beta hairpin loop motif, Psi-loop motif, greek key motif, beta-meander motif, Rossman fold, hemoglobin fold and the immunoglobin fold
 • Effects of protein misfolding causing diseases such as Alzheimer's disease 
• Protein over-production and purification methods for structural and functional studies using recombinant technology 
• The importance of over-production and purification of recombinant proteins in industry and health care 
• The protein data bank and the use of analytical methods for structural analysis 
• Databases and software used to check and analyse the sequence, structure and function of proteins (e.g. Expasy, NCBI, EBI and UniProt)
 • A look at the structure and function of proteins in human diseases through the bacterium Shigella flexneri (for example) 
• A look at the structure and function of proteins in human diseases through the bacterium Listeria monocytogenes (for example) 
• A look at the structure and function of proteins in plant pests through the bacterium Bacillus subtilis (for example)
 • A look at the structure and function of proteins in the biosynthesis of vitamin B12 
• A look at the structure and function of proteins involved in angiogenesis and neurogenesis 
 
References: 
1. Amit Kessel and Nir Ben-Tal, Introduction to Proteins: Structure, Function, and Motion, Second Edition, Chapman and Hall/CRC Publishers, 2018. 
2. Arthur M. Lesk, Introduction to Protein Science, architecture, function and genomics, Oxford University Press, 2012. 
3. Engelbert Buxbaum, Fundamental of Protein Structure and Function, Wiley, 2007. 4. David Whitford, Protein Structure and Function, Wiley, 2005. 
 
2. Introductory Macromolecular X-ray Crystallography (Basic level; optional course for MSc/PhD level students) 
 
Course Objectives: 
An introductory course on the macromolecular X-ray crystallography technique and the steps required to obtain a three-dimensional protein structure from the start, that is, the expression and purification of proteins, to the end, i.e. the deposition of a protein structure into the Protein Data Bank.
 
Course contents: 
• An introduction to macromolecular X-ray crystallography
• Expression and purification of proteins for crystallography
• Protein crystallisation
• Crystal preparation for crystallography 
• Sources and detectors for data collection 
• Diffraction, symmetry and space group 
• Bragg's law and the reciprocal space 
• Data collection and processing
• Understanding the Ewald Sphere 
• Introduction to phasing and the Phase problem 
• Understanding the Fourier Transform 
• Necessary software for data analysis and structure determination: Mosflm, Scala , Molrep or PHASER,  Refmac5 and Coot 
• Validation and structure deposition in the Protein Data Bank
 
References: 
1. Outline of Crystallography for biologists, David Blow Oxford University Press, First published 2002, reprinted 2009. 
2. Crystallography made crystal clear (Third Edition), Gale Rhodes Academic Press, 2006 
3. Andreas Forster and Clemens Schulze-Briese, A shared vision for macromolecular crystallography over the next five years, Struct. Dyn. 6, 064302, 2019; https://doi.org/10.1063/1.5131017 
 
3. Advanced Macromolecular X-ray Crystallography (Advanced level; optional course for MSc/PhD level students)  
 
Course Objectives:
After being familiarised with the macromolecular X-ray crystallography technique in the "Introductory Macromolecular X-ray Crystallography" course, the "Advanced Macromolecular X-ray Crystallography" course deals with more details about the necessary programs used to collect, process, analyse and finalise the experimental data to solve a given protein structure and deposit it in the protein data bank. This course sets out the necessary details for someone who wants to apply the macromolecular X-ray crystallography technique and determine a protein structure.
 
Course contents: 
• A reminder on the 'Introductory Macromolecular X-ray crystallography' course
• X-ray diffraction from protein crystals and the use of Mosflm/iMosflm programs 
• Evaluation of data quality and information given using Scala, pointless, Matthews coefficient and Aimless programs 
• Introduction to routine programs including SAD, MAD and MR, which are used to gain phase information and solve protein structures 
• An example of a structure solved with MR using Molrep or Phaser programs 
• Electron density map analysis and validation using the Coot program 
• The use of the JLigand program to build the required ligands • Refinement of data using the Refmac program from CCP4
• Validation of the final model using the Ramachandran plot in Coot 
• Deposition of the final structure in the Protein Data Bank 
• Assessing and visualising the final structure using Pymol, Chimera and CCP4MG programs 
 
References: 
1. Outline of Crystallography for biologists, David Blow Oxford University Press, First published 2002, reprinted 2009. 
2. Crystallography made crystal clear (Third Edition), Gale Rhodes Academic Press, 2006. 
3. Ivan G. Shabalin, Przemyslaw J. Porebski and Wladek Minor, Refining the macromolecular model – achieving the best agreement with the data from X-ray diffraction experiment, Crystallography Reviews, Volume 24(4), 2018; https://doi.org/10.1080/0889311X.2018.1521805