Institute for Advanced Studies in Basic Sciences (IASBS)

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Department of Biological Sciences
Hamid Hadi-Alijanvand  
Assistant Professor
Room: Building
Tel: 33153316
Personal Homepage

Teaching Experiences:
  1. Computational Biophysics
  2. Bioinformatics
  3. Biophysical Chemistry
  4. Advanced Molecular Biology (Structural Approach)


Research area:
  1. Computational Biophysics
  2. Protein Folding
  3. Computer-Aided Drug Design

1- Hadi-Alijanvand, H., Proctor, E. A., Ding, F., Dokholyan, N. V., Moosavi-Movahedi, A. A., "A hidden aggregation-prone structure in the heart of hypoxia inducible factor prolyl hydroxylase", Proteins: Structure, Function, and Bioinformatics, 84: (5), 611-623, (2016).

Prolyl hydroxylase domain-containing protein 2 (PHD2), as one of the most important regulators of angiogenesis and metastasis of cancer cells, is a promising target for cancer therapy drug design. Progressive studies imply that abnormality in PHD2 function may be due to misfolding. Therefore, study of the PHD2 unfolding pathway paves the way for a better understanding of the influence of PHD2 mutations and cancer cell metabolites on the protein folding pathway. We study the unfolding of the PHD2 catalytic domain using differential scanning calorimetry (DSC), fluorescence spectroscopy, and discrete molecular dynamics simulations (DMD). Using computational and experimental techniques, we find that PHD2 undergoes four transitions along the thermal unfolding pathway. To illustrate PHD2 unfolding events in atomic detail, we utilize DMD simulations. Analysis of computational results indicates an intermediate species in the PHD2 unfolding pathway that may enhance aggregation propensity, explaining mutation-independent PHD2 malfunction.
2- Hadi-Alijanvand, H., Rouhani, M., "Journey of Poly-Nucleotides through OmpF Porin", J. Phys. Chem. B, 119, 6113-6128, (2015).

OmpF is an abundant porin in many bacteria which attracts attention as a promising biological nanopore for DNA sequencing. We study the interactions of OmpF with pentameric poly-nucleotides (poly-Ns) in silico. The poly-N molecule is forced to translocate through the lumen of OmpF. Subsequently, the structural and dynamical effects of translocation steps on protein and poly-N molecules are explored in detail. The external loops of OmpF are introduced as the main region for discrimination of poly-Ns based on their organic bases. Structural network analyses of OmpF in the presence or absence of poly-Ns characterize special residues in the structural network of porin. These residues pave the way for engineering OmpF protein. The poly-N-specific pattern of OmpF's local conductance is detected in the current study. Computing the potential of mean force for translocation steps, we define the energetic barrier ahead of poly-N to move through OmpF's lumen. We suggest that fast translocation of the examined poly-N molecules through OmpF seems unattainable by small external driving forces. Our computational results suggest some abilities for OmpF porin like OmpF's potential for being used in poly-N sequencing.
3- Moosavi-Movahedi, Z., Gharibi, H., Hadi-Alijanvand, H., Akbarzadeh, M., Esmaili, M., Atri, M. S., Sefidbakht, Y., Bohlooli, M., Nazari, K.,Javadian, S., Hong, J., Saboury, A .A., Sheibani, N., Moosavi-Movah., "Caseoperoxidase, mixed β-casein-SDS-hemin-imidazole complex: a nano artificial enzyme", J. Biomol. Struct. Dyn, 1-14, (2015).

A novel peroxidase-like artificial enzyme, named "caseoperoxidase", was biomimetically designed using a nano artificial amino acid apo-protein hydrophobic pocket. This four-component nano artificial enzyme containing heme-imidazole-β-casein-SDS exhibited high activity growth and kcat performance toward the native horseradish peroxidase demonstrated by the steady state kinetics using UV-vis spectrophotometry. The hydrophobicity and secondary structure of the caseoperoxidase were studied by ANS fluorescence and circular dichroism spectroscopy. Camel β-casein (Cβ-casein) was selected as an appropriate apo-protein for the heme active site because of its innate flexibility and exalted hydrophobicity. This selection was confirmed by homology modeling method. Heme docking into the newly obtained Cβ-casein structure indicated one heme was mainly incorporated with Cβ-casein. The presence of a main electrostatic site for the active site in the Cβ-casein was also confirmed by experimental methods through Wyman binding potential and isothermal titration calorimetry. The existence of Cβ-casein protein in this biocatalyst lowered the suicide inactivation and provided a suitable protective role for the heme active-site. Additional experiments confirmed the retention of caseoperoxidase structure and function as an artificial enzyme.
4- Naderi, M., Moosavi-Movahedi, A. A., Hosseinkhani, S., Nazari, Mahboobeh ., Bohlooli, M., Hong, J., Hadi-Alijanvand, H., Sheibani, N., "Implication of disulfide bridge induced thermal reversibility, structural and functional stability for luciferase", Protein Pept. Lett, 22: (1), 23-30, (2015).

Firefly luciferase is a relatively unstable protein and commonly loses its activity at room temperature because of structural changes. The structural and functional stability of this protein is critical for its enzymatic applications. Different approaches are applied to increase the stability of this enzyme such as designing of covalent cross-links (disulfide bonds). In this study, luciferase mutants containing one or two disulfide bonds were compared to the native protein for their for their structural, thermodynamic, and functional properties. Mutant forms of P. Pyralis luciferase A²⁹⁶C-A³²⁶C and A²⁹⁶C-A³²⁶C/P⁴⁵¹C-V⁴⁶⁹C were used. Thermodynamic and biophysical studies were carried out using UV-Vis, fluorescence, circular dichroism, luminescence spectroscopy and differential scanning calorimetry (DSC). We observed that both mutant forms of the protein were more stable than the wild-type enzyme. However, the single disulfide bond containing mutant was structurally and functionally more stable than the mutant protein containing two disulfide bonds. Furthermore, the enzymatic activity of the single disulfide bond containing mutant protein was 7-folds greater than the wild type and the double disulfide bond proteins. The A²⁹⁶C-A³²⁶C mutation also increased the reversibility and disaggregation of the protein. The enhanced activity of the single disulfide bond mutant protein was contributed to the expansion of its active site cleft, which was confirmed by bioinformatics tools.
5- Hadi-Alijanvand, S., Mobasheri, H., Hadi-Alijanvand, H., "Application of OmpF nanochannel forming protein in polynucleotide sequence recognition", J. Mol. Recognit, 27: (10), 575-587, (2014).

Recognition of the sequence of human genome sequence is vital to address malfunctions occurring at molecular, cellular and tissue levels and requires a great deal of time, cost and efforts. Thus, various synthetic and natural pores were considered to fabricate high-throughput systems capable to fulfill the task in an efficient manner. Here, voltage gating OmpF nanochannel, whose structure is known at an atomic level, was used to recognize and differentiate between polynucleotide primers through voltage clamp technique. Our results showed that poly(T) occasionally blocked the channel at both polarities, while poly(C) and poly(G) obstructed it only at positive polarity. The channel was blocked at potential differences of as low as 80 mV in the presence of poly(T). The conductance of channel decreased in the presence of poly(C) and poly(G) by 61 and 5% respectively. Analysis of the number of events showed that poly(T) caused more closing events at higher voltages, while poly(G) and poly(C) induced it at lower voltages. Application of the hazard function as a statistical parameter and analysis of event closing times in various voltages demonstrated the most efficient differentiation at 60 mV. The results of practical and theoretical approaches presented here show that OmpF porin channel possesses the structural and dynamic characteristics required to be considered as a biosensor capable for continuous polynucleotide sequencing.
1- Alijanianzadeh, M., Saboury, A. A., Ganjali, M. R., Hadi-Alijanvand, H., "Computational and experimental study of tyrosinase inhibition by a new synthesized ligand", Annual Meeting of the German Biophysical Society, University Göttingen, Germany, (2012).
2- Moosavi-Movahedi, Z., Hadi-Alijanvand, H., Gharibi, H., Esmaili, M., Nazari, M., Javadian, S., Moosavi-Movahedi, A. A., "Caseoperoxidase: Novel Peroxidase-Like Nano-Artificial Enzyme", First International Conference on Biophysical Chemistry, Ardabil University of Medical Sciences, Iran, (2012).
3- Moosavi-Movahedi, F., Saboury, A. A., Hadi-Alijanvand, H., Moosavi-Movahedi, A. A., "Thermal Inactivation and Conformational Lock Study on Horse Liver Alcohol Dehydrogenase", First International Conference on Biophysical Chemistry, Ardabil University of Medical Sciences, Iran , (2012).
4- Hadi-Alijanvand, H., Rouhani, M., Moosavi-Movahedi, A. A., "HAMDAM-1 as a sequence-based software for studying the physical properties of proteins", Joint Meeting of the Biophysical Society 54th annual meeting & 18th International biophysics congress. , San Francisco, California, USA, 98: (3), 197a-197a, (2010).

In the field of protein evolution there are a few studies that focus on the physical parameters of the protein. For a comprehensive study of physical parameters it is necessary to consider biothermodynamic parameters, structural and statistical properties simultaneously. We developed the HAMDAM-1 as a sequence-based software which is capable of calculating different physical parameters of proteins synchronously based on their amino acid sequences. Our results could confirm the co-evolution among three interacting proteins Cav 1, α-actinin and rSK2.
5- Hadi-Alijanvand, H., Moosavi-Movahedi, A. A., "Thermodynamic Aspect of Evolution for Insulin and Insulin Receptor", VIII European Symposium of the Protein Society, Zurich, Switzerland, (2009).
1- Fallah, J., Kouhzaei, S., Sabaghian, M., Hadi-Alijanvand, H., Fazeli, G., Rafatian, N., "The NCBI; Data Analysis Tools", Andishe Zohour Press, Tehran, Iran, ISBN 978-964-6131-02-6. (This book is a compilation), (2008).
2- Khoei, S., Fazeli, G., Hadi-Alijanvand, H., Khabiri, M., "Calculations for Molecular Biology and Biotechnology: A Guide to Mathematics in the Laboratory", House of Biology Press, Tehran, Iran, ISBN 964-2605-05-8. (This book is a translation), (2006).
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