Hamid Hadi-Alijanvand

Hamid Hadi-Alijanvand
Institute for Advanced Studies in Basic Sciences | IASBS · Department of Biological Sciences

Ph.D in Biophysics

About

35
Publications
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311
Citations
Introduction
Hamid Hadi-Alijanvand currently works at the Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences. Hamid does research in Computational Biophysics, Biophysics and Cancer Research. His most recent publication is 'Complex Stability is Encoded in Binding Patch Softness: a Monomer-Based Approach to Predict Inter-Subunit Affinity of Protein Dimers'.
Education
September 2007 - September 2012
September 2005 - March 2007
September 2000 - July 2004

Publications

Publications (35)
Article
Protein complexes play deterministic roles in the live entities in sensing, compiling, controlling, and responding to the external and internal stimuli. Thermodynamic stability is an important property of protein complexes; having knowledge about complex stability helps us to understand the basics of protein-assembly-related diseases and the mechan...
Article
By having knowledge about the characteristics of protein interaction interfaces, we will be able to manipulate protein complexes for therapies. Dimer state is considered as the primary alphabet of the most proteins’ quaternary structure. The properties of binding interface between subunits and of noninterface region define the specificity and stabi...
Article
Knowledge about the structure and stability of PPIs is inevitable to decipher the behavior of protein systems. Prediction of protein complexes’ stability is an interesting topic in the field of structural biology. There are some promising published computational approaches that predict the affinity between subunits of protein dimers using 3D struct...
Article
A highly infectious coronavirus, SARS-CoV-2, spreads in many countries. This virus recognizes its receptor, angiotensin-converting enzyme 2 (ACE2) using receptor binding domain of its spike protein subunit S1. Many missense mutations are reported in various human populations for ACE2 gene. In current study, we predict the affinity of many ACE2 vari...
Article
Full-text available
At the center of the SARS-CoV2 infection, the spike protein and its interaction with the human receptor ACE2 play a central role in the molecular machinery of SARS-CoV2 infection of human cells. Vaccine therapies are a valuable barrier to the worst effects of the virus and to its diffusion, but the need of purposed drugs is emerging as a core targe...
Article
Full-text available
ABSTRACT: At the center of the SARS-CoV2 infection, the spike protein and its interaction with the human receptor ACE2 play a central role in the molecular machinery of SARS-CoV2 infection of human cells. Vaccine therapies are a valuable barrier to the worst effects of the virus and to its diffusion, but the need of purposed drugs is emerging as a...
Article
Full-text available
SARS-CoV-2 has caused the largest pandemic of the XXI (COVID-19), threatening the life and economy of all countries in the world. Finding therapies and vaccines to mitigate or even fight this sanitary and health threat is among the most important challenges of biomedical sciences in the century. To build up a long-term strategy to fight not only SA...
Conference Paper
Full-text available
Microarray is a powerful technology for simultaneously analyzing thousands of genes and can be used as a tool to discover methods of treat in variety of diseases especially in cancer. The most challenging aspect in the microarray data analysis is the large number of genes versus the small number of samples. Thus, in order to provide a simpler and m...
Article
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...
Article
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...
Article
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Abstract 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 towards the native horseradish peroxidase (H...
Article
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...
Article
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...
Article
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Alzheimer, a neurodegenerative disease, and a large variety of pathologic conditions are associated with a form of protein aggregation known as amyloid fibrils. Since fibrils and prefibrillar intermediates are cytotoxic, numerous attempts have been made to inhibit fibrillation process as a therapeutic strategy. Peptides, surfactants, and aromatic s...
Article
Advanced glycation end products (AGEs) are the predominant intermediates of glycation process, and mediate oxidative stress and complications of diabetes. Potassium sorbate (PS) as a widespread preservative is an oxidative agent and used in different dairy and drug products, which can readily enter biological matrices. Here we studied the PS interf...
Article
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Ca(2+) is an essential second messenger, playing a fundamental role in maintaining cell viability and neuronal activity. Two specific endoplasmic reticulum calcium channels, ryanodine receptors (RyRs) and inositol 1,4,5-trisphosphate receptors (IP3Rs) play an important role in Ca(2+) regulation. In the present study, we provided a 3D structure of R...
Article
Sodium benzoate (SB), a powerful inhibitor of microbial growth, is one of the most commonly used food preservative. Here, we determined the effects of SB on human serum albumin (HSA) structure in the presence or absence of glucose after 35 days of incubation under physiological conditions. The biochemical, biophysical, and molecular approaches incl...
Article
Horse liver alcohol dehydrogenase (HLADH) is a two subunits metal enzyme that has two catalytic sites and two coenzyme domains for each subunit. These subunits are connected together by coenzyme domains. In this study, we investigated the number and sequences of residues that participated in interface locks of HLADH. For this purpose, the kinetics...
Article
Full-text available
Prolyl hydroxylase domain 2 containing protein (PHD2) is a central protein in regulation of cellular response to hypoxia. This protein controls the responses of cell to oxygen level via the regulation of hypoxia inducible factor (HIF) stability. HIF induces the expression of many genes, especially ones orchestrate angiogenesis. There are some repor...
Article
Full-text available
Prolyl hydroxylase domain 2 containing protein (PHD2) is a key protein in regulation of angiogenesis and metastasis. In normoxic condition, PHD2 triggers the degradation of hypoxia-inducible factor 1 (HIF-1α) that induces the expression of hypoxia response genes. Therefore the correct function of PHD2 would inhibit angiogenesis and consequent metas...
Article
Alterations in the synthesis of melanin contribute to a number of diseases; therefore, the design of new tyrosinase inhibitors is very important. Mushroom tyrosinase (MT) is a metalloenzyme, which plays an important role in melanin biosynthesis. In this study, the inhibitory effect of a novel designed compound, i.e. 2-((1Z)-(2-(2,4-dinitrophenyl)hy...
Article
Full-text available
Protein aggregation and denaturation are two major limitations in bioprocess engineering and protein processing. In the present study, we investigated the effects of β-cyclodextrin, as an artificial chaperone, on the structure and function of lysozyme using UV-Vis, fluorescence spectrophotometry, isothermal titration calorimetry (ITC) and theoretic...
Article
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The kinetics of thermal inactivation of bovine carbonic anhydrase (BCA) was studied in a 50 mM Tris-HCl buffer, pH 7.8 using p-nitrophenyl acetate as substrate in absorbance of 400 nm by UV-VIS spectrophotometry. The number of conformational locks and inter-subunit amino acid residues of BCA were obtained by thermal inactivation analysis. The cleav...
Article
The inhibitory effect of ethylenediamine on both activities of mushroom tyrosinase (MT) at 20 °C in a 10 mM phosphate buffer solution (pH 6.8), was studied. L-DOPA and L-tyrosine were used as substrates of catecholase and cresolase activities, respectively. The results showed that ethylenediamine competitively inhibits both activities of the enzyme...
Article
Arsenical compounds exhibit a differential toxicity to cancer cells. Microtubules are a primary target of a number of anticancer drugs, such as arsenical compounds. The interaction of 1-NAA (1-naphthylarsonic acid) has been investigated on microtubule polymerization under in vitro and cellular conditions. Microtubules were extracted from sheep brai...
Article
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An important factor in medicine and related industries is the use of chaperones to reduce protein aggregation. Here we show that chaperone ability is induced in β-casein by modification of its acidic residues using Woodward's Reagent K (WRK). Lysozyme at pH 7.2 was used as a target protein to study β-casein chaperone activities. The mechanism for c...
Article
2A protease of the pathogenic coxsackievirus B3 is key to the pathogenesis of inflammatory myocarditis and, therefore, an attractive drug target. However lack of a crystal structure impedes design of inhibitors. Here we predict 3D structure of CVB3 2A(pro) based on sequence comparison and homology modeling with human rhinovirus 2A(pro). The two enz...
Article
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α-Lactalbumin α-La), together with oleic acid can be converted to a complex, which kills tumor cells selectively. Cytotoxic α-La -oleic acid and α-La -linoleic acid complexes were generated by adding fatty acid to camel holo α-La at 60 ° C (referred to as La-OA-60 and La-LA-60 state, respectively). Structural properties of these complexes were stud...
Article
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While various approaches exist to study protein localization, it is still a challenge to predict where proteins localize. Here, we consider a mechanistic viewpoint for membrane localization. Taking into account the steps for the folding pathway of α-helical membrane proteins and relating biophysical parameters to each of these steps, we create a sc...
Article
Enteroviridae such as coxsackievirus are important infectious agents causing viral heart diseases. Viral protease 2A (2Apro) initiates the virus life cycle, and is an excellent target for developing antiviral drugs. Here, to evaluate the validity of the 2Apro as a proper therapeutic target, and based on the existing information and molecular dynami...
Conference Paper
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 cal...
Article
Fibril formation seems to be a general property of all proteins. Its occurrence in hen or human lysozyme depends on certain conditions, namely acidic pHs or the presence of some additives. This paper studies the interaction of lysozyme with sodium dodecyl sulfate (SDS) at pH 9.2, using UV-visible spectrophotometry, circular dichroism (CD) spectropo...
Article
Full-text available
Cold denaturation is an intriguing phenomenon in protein denaturation for elucidating protein accessible surface area (ASA). Compared to the impact of protein surface, the importance of protein-water interactions in cold denaturation may be ruled out significantly. Here, based on the ASA, we have defined a new factor, the surface stability factor (...