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    StrongestPath: a Cytoscape application for protein-protein interaction analysis

    , Article BMC bioinformatics ; Volume 22, Issue 1 , 2021 , Pages 352- ; 14712105 (ISSN) Mousavian, Z ; Khodabandeh, M ; Sharifi Zarchi, A ; Nadafian, A ; Mahmoudi, A ; Sharif University of Technology
    NLM (Medline)  2021
    Abstract
    BACKGROUND: StrongestPath is a Cytoscape 3 application that enables the analysis of interactions between two proteins or groups of proteins in a collection of protein-protein interaction (PPI) network or signaling network databases. When there are different levels of confidence over the interactions, the application is able to process them and identify the cascade of interactions with the highest total confidence score. Given a set of proteins, StrongestPath can extract a set of possible interactions between the input proteins, and expand the network by adding new proteins that have the most interactions with highest total confidence to the current network of proteins. The application can... 

    Understanding the nanoparticle-protein corona complexes using computational and experimental methods

    , Article International Journal of Biochemistry and Cell Biology ; Volume 75 , 2016 , Pages 162-174 ; 13572725 (ISSN) Kharazian, B ; Hadipour, N. L ; Ejtehadi, M. R ; Sharif University of Technology
    Elsevier Ltd 
    Abstract
    Nanoparticles (NP) have capability to adsorb proteins from biological fluids and form protein layer, which is called protein corona. As the cell sees corona coated NPs, the protein corona can dictate biological response to NPs. The composition of protein corona is varied by physicochemical properties of NPs including size, shape, surface chemistry. Processing of protein adsorption is dynamic phenomena; to that end, a protein may desorb or leave a surface vacancy that is rapidly filled by another protein and cause changes in the corona composition mainly by the Vroman effect. In this review, we discuss the interaction between NP and proteins and the available techniques for identification of... 

    SimDiv: A new solution for protein comparison

    , Article Lecture Notes in Electrical Engineering ; Volume 6 , 2008 , Pages 467-483 ; 18761100 (ISSN); 9780387749341 (ISBN) Sayyadi, H ; Salehi, S ; Ghodsi, M ; Sharif University of Technology
    2008
    Abstract
    The number of known proteins is increasing every day; tens of thousands have been studied and categorized by now. In this chapter, we propose amodel for protein matching or extracting similar parts of two given proteins. We focus on the computational geometric approach and the graph matching method that are used to model and compare the sequence and 3D structure of proteins. The remainder ofthis chapter is organized as follows. We first have a glance at the related works. There are two major methods used in the literature: Delaunay tetrahedralization and similarity flooding.We explain the required information in the next section as background knowledge, and then propose a new idea in Sect.... 

    Three-body interactions improve the prediction of rate and mechanism in protein folding models

    , Article Proceedings of the National Academy of Sciences of the United States of America ; Volume 101, Issue 42 , 2004 , Pages 15088-15093 ; 00278424 (ISSN) Ejtehadi, M. R ; Avall, S. P ; Plotkin, S. S ; Sharif University of Technology
    2004
    Abstract
    Here we study the effects of many-body interactions on rate and mechanism in protein folding by using the results of molecular dynamics simulations on numerous coarse-grained Cα-model single-domain proteins. After adding three-body interactions explicitly as a perturbation to a Gō-like Hamiltonian with native pairwise interactions only, we have found (i) a significantly increased correlation with experimental φ values and folding rates, (ii) a stronger correlation of folding rate with contact order, matching the experimental range in rates when the fraction of three-body energy in the native state is ≈20%, and (iii) a considerably larger amount of three-body energy present in chymotripsin... 

    Effects of temperature shifts and oscillations on recombinant protein production expressed in Escherichia coli

    , Article Bioprocess and Biosystems Engineering ; Volume 36, Issue 11 , 2013 , Pages 1571-1577 ; 16157591 (ISSN) Jazini, M ; Herwig, C ; Sharif University of Technology
    2013
    Abstract
    Escherichia coli is widely used host for the intracellular expression of many proteins. However, in some cases also secretion of protein from periplasm was observed. Improvement of both intracellular and extracellular production of recombinant protein in E. coli is an attractive goal in order to reduce production cost and increase process efficiency and economics. Since heat shock proteins in E. coli were reported to be helpful for protein refolding and hindering aggregation, in this work different types of single and periodic heat shocks were tested on lab scale to enhance intracellular and extracellular protein production. A single heat shock prior to induction and different oscillatory... 

    Gating and conduction of nano-channel forming proteins: A computational approach

    , Article Journal of Biomolecular Structure and Dynamics ; Volume 31, Issue 8 , 2013 , Pages 818-828 ; 07391102 (ISSN) Besya, A. B ; Mobasheri, H ; Ejtehadi, M. R ; Sharif University of Technology
    2013
    Abstract
    Monitoring conformational changes in ion channels is essential to understand their gating mechanism. Here, we explore the structural dynamics of four outer membrane proteins with different structures and functions in the slowest nonzero modes of vibration. Normal mode analysis was performed on the modified elastic network model of channel in the membrane. According to our results, when membrane proteins were analyzed in the dominant mode, the composed pores, TolC and α-hemolysin showed large motions at the intramembrane β-barrel region while, in other porins, OmpA and OmpF, largest motions observed in the region of external flexible loops. A criterion based on equipartition theorem was used... 

    NETAL: A new graph-based method for global alignment of protein-protein interaction networks

    , Article Bioinformatics ; Volume 29, Issue 13 , 2013 , Pages 1654-1662 ; 13674803 (ISSN) Neyshabur, B ; Khadem, A ; Hashemifar, S ; Arab, S. S ; Sharif University of Technology
    2013
    Abstract
    Motivation: The interactions among proteins and the resulting networks of such interactions have a central role in cell biology. Aligning these networks gives us important information, such as conserved complexes and evolutionary relationships. Although there have been several publications on the global alignment of protein networks; however, none of proposed methods are able to produce a highly conserved and meaningful alignment. Moreover, time complexity of current algorithms makes them impossible to use for multiple alignment of several large networks together.Results: We present a novel algorithm for the global alignment of protein-protein interaction networks. It uses a greedy method,... 

    Evolution of 'ligand-deffusion chreodes' on protein-surface models: A genetic-algorithm study

    , Article Chemistry and Biodiversity ; Volume 4, Issue 12 , 2007 , Pages 2766-2771 ; 16121872 (ISSN) Marashi, A ; Kargar, M ; Katanforoush, A ; Abolhassani, H ; Sadeghi, M ; Sharif University of Technology
    2007
    Abstract
    Lattice models have been previously used to model ligand diffusion on protein surfaces. Using such models, it has been shown that the presence of pathways (or 'chreodes') of consecutive residues with certain properties can decrease the number of steps required for the arrival of a ligand at the active site. In this work, we show that, based on a genetic algorithm, ligand-diffusion pathways can evolve on a protein surface, when this surface is selected for shortening the travel length toward the active site. Biological implications of these results are discussed. © 2007 Verlag Helvetica Chimica Acta AG, Zürich  

    Expression of PIAS genes in migraine patients

    , Article Journal of Molecular Neuroscience ; Volume 71, Issue 10 , 2021 , Pages 2053-2059 ; 08958696 (ISSN) Ghafouri Fard, S ; Hesami, O ; Nazer, N ; Sayad, A ; Taheri, M ; Sharif University of Technology
    Humana Press Inc  2021
    Abstract
    Migraine is a complex disabling condition which is associated with dysregulation of several pathways particularly those being associated with immune responses. In order to assess contribution of protein inhibitor of activated STAT (PIAS) in the pathogenesis of migraine, we quantified expression levels of PIAS1–PIAS4 genes in the circulation of patients with migraine compared with controls. Expression of PIAS1 was substantially lower in total migraineurs compared with controls (ratio of mean expressions (RME) = 0.18, SE = 0.29, P value < 0.001) and in both male and female migraineurs compared with sex-matched controls. Expression of PIAS2 was lower in migraineurs without aura compared with... 

    PFP-WGAN: Protein function prediction by discovering gene ontology term correlations with generative adversarial networks

    , Article PLoS ONE ; Volume 16, Issue 2 , 2021 ; 19326203 (ISSN) Seyyedsalehi, S. F ; Soleymani, M ; Rabiee, H. R ; Kaazempur Mofrad, M. R ; Sharif University of Technology
    Public Library of Science  2021
    Abstract
    Understanding the functionality of proteins has emerged as a critical problem in recent years due to significant roles of these macro-molecules in biological mechanisms. However, in-laboratory techniques for protein function prediction are not as efficient as methods developed and processed for protein sequencing. While more than 70 million protein sequences are available today, only the functionality of around one percent of them are known. These facts have encouraged researchers to develop computational methods to infer protein functionalities from their sequences. Gene Ontology is the most well-known database for protein functions which has a hierarchical structure, where deeper terms are... 

    Codon usage and protein sequence pattern dependency in different organisms: A Bioinformatics approach

    , Article Journal of Bioinformatics and Computational Biology ; Volume 13, Issue 2 , April , 2015 ; 02197200 (ISSN) Foroughmand Araabi, M. H ; Goliaei, B ; Alishahi, K ; Sadeghi, M ; Goliaei, S ; Sharif University of Technology
    World Scientific Publishing Co. Pte Ltd  2015
    Abstract
    Although it is known that synonymous codons are not chosen randomly, the role of the codon usage in gene regulation is not clearly understood, yet. Researchers have investigated the relation between the codon usage and various properties, such as gene regulation, translation rate, translation efficiency, mRNA stability, splicing, and protein domains. Recently, a universal codon usage based mechanism for gene regulation is proposed. We studied the role of protein sequence patterns on the codons usage by related genes. Considering a subsequence of a protein that matches to a pattern or motif, we showed that, parts of the genes, which are translated to this subsequence, use specific ratios of... 

    An accurate alignment-free protein sequence comparator based on physicochemical properties of amino acids

    , Article Scientific Reports ; Volume 12, Issue 1 , 2022 ; 20452322 (ISSN) Akbari Rokn Abadi, S ; Abdosalehi, A. S ; Pouyamehr, F ; Koohi, S ; Sharif University of Technology
    Nature Research  2022
    Abstract
    Bio-sequence comparators are one of the most basic and significant methods for assessing biological data, and so, due to the importance of proteins, protein sequence comparators are particularly crucial. On the other hand, the complexity of the problem, the growing number of extracted protein sequences, and the growth of studies and data analysis applications addressing protein sequences have necessitated the development of a rapid and accurate approach to account for the complexities in this field. As a result, we propose a protein sequence comparison approach, called PCV, which improves comparison accuracy by producing vectors that encode sequence data as well as physicochemical properties... 

    Oncolytic paramyxoviruses-induced autophagy; A prudent weapon for cancer therapy

    , Article Journal of Biomedical Science ; Volume 26, Issue 1 , 2019 ; 10217770 (ISSN) Keshavarz, M ; Solaymani Mohammadi, F ; Miri, S. M ; Ghaemi, A ; Sharif University of Technology
    BioMed Central Ltd  2019
    Abstract
    Oncolytic virotherapy has currently emerged as a promising approach upon which scientists have been able to induce tumor-specific cell death in a broad spectrum of malignancies. Paramyxoviruses represent intrinsic oncolytic capability, which makes them excellent candidates to be widely used in oncolytic virotherapy. The mechanisms through which these viruses destroy the cancerous cells involve triggering the autophagic machinery and apoptosis in target cells. Interestingly, oncolytic paramyxoviruses have been found to induce autophagy and lead to tumor cells death rather than their survival. Indeed, the induction of autophagy has been revealed to enhance the immunogenicity of tumor cells via... 

    Site-specific protein conjugation onto fluorescent single-walled carbon nanotubes

    , Article Chemistry of Materials ; Volume 32, Issue 20 , 2020 , Pages 8798-8807 Zubkovs, V ; Wu, S. J ; Rahnamaee, S. Y ; Schuergers, N ; Boghossian, A. A ; Sharif University of Technology
    American Chemical Society  2020
    Abstract
    Semiconducting single-walled carbon nanotubes (SWCNTs) are among the few photostable optical emitters that are ideal for sensing, imaging, drug delivery, and monitoring of protein activity. These applications often require strategies for immobilizing proteins onto the nanotube while preserving the optical properties of the SWCNTs. Site-specific and oriented immobilization strategies, in particular, offer advantages for improving sensor and optical signaling responses. In this study, we demonstrate site-specific protein immobilization of a model of enhanced yellow fluorescent protein with a single engineered cysteine residue, using either single-stranded DNA or a pyrene-containing linker to... 

    TripletProt: Deep Representation Learning of Proteins Based On Siamese Networks

    , Article IEEE/ACM Transactions on Computational Biology and Bioinformatics ; Volume 19, Issue 6 , 2022 , Pages 3744-3753 ; 15455963 (ISSN) Nourani, E ; Asgari, E ; McHardy, A. C ; Mofrad, M. R. K ; Sharif University of Technology
    Institute of Electrical and Electronics Engineers Inc  2022
    Abstract
    Pretrained representations have recently gained attention in various machine learning applications. Nonetheless, the high computational costs associated with training these models have motivated alternative approaches for representation learning. Herein we introduce TripletProt, a new approach for protein representation learning based on the Siamese neural networks. Representation learning of biological entities which capture essential features can alleviate many of the challenges associated with supervised learning in bioinformatics. The most important distinction of our proposed method is relying on the protein-protein interaction (PPI) network. The computational cost of the generated... 

    Finding correlation between protein protein interaction modules using semantic web techniques

    , Article 13th International Computer Society of Iran Computer Conference on Advances in Computer Science and Engineering, CSICC 2008, Kish Island, 9 March 2008 through 11 March 2008 ; Volume 6 CCIS , 2008 , Pages 1009-1012 ; 18650929 (ISSN); 3540899847 (ISBN); 9783540899846 (ISBN) Kargar, M ; Moaven, S ; Abolhassani, H ; Sharif University of Technology
    2008
    Abstract
    Many complex networks such as social networks and computer show modular structures, where edges between nodes are much denser within modules than between modules. It is strongly believed that cellular networks are also modular, reflecting the relative independence and coherence of different functional units in a cell. In this paper we used a human curated dataset. In this paper we consider each module in the PPI network as ontology. Using techniques in ontology alignment, we compare each pair of modules in the network. We want to see that is there a correlation between the structure of each module or they have totally different structures. Our results show that there is no correlation... 

    A theoretical study of repeating sequence in HRP II: A combination of molecular dynamics simulations and 17O quadrupole coupling tensors

    , Article Biophysical Chemistry ; Volume 137, Issue 2-3 , 2008 , Pages 76-80 ; 03014622 (ISSN) Behzadi, H ; Esrafili, M. D ; van der spoel, D ; Hadipour, N. L ; Parsafar, G ; Sharif University of Technology
    2008
    Abstract
    Histidine rich protein II derived peptide (HRP II 169-182) was investigated by molecular dynamics, MD, simulation and 17O electric field gradient, EFG, tensor calculations. MD simulation was performed in water at 300 K with α-helix initial structure. It was found that peptide loses its initial α-helix structure rapidly and is converted to random coil and bent secondary structures. To understand how peptide structure affects EFG tensors, initial structure and final conformations resulting from MD simulations were used to calculate 17O EFG tensors of backbone carbonyl oxygens. Calculations were performed using B3LYP method and 6-31 + G* basis set. Calculated 17O EFG tensors were used to... 

    Plant protein-based hydrophobic fine and ultrafine carrier particles in drug delivery systems

    , Article Critical Reviews in Biotechnology ; Volume 38, Issue 1 , 2018 , Pages 47-67 ; 07388551 (ISSN) Malekzad, H ; Mirshekari, H ; Sahandi Zangabad, P ; Moosavi Basri, S. M ; Baniasadi, F ; Sharifi Aghdam, M ; Karimi, M ; Hamblin, M. R ; Sharif University of Technology
    Taylor and Francis Ltd  2018
    Abstract
    For thousands of years, plants and their products have been used as the mainstay of medicinal therapy. In recent years, besides attempts to isolate the active ingredients of medicinal plants, other new applications of plant products, such as their use to prepare drug delivery vehicles, have been discovered. Nanobiotechnology is a branch of pharmacology that can provide new approaches for drug delivery by the preparation of biocompatible carrier nanoparticles (NPs). In this article, we review recent studies with four important plant proteins that have been used as carriers for targeted delivery of drugs and genes. Zein is a water-insoluble protein from maize; Gliadin is a 70% alcohol-soluble... 

    Design and Construction of Novel Intein Mediated Biosensor in Order to Detect Amyloid Fibrils

    , M.Sc. Thesis Sharif University of Technology Miri, Mohammad (Author) ; Kalhor, Hamid Reza (Supervisor)
    Abstract
    The most important factor in protein's function and its 3D structure is folding. Misfolding or native folding perturbation in some peptides and proteins force them get into amyloid fibril aggregation. It has been observed that these aggregations are the cause of some debilitative diseases especially ones that are related to aging like Alzheimer disease, Hantington's disease, typeII diabets etc. Recently it has been shown that specific regions in human catalase protein interact with some amyloid fibrils, such as Aß, IAPP, PrP etc. Inteins are self-splicing protein enzymes, which excise themselves from the mature protein and join the two flanking adjacent sequences by a new peptide bond in a... 

    Directed Evolution of the Asparaginase Enzyme to Alter Substrate Specificity

    , M.Sc. Thesis Sharif University of Technology Yousefi, Danial (Author) ; Kalhor, Hamid Reza (Supervisor)
    Abstract
    Asparagainase is a therapeutic enzyme which has been a subject of research for decades. The enzyme catalyzes the hydrolysis of the amide group in asparagine and similar amides. Altering the substrate specificity and stabilization of this enzyme can increase its therapeutic properties. Moreover, asparaginases may be evolved to catalyze the hydrolysis of other similar compounds. These can be achieved through directed evolution and computational methods.In this study, the gene encoding L-asparaginase II enzyme from E. coli was amplified by polymerase chain reaction (PCR) and was cloned into an expression vector. The recombinant protein was expressed by an appropriate host secreting the...