Sharif Digital Repository

We use coarse grained molecular dynamics simulations to investigate diffusion properties of sheared lipid membranes with embedded transmembrane proteins. In membranes without proteins, we find normal in-plane diffusion of lipids in all flow conditions. Protein embedded membranes behave quite differently: by imposing a simple shear flow and sliding the monolayers of the membrane over each other, the motion of protein clusters becomes strongly superdiffusive in the shear direction. In such a circumstance, the subdiffusion regime is predominant perpendicular to the flow. We show that superdiffusion is a result of accelerated chaotic motions of protein-lipid complexes within the membrane voids,... 

The cell membrane is responsible for the transportation of heat between inside and outside the cell. Whether the thermal properties of the cell membrane are affected by the cholesterol concentration or the membrane proteins has not been investigated so far. Although the experimental measurement of the membrane thermal conductivity was not available until very recently, computational methods have been widely used for this purpose. In this study, we carry out molecular dynamics simulations to investigate the relation between the concentration of cholesterol and the thermal conductivity of a model membrane. Our results suggest an increase in the membrane thermal conductivity upon increasing the... 

This study aims to identify genetic causes of familial female infertility characterized by embryonic developmental arrest (EDA) and repeated implantation failure (RIF) with oocyte donation IVF cycle. We used Whole-exome sequencing and Sanger validation to find causative genes in an Iranian consanguineous family that had 3 infertile daughters, 4 fertile daughters, and 2 fertile sons. All patients in this consanguineous family exhibited typical manifestations of unexplained RIF and EDA. Genetic analysis identified a homozygous missense variant (c.G1054C:p.G352R) in exon 13 of the TLE6 gene that cosegregated with the EDA phenotype in an autosomal recessive pattern. Other members of the family,... 

Syndapin 1 FBAR, a member of the Bin-amphiphysin-Rvs (BAR) domain protein family, is known to induce membrane curvature and is an essential component in biological processes like endocytosis and formation and growth of neurites. We quantify the curvature sensing of FBAR on reconstituted porcine brain lipid vesicles and show that it senses membrane curvature at low density whereas it induces and reinforces tube stiffness at higher density. FBAR strongly up-concentrates on the high curvature tubes pulled out of Giant Unilamellar lipid Vesicles (GUVs), this sorting behavior is strongly amplified at low protein densities. Interestingly, FBAR from syndapin 1 has a large affinity for tubular... 

Complex networks serve as generic models for many biological systems that have been shown to share a number of common structural properties such as power-law degree distribution and small-worldness. Real-world networks are composed of building blocks called motifs that are indeed specific subgraphs of (usually) small number of nodes. Network motifs are important in the functionality of complex networks, and the role of some motifs such as feed-forward loop in many biological networks has been heavily studied. On the other hand, many biological networks have shown some degrees of robustness in terms of their efficiency and connectedness against failures in their components. In this paper we... 

The dependency of amino acid chemical shifts on φ and ψ torsion angle is, independently, studied using a five-residue fragment of ubiquitin and ONIOM(DFT:HF) approach. The variation of absolute deviation of 13Cα chemical shifts relative to φ dihedral angle is specifically dependent on secondary structure of protein not on amino acid type and fragment sequence. This dependency is observed neither on any of 13Cβ, and 1Hα chemical shifts nor on the variation of absolute deviation of 13Cα chemical shifts relative to ψ dihedral angle. The 13Cα absolute deviation chemical shifts (ADCC) plots are found as a suitable and simple tool to predict secondary structure of protein with no requirement of... 

ApolipoproteinD (ApoD) is a human glycoprotein from the lipocalin family. ApoD contains a conserved central motif of an 8-stranded antiparallel β-sheet, which forms a beta-barrel that can be used for transport and storage of diverse hydrophobic ligands. Due to hydrophobic nature of ApoD, it has been difficult to generate a recombinant version of this protein. In the present work, we aimed at the production of ApoD in the robust Pichia pastoris expression system. To this end, the ApoD gene sequence was synthesized and subcloned for expression in the yeast host cells. Following integration of the ApoD gene into the yeast genomic region using homologous recombination, the ApoD recombinant... 

Fibrillation of amyloid beta (Aβ) peptide is the hallmark of Alzheimer's disease. Given that interactions at the bio–nano interface affect the fibrillation tendency of this peptide, an understanding of the interactions at Aβ peptide–inorganic surfaces on the microscopic level can help to determine the possible neurotoxicity of nanoparticles. Here, the interactions between a fibril-forming peptide, Aβ25–35, and (111) and (100) facets of gold and silver surfaces have been studied by conducting atomistic molecular dynamics simulations. The obtained results indicate that the adsorption onto gold and silver surfaces force the peptide into the β-sheet-rich conformations, which is prone to... 

Protein separation and purification technologies play an essential role in various industries including but not limited to pharmaceuticals, dairy as well as the food sector. Accordingly, a wide variety of techniques such as chromatography and electrophoresis have been developed and utilized extensively over the years for this purpose. Despite their widespread acceptance, conventional techniques still suffer from major limitations and complexities such as short lifetime, low productivity, high-pressure drop and difficulty in scale-up among others. Membrane separation processes have received significant attention in recent years as a promising alternative that can potentially overcome the... 

Humanity's challenges are becoming increasingly difficult, and as these challenges become more advanced, the need for effective and intelligent action becomes more apparent. Meanwhile, the novel coronavirus disease (COVID-19) pandemic, which has plagued the world, could be considered as an opportunity to take a step toward the need for atomic engineering, compared to molecular engineering, as well as to accelerate this type of research. This approach, which can be expressed in terms of picotechnology, makes it possible to identify living cell types or in general, chemical and biological surfaces using their atomic arrays, and applied for early diagnosis even treatment of the disease. © 2020... 

Discontinuous molecular dynamics simulations, together with the protein intermediate resolution model, an intermediate-resolution model of proteins, are used to carry out several microsecond-long simulations and study folding transition and stability of α -de novo-designed proteins in slit nanopores. Both attractive and repulsive interaction potentials between the proteins and the pore walls are considered. Near the folding temperature Tf and in the presence of the attractive potential, the proteins undergo a repeating sequence of folding/partially folding/unfolding transitions, with Tf decreasing with decreasing pore sizes. The unfolded states may even be completely adsorbed on the pore's... 

In the past decade, assays that profile different aspects of the epigenome have grown exponentially in number and variation. However, standard guidelines for researchers to choose between available tools depending on their needs are lacking. Here, we introduce a comprehensive collection of the most commonly used bulk and single-cell epigenomic assays and compare and contrast their strengths and weaknesses. We summarize some of the most important technical and experimental parameters that should be considered for making an appropriate decision when designing epigenomic experiments. © Copyright © 2021 Mehrmohamadi, Sepehri, Nazer and Norouzi  

Bacterial populations are promising candidates for the development of the receiver and transmitter nanomachines for molecular communication (MC). A bacterial receiver is required to uptake the information molecules and produce the detectable molecules following a regulation mechanism. We have constructed a novel bacterial MC receiver using an inducible bacterial L-rhamnose-regulating operon. The proposed bacterial receiver produces green fluorescent protein (GFP) in response to the L-rhamnose information molecules following a quite fast regulation mechanism. To fabricate the receiver, the bacterial population has been transformed using a plasmid harboring L-rhamnose operon genes and gene... 

It is reported that approximately 40 million people are suffering from dementia, globally. Dementia is a group of symptoms that affect neurons and cause some mental disorders, such as losing memory. Alzheimer's disease (AD) which is known as the most common cause of dementia, is one of the top medical care concerns across the world. Although the exact sources of the disease are not understood, is it believed that aggregation of amyloid-beta (Aβ) outside of neuron cells and tau aggregation or neurofibrillary tangles (NFTs) formation inside the cell may play crucial roles. In this paper, we are going to review studies that targeted inhibition of amyloid plaque and tau protein tangle formation,... 

Different techniques including toluene-ethanol, guanidine hydrochloride, guanidine hydrochloride-EDTA, lysozyme, lysozyme-EDTA and sonication treatments were used to extract penicillin G acylase from Escherichia coli ATCC 11105 cells. The obtained results show that penicillin G acylase extraction by guanidine-EDTA treatment is more specific in comparison to the other applied methods. The maximum specific activity of the enzyme (5.61 U/mg), i.e. the maximum purification was found when 1 M guanidine + 100 mM EDTA solution was used for penicillin G acylase extraction at culture condition including 0.50% (w/v) yeast extract as carbon source. In such a condition more than 95% of the enzyme was... 

To control liposomes fate and transport upon contact with biofluids, it is essential to consider several parameters affecting the synthetic and biological identity of liposomes, as well as liposome-protein corona (PC) aspects. As a powerful tool in this data mining adventure, quantitative structure-activity relationship (QSAR) approach is used to correlate physicochemical properties of liposomes and their PC fingerprints to multiple quantified biological responses. In the present study, the relationship between cellular interactions of a set of structurally diverse liposomal formulations and their physicochemical and PC properties has been investigated via linear and nonlinear QSAR models.... 

Proteins are the main players in the game of life. Good understanding of their structures, functions, and behaviors leads to good understanding of drugs, diseases, and thus our health. So, much effort has been done to study and categorize proteins. Nowadays, tens of thousands of proteins have been found. Moreover, the problem of comparing the proteins is hard. Therefore efficient methods are needed to deal with this problem. In this paper, we used one important computational geometric method and one graph matching method: "Delaunay Tetrahedral-ization" and "Similarity Flooding" to propose a new idea to extract similar parts of proteins by combining both of these methods