Sharif Digital Repository

Background: It has been previously shown that palindromic sequences are frequently observed in proteins. However, our knowledge about their evolutionary origin and their possible importance is incomplete. Results: In this work, we tried to revisit this relatively neglected phenomenon. Several questions are addressed in this work. (1) It is known that there is a large chance of finding a palindrome in low complexity sequences (i.e. sequences with extreme amino acid usage bias). What is the role of sequence complexity in the evolution of palindromic sequences in proteins? (2) Do palindromes coincide with conserved protein sequences? If yes, what are the functions of these conserved segments?... 

The interaction of n-dodecyl trimethylammonium bromide (DTAB) with oxyhemoglobin A and oxyhemoglobin S is investigated using UV-visible absorption spectra and chemometric resolution techniques. Oxyhemoglobins (A and S) induced to partial oxidized form (ferrihemoglobin) by DTAB and finally transform to fully oxidized hemichrome. Hemichrome mole fractions of HbS are more than HbA because of more hydrophobic interaction of DTAB-HbS in second set of binding site relative to DTAB-HbA. The visible spectra between 500 and 650 nm are used for identifying the present components in solution because each species of hemoglobin has a specific spectrum in this region. The number of components and mole... 

D-glucosamine, as a representative polyfunctional compound, is a bioactive amino sugar. In this study, the gas phase thermochemical properties of D-glucosamine, including its Metal Ion Affinity (MIA), metal binding sites, Anion Affinity (AA), acidity and proton affinity, have been explored, using the Density Functional Theory (DFT) and a 6-311++G**basis set. The summary of the MIA and AA results (in kcal/mol-1) are: Li+ = 67.6, Na+ = 51.1, K+ = 37.3, Mg2+ = 207.9, Ca2+ = 150.4, Zn2+ = 251.2, Cl- = 27.4, CN- = 28.0. The acidity values calculated at different sites, including four -OH groups and one -NH2 group, range from 344.0 to 373.0 kcal/mol-1. These results, surprisingly, indicate how... 

SARS-CoV-2 is a strain of Coronavirus family that caused the ongoing pandemic of COVID-19. Several studies showed that the glycosylation of virus spike (S) protein and the Angiotensin-Converting Enzyme 2 (ACE2) receptor on the host cell is critical for the virus infectivity. Molecular Dynamics (MD) simulations were used to explore the role of a novel mutated O-glycosylation site (D494S) on the Receptor Binding Domain (RBD) of S protein. This site was suggested as a key mediator of virus-host interaction. By exploring the dynamics of three O-glycosylated models and the control systems of unglcosylated S4944 and S494D complexes, it was shown that the decoration of S494 with elongated O-glycans... 

We show that the hydrophobicity of sequences is the leading term in Miyazawa-Jernigan interactions. Being the source of additive (solvation) terms in pair-contact interactions, they were used to reduce the energy parameters while resulting in a clear vector manipulation of energy. The reduced (additive) potential performs considerably successful in predicting the statistical properties of arbitrary structures. The evaluated designabilities of the structures by both models are highly correlated. Suggesting geometrically nondegenerate vectors (structures) as proteinlike structures, the additive model is a powerful tool for protein design. Moreover, a crossing point in the log-linear diagram of... 

Two-dimensional MXenes are the newly emerging family of nanomaterials with competitive performance for nano-device development. Surface functional groups and abundant binding sites make these materials ideal candidates for sensor applications. Herein, we report the successful fabrication of a MXene-based nano-bio device for capturing, sensing, and filtering the Escherichia coli (E. coli) bacteria. Mannose carbohydrate, which binds strongly to E.coli's fimH protein via glucan multivalent interactions, is used as the bio-receptor element. MXene's structure was engineered to guarantee efficient E. coli capturing without mannose detachment. Electrochemical impedance spectroscopy (EIS) and cyclic... 

In this study, the potential of using MIL-100(Fe) metal–organic framework (MOF) for loading and controlling the release of dacarbazine (DTIC) was evaluated for in vitro treatment of melanoma. The drug loading was performed during the green synthesis of MIL-100(Fe) in an aqueous media without using any harmful solvents, to obtain MIL-DTIC. The surface of this structure was then coated with polyethylene glycol (PEG) in the same aqueous solution to synthesize MIL-DTIC-PEG. The synthesized samples were characterized using various methods. Their release profile was studied in phosphate-buffered saline (PBS) and simulated cutaneous medium (SCM). The cytotoxicity of DTIC and its nano-MOF... 

Hi-C is a genome-wide chromosome conformation capture technology that detects interactions between pairs of genomic regions and exploits higher order chromatin structures. Conceptually Hi-C data counts interaction frequencies between every position in the genome and every other position. Biologically functional interactions are expected to occur more frequently than transient background and artefactual interactions. To identify biologically relevant interactions, several background models that take biases such as distance, GC content and mappability into account have been proposed. Here we introduce MaxHiC, a background correction tool that deals with these complex biases and robustly...