Bioinformatics analysis of myelin-microbe interactions suggests multiple types of molecular mimicry in the pathogenesis of multiple sclerosis.

Multiple sclerosis (MS) is a devastating autoimmune disease that leads to the destruction of the myelin sheath in the human central nervous system (CNS). Infection by viruses and bacteria has been found to be strongly associated with the onset of MS or its severity. We postulated that the immune system's attack on the myelin sheath could be triggered by viruses and bacteria antigens that resemble myelin sheath components.

Evaluation of pH change effects on the HSA folding and its drug binding characteristics, a computational biology investigation.

The binding of therapeutics to human serum albumin (HSA), which is an abundant protein in plasma poses a major challenge in drug discovery. Although HSA has several binding pockets, the binding site I on D2 and binding site II on D3 are the main binding pockets of HSA. To date, a few experiments have been conducted to examine the effects of the potential of hydrogen (pH) changes on HSA attributes.

Topological Analysis of Regulatory Networks Reveals Functionally Key Genes and miRNAs Involved in the Differentiation of Mesenchymal Stem Cells.

Background: The details of molecular mechanisms underlying the differentiation of Mesenchymal Stem Cells (MSCs) into specific lineages are not well understood.

Objectives: We aimed to construct the interactome network and topology analysis of bone marrow mesenchymal stem cell of CAGE data. Applying the enrichment results, we wanted to introduce the common genes and hub-microRNA and hub-genes of these giant network.

Reconstruction of Intercellular Signaling Network by Cytokine-Receptor Interactions.

Background: The immune system function depends on the coordination activity of the components of system and communications between them which leads to the formation of a complex communication network between immune cells. In this network, cytokines have an important role in the communication between immune cells through the interaction to their specific receptors. These molecules cause to cellular communications and normal function of a tissue.

Directed Blocking of TGF-β Receptor I Binding Site Using Tailored Peptide Segments to Inhibit its Signaling Pathway.

Background: TGF-β isoforms play crucial roles in diverse cellular processes. Therefore, targeting and inhibiting TGF-β signaling pathway provides a potential therapeutic opportunity. TGF-β isoforms bind and bring the receptors (TβRII and TβRI) together to form a signaling complex in an ordered manner.

Development of a highly-potent anti-angiogenic VEGF8-109 heterodimer by directed blocking of its VEGFR-2 binding site.

Angiogenesis is a hallmark of various pathological conditions and is controlled by a variety of angiogenic factors. Blockade of vascular endothelial growth factor (VEGF) as the most pivotal stimulator of angiogenesis offers a promising therapeutic approach for some diseases, typically cancer. In the present study, a heterodimeric antagonistic VEGF was precisely designed based on structural information of recently-crystallized VEGF/VEGF receptor-2 (VEGFR-2/fetal liver kinase 1/kinase domain region) complex.

A pairwise residue contact area-based mean force potential for discrimination of native protein structure.

Background: Considering energy function to detect a correct protein fold from incorrect ones is very important for protein structure prediction and protein folding. Knowledge-based mean force potentials are certainly the most popular type of interaction function for protein threading. They are derived from statistical analyses of interacting groups in experimentally determined protein structures.

STON: A novel method for protein three-dimensional structure comparison.

Protein structure comparison is an important problem in bioinformatics and has many applications in the study of structural and functional genomics. During the last decades, various heuristic methods have been developed to solve the protein structure comparison problem. Most of the protein structure comparison methods give the alignment based on the minimum RMSD (root mean square deviation) and ignore many significant local alignments that may be important for evolutional or functional studies.

A tale of two symmetrical tails: structural and functional characteristics of palindromes in proteins.

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.

A method for protein accessibility prediction based on residue types and conformational states.

Prediction of protein accessibility from sequence, as prediction of protein secondary structure is an intermediate step for predicting structures and consequently functions of proteins. Most of the currently used methods are based on single residue prediction, either by statistical means or evolutionary information, and accessibility state of central residue in a window predicted. By expansion of databases of proteins with known 3D structures, we extracted information of pairwise residue types and conformational states of pairs simultaneously.

Prediction of protein secondary structure based on residue pair types and conformational states using dynamic programming algorithm.

We have used a statistical approach for protein secondary structure prediction based on information theory and simultaneously taking into consideration pairwise residue types and conformational states. Since the prediction of residue secondary structure by one residue window sliding make ambiguity in state prediction, we used a dynamic programming algorithm to find the path with maximum score. A score system for residue pairs in particular conformations is derived for adjacent neighbors up to ten residue apart in sequence.