A framework for protein structure classification and identification of novel protein structures

BACKGROUND: Protein structure classification plays a central role in understanding the function of a protein molecule with respect to all known proteins in a structure database. With the rapid increase in the number of new protein structures, the need for automated and accurate methods for protein classification is increasingly important. RESULTS: In this paper we present a unified framework for protein structure classification and identification of novel protein structures. The framework consists of a set of components for comparing, classifying, and clustering protein structures. These components allow us to accurately classify proteins into known folds, to detect new protein folds, and to provide a way of clustering the new folds. In our evaluation with SCOP 1.69, our method correctly classifies 86.0%, 87.7%, and 90.5% of new domains at family, superfamily, and fold levels. Furthermore, for protein domains that belong to new domain families, our method is able to produce clusters that closely correspond to the new families in SCOP 1.69. As a result, our method can also be used to suggest new classification groups that contain novel folds. CONCLUSION: We have developed a method called proCC for automatically classifying and clustering domains. The method is effective in classifying new domains and suggesting new domain families, and it is also very efficient. A web site offering access to proCC is freely available a

Practical methods for constructing suffix trees

Sequence datasets are ubiquitous in modern life-science applications, and querying sequences is a common and critical operation in many of these applications. The suffix tree is a versatile data structure that can be used to evaluate a wide variety of queries on sequence datasets, including evaluating exact and approximate string matches, and finding repeat patterns. However, methods for constructing suffix trees are often very time-consuming, especially for suffix trees that are large and do not fit in the available main memory. Even when the suffix tree fits in memory, it turns out that the processor cache behavior of theoretically optimal suffix tree construction methods is poor, resulting in poor performance. Currently, there are a large number of algorithms for constructing suffix trees, but the practical tradeoffs in using these algorithms for different scenarios are not well characterized.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47869/1/778_2005_Article_154.pd

Report from the American Society of Transplantation on frailty in solid organ transplantation

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/148387/1/ajt15198_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/148387/2/ajt15198.pd

Mitochondria-Associated MicroRNAs in Rat Hippocampus Following Traumatic Brain Injury

Traumatic brain injury (TBI) is a major cause of death and disability. However, the molecular events contributing to the pathogenesis are not well understood. Mitochondria serve as the powerhouse of cells, respond to cellular demands and stressors, and play an essential role in cell signaling, differentiation, and survival. There is clear evidence of compromised mitochondrial function following TBI; however, the underlying mechanisms and consequences are not clear. MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate gene expression post-transcriptionally, and function as important mediators of neuronal development, synaptic plasticity, and neurodegeneration. Several miRNAs show altered expression following TBI; however, the relevance of mitochondria in these pathways is unknown. Here, we present evidence supporting the association of miRNA with hippocampal mitochondria, as well as changes in mitochondria-associated miRNA expression following a controlled cortical impact (CCI) injury in rats. Specifically, we found that the miRNA processing proteins Argonaute (AGO) and Dicer are present in mitochondria fractions from uninjured rat hippocampus, and immunoprecipitation of AGO associated miRNA from mitochondria suggests the presence of functional RNA-induced silencing complexes. Interestingly, RT-qPCR miRNA array studies revealed that a subset of miRNA is enriched in mitochondria relative to cytoplasm. At 12h following CCI, several miRNAs are significantly altered in hippocampal mitochondria and cytoplasm. In addition, levels of miR-155 and miR-223, both of which play a role in inflammatory processes, are significantly elevated in both cytoplasm and mitochondria. We propose that mitochondria-associated miRNAs may play an important role in regulating the response to TBI

Luminal-Applied Flagellin Is Internalized by Polarized Intestinal Epithelial Cells and Elicits Immune Responses via the TLR5 Dependent Mechanism

Bacteria release flagellin that elicits innate responses via Toll-like receptor 5 (TLR5). Here, we investigated the fate of apically administrated full length flagellin from virulent and avirulent bacteria, along with truncated recombinant flagellin proteins in intestinal epithelial cells and cellular responses. Flagellin was internalized by intestinal epithelial cell (IEC) monolayers of IEC-18. Additionally, apically applied flagellin was internalized by polarized human Caco-2BBe and T-84 cells in a TLR5 dependent mechanism. More, flagellin exposure did not affect the integrity of intestinal monolayers. With immunofluorescent staining, internalized flagellin was detected in both early endosomes as well as lysosomes. We found that apical exposure of polarized Caco-2BBe and T-84 to flagellin from purified Salmonella, Escherichia coli O83:H1 (isolate from Crohn’s lesion) or avirulent E. coli K12 induced comparable levels of basolateral IL-8 secretion. A recombinant protein representing the conserved amino (N) and carboxyl (C) domains (D) of the flagellin protein (ND1/2ECHCD2/1) induced IL-8 secretion from IEC similar to levels elicited by full-length flagellins. However, a recombinant flagellin protein containing only the D3 hypervariable region elicited no IL-8 secretion in both cell lines compared to un-stimulated controls. Silencing or blocking TLR5 in Caco-2BBe cells resulted in a lack of flagellin internalization and decreased IL-8 secretion. Furthermore, apical exposure to flagellin stimulated transepithelial migration of neutrophils and dendritic cells. The novel findings in this study show that luminal-applied flagellin is internalized by normal IEC via TLR5 and co-localizes to endosomal and lysosomal compartments where it is likely degraded as flagellin was not detected on the basolateral side of IEC cultures

Synthesis and characterization of ether linkage containing bis-fluoran compounds

2-Chloro-6-diethylaminofluoran and 2-chloro-3-methyl-6-diethylaminofluoran were reacted with various diphenols in dimethyl formamide in the presence of potassium carbonate to give the related bis-fluoran compounds. All the synthesized derivatives were identified by conventional methods (IR, 1H-NMR), elemental analysis and UV-visible spectroscopy in organic solvent and 95 % acetic acid. All the fluoran compounds change their colour in acidic media

Homology Modeling of Human α~2A~-Adrenoceptor

α~2A~-adrenoceptor (ADA2A) is a membrane bound receptor which has been classified as the member of larger superfamily G-protein coupled receptors (GPCRs); also known as seven transmembrane (7-TM) domains receptor. Around 50% drugs currently available in the market exert their effects through GPCRs. Membrane proteins are difficult to crystallize as compared to soluble proteins. There is a need of 3D-structure of ADA2A to understand binding modes of various agonists and antagonists and hence homology model of ADA2A was developed. Homology model of ADA2A constructed based on crystal structure of β~2~-adrenoceptor. The crystal structure of β~2~-adrenoceptor (PDB ID: 2RH1) was used as template, which has good sequence identity and higher resolution (2.4 Å) and models were generated using MODELLER9v7, among them some models were selected based on molpdf and DOPE score. The built homology model was evaluated using various programs like ERRAT, PROCHECK, PROSA2003, and WHAT_IF. The built homology model can be useful for designing more potent subtype selective antagonists or/and agonists and can provide guidance for mutagenesis studies