• signaling pathway
  • We found that phosphorylation of Chk1 by ATR also requires checkpoint proteins Rad17 and replication protein A. In contrast, phosphorylation of SMC1 by ATR is independent of Rad17 and replication protein A, suggesting that the signaling pathway leading to SMC1 phosphorylation is distinct from that mediated by the checkpoint proteins. (pnas.org)
  • ATPase
  • The ATPase activity associated with MutS alpha regulates binding similar to a molecular switch: mismatched DNA provokes ADP-->ATP exchange, resulting in a discernible conformational transition that converts MutS alpha into a sliding clamp capable of hydrolysis-independent diffusion along the DNA backbone. (uniprot.org)
  • As with other MutS homologs, hMSH6 has an intrinsic ATPase activity. (wikipedia.org)
  • It has been proposed that histone proteins are evolutionarily related to the helical part of the extended AAA+ ATPase domain, the C-domain, and to the N-terminal substrate recognition domain of Clp/Hsp100 proteins. (wikipedia.org)
  • tumor
  • 1 , 2 If this function is lost in a cell due to MUTYH mutation of both alleles, there are increased G:C→T:A transversions (a guanine-cytosine pair to a thymine-adenine pair) 2 in other genes including tumor suppressors, which could increase cancer risk. (pubmedcentralcanada.ca)
  • These interactions form protein complexes that are typically involved in tumor suppression and DNA repair activities. (wikipedia.org)
  • MSH5
  • These findings in mouse and human indicate that the MSH5 protein plays an important role in meiotic recombination. (wikipedia.org)
  • In the worm Caenorhabditis elegans, the MSH5 protein is required during meiosis both for normal spontaneous and for gamma-irradiation induced crossover recombination and chiasma formation. (wikipedia.org)
  • genes
  • So CCDS's gene number prediction represents a lower bound on the total number of human protein-coding genes. (wikipedia.org)
  • While the exact criteria as defined in the scientific literature vary, giant viruses are generally described as viruses having large pseudo-icosahedral capsids (200 to 400 nanometers) which can be surrounded by a thick (approximately 100 nm) layer of filamentous protein fibers with large double-stranded DNA genomes (300 to 1000 kilobase pairs or larger) encoding a large contingent of genes (of the order of 1000 genes). (wikipedia.org)
  • Two microRNAs, miR21 and miR-155, target the DNA mismatch repair (MMR) genes hMSH6 and hMSH2, to cause reduced expression of their proteins. (wikipedia.org)
  • hMSH2
  • hMSH6 combines with hMSH2 to form the active protein complex, hMutS alpha, also called hMSH2-hMSH6. (wikipedia.org)
  • If one or the other of these two microRNAs is over-expressed, hMSH2 and hMSH6 proteins are under-expressed, resulting in reduced DNA mismatch repair and increased microsatellite instability. (wikipedia.org)
  • Transitional Cell
  • OBJECTIVES: To establish whether high microsatellite instability (MSI) (present in almost 20% of cases) and loss of MSH2 protein expression (sometimes used to predict MSI status) are prognostic factors of overall survival for patients with invasive upper urinary tract transitional cell carcinoma (UUT-TCC). (ox.ac.uk)
  • degradation
  • Phosphorylated by PRKCZ, which may prevent MutS alpha degradation by the ubiquitin-proteasome pathway. (waw.pl)
  • amino acid
  • Computational protein design algorithms seek to identify novel amino acid sequences that are low in energy when folded to the pre-specified target structure. (wikipedia.org)
  • recognizes
  • MutS alpha recognizes single base mismatches and dinucleotide insertion-deletion loops (IDL) in the DNA. (uniprot.org)
  • sequences
  • While the sequence-conformation space that needs to be searched is large, the most challenging requirement for computational protein design is a fast, yet accurate, energy function that can distinguish optimal sequences from similar suboptimal ones. (wikipedia.org)
  • These techniques involve alignment of target protein sequences with other related protein sequences. (wikipedia.org)
  • Multiple sequence alignment utilizes data bases such as PREFAB, SABMARK, OXBENCH, IRMBASE, and BALIBASE in order to cross reference target protein sequences with known sequences. (wikipedia.org)
  • deletion loops
  • This dimer repairs longer insertion/deletion loops than MutSα. (wikipedia.org)
  • MutSα is responsible for base-base mispairs and short insertion/deletion loops, while MutSβ reapirs long insertion/deletion loops in DNA. (wikipedia.org)
  • While both proteins have redundant function in base-base repairs, MutSα typically effects base-base mispair repairs and also performs repairs on the more common short inertion/deletion loops. (wikipedia.org)
  • MutSβ can compensate somewhat for loss of base-base mispair correction functions, but is not suited for repairing many short, 1-2 base pair insertion/deletion loops. (wikipedia.org)
  • sequence
  • Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed. (uniprot.org)
  • They were the first to perform "exomic sequencing", meaning determination of the sequence of every protein-encoding gene in the human genome. (wikipedia.org)
  • The 4 'core' histones (H2A, H2B, H3 and H4) are relatively similar in structure and are highly conserved through evolution, all featuring a 'helix turn helix turn helix' motif (DNA-binding protein motif that recognize specific DNA sequence). (wikipedia.org)
  • Without structural information about a protein, sequence analysis is often useful in elucidating information about the protein. (wikipedia.org)
  • interactions
  • In the case of endonucleases such as EcoRV, BamHI, and PvuII, this nonspecific binding involves electrostatic interactions between minimal surface area of the protein and the DNA. (wikipedia.org)
  • complexes
  • Crossing over and DNA repair are very similar processes, which utilize many of the same protein complexes. (wikipedia.org)
  • A drastic shift in the relative levels of these protein complexes can lead to diminished capacity for MMR. (wikipedia.org)
  • chromatin
  • Using a murine model of inflammation-induced tumorigenesis, we tested the hypothesis that inflammation promotes recruitment of epigenetic proteins to chromatin, initiating methylation and gene silencing in tumors. (aacrjournals.org)
  • They are the chief protein components of chromatin, acting as spools around which DNA winds, and playing a role in gene regulation. (wikipedia.org)
  • evolutionarily
  • It down-regulates BCL6 (B-cell lymphoma 6) protein [ 8 ], which is an evolutionarily conserved zinc finger transcription factor that contains an N-terminal POZ/BTB domain. (biomedcentral.com)
  • nicks
  • Recent work has shown that nicks are sites for RFC-dependent loading of the replication sliding clamp PCNA, in an orientation-specific manner, such that one face of the donut-shape protein is juxtaposed toward the 3'-OH end at the nick. (wikipedia.org)
  • Upon activation by the MutS-DNA complex, MutH nicks the daughter strand near the hemimethylated site. (wikipedia.org)
  • polymerase
  • Detection methods for microsatellite instability include polymerase chain reaction (PCR) and immunohistochemical (IHC) methods, polymerase chain checking the DNA and immunohistochemical surveying mismatch repair protein levels. (wikipedia.org)
  • The single-strand gap created by the exonuclease can then be repaired by DNA Polymerase III (assisted by single-strand-binding protein), which uses the other strand as a template, and finally sealed by DNA ligase. (wikipedia.org)
  • replication
  • One mechanism of DNA damage recognition has been elucidated recently, in which binding of replication protein A (RPA) to single-stranded DNA (ssDNA) results in recruitment of the ATR-interacting protein ATRIP to load the ATR/ATRIP complex to ssDNA, leading to activation of ATR ( 4 ). (pnas.org)
  • Proliferating cell nuclear antigen (PCNA) is a protein involved in post-replication MMR. (wikipedia.org)
  • Bound PCNA then localizes the MutSβ complex to replication foci, indicating that PCNA assists in initiating repair by guiding MutSβ and other repair proteins to free termini in recently replicated DNA. (wikipedia.org)
  • form
  • Duchenne Muscular Dystrophy (DMD) is an X-linked genetic disorder that results in the production of a dysfunctional form of the protein, dystrophin. (nih.gov)
  • yeast
  • Genetic work from yeast has established the current conceptual framework of DNA damage response ( 2 ). (pnas.org)
  • recombinase
  • We also report that the frequency of genetic repair of the mdx mutation can be enhanced if RNAi is used to suppress expression of the recombinase inhibitor protein Msh2 in cultures containing myoblasts but not in those heavily enriched in myoblasts. (nih.gov)
  • One such particular protein complex that is conserved between processes is RAD51, a well conserved recombinase protein that has been shown to be crucial in DNA repair as well as cross over. (wikipedia.org)
  • alterations
  • Loss of MutS homolog 2 (MSH2), a mismatch repair (MMR) protein, abrogated early inflammation-induced epigenetic alterations and DNA hypermethylation alterations observed in inflammation-induced tumors. (aacrjournals.org)
  • These results indicate that early epigenetic alterations initiated by inflammation and MMR proteins lead to gene silencing during tumorigenesis, revealing a novel mechanism of epigenetic alterations in inflammation-driven cancer. (aacrjournals.org)
  • tumors
  • In contrast, γδ-T cells bearing the Vδ2 gene with the co-expression of the Vγ9 chain (Vγ9Vδ2-T cells) are abundant in the peripheral blood and lymphoid organs of most healthy individuals, and they are involved in the first line of the immune responses to mycobacteria, Epstein-Barr virus (EBV), and some solid tumors ( 1 , 2 , 4 - 10 ). (frontiersin.org)