scholarly journals Learning conjunctive concepts in structural domains

1989 ◽  
Vol 4 (1) ◽  
pp. 7-40 ◽  
Author(s):  
David Haussler
Keyword(s):  
Structural Domains ◽  
Conjunctive Concepts

scholarly journals Structural Domains of Human Apolipoprotein B-100

1989 ◽  
Vol 264 (24) ◽  
pp. 14369-14375 ◽  
Author(s):  
G C Chen ◽  
S Zhu ◽  
D A Hardman ◽  
J W Schilling ◽  
K Lau ◽  
...  
Keyword(s):  
Apolipoprotein B ◽  
Structural Domains ◽  
Human Apolipoprotein

scholarly journals Functional Roles of Bromodomain Proteins in Cancer

Cancers ◽  
2021 ◽  
Vol 13 (14) ◽  
pp. 3606
Author(s):  
Samuel P. Boyson ◽  
Cong Gao ◽  
Kathleen Quinn ◽  
Joseph Boyd ◽  
Hana Paculova ◽  
...  
Keyword(s):  
Open Chromatin ◽  
Structural Domains ◽  
Pharmacological Agents ◽  
Functional Roles ◽  
Cellular Processes ◽  
Protein Interactome ◽  
Interaction Partners ◽  
Recent Developments ◽  
Bromodomain Proteins ◽  
Chromatin Configuration

Histone acetylation is generally associated with an open chromatin configuration that facilitates many cellular processes including gene transcription, DNA repair, and DNA replication. Aberrant levels of histone lysine acetylation are associated with the development of cancer. Bromodomains represent a family of structurally well-characterized effector domains that recognize acetylated lysines in chromatin. As part of their fundamental reader activity, bromodomain-containing proteins play versatile roles in epigenetic regulation, and additional functional modules are often present in the same protein, or through the assembly of larger enzymatic complexes. Dysregulated gene expression, chromosomal translocations, and/or mutations in bromodomain-containing proteins have been correlated with poor patient outcomes in cancer. Thus, bromodomains have emerged as a highly tractable class of epigenetic targets due to their well-defined structural domains, and the increasing ease of designing or screening for molecules that modulate the reading process. Recent developments in pharmacological agents that target specific bromodomains has helped to understand the diverse mechanisms that bromodomains play with their interaction partners in a variety of chromatin processes, and provide the promise of applying bromodomain inhibitors into the clinical field of cancer treatment. In this review, we explore the expression and protein interactome profiles of bromodomain-containing proteins and discuss them in terms of functional groups. Furthermore, we highlight our current understanding of the roles of bromodomain-containing proteins in cancer, as well as emerging strategies to specifically target bromodomains, including combination therapies using bromodomain inhibitors alongside traditional therapeutic approaches designed to re-program tumorigenesis and metastasis.

scholarly journals Sequence analysis of phospholamban. Identification of phosphorylation sites and two major structural domains.

1986 ◽  
Vol 261 (28) ◽  
pp. 13333-13341 ◽  
Author(s):  
H K Simmerman ◽  
J H Collins ◽  
J L Theibert ◽  
A D Wegener ◽  
L R Jones
Keyword(s):  
Sequence Analysis ◽  
Phosphorylation Sites ◽  
Structural Domains

Likelihood Models of Somatic Mutation and Codon Substitution in Cancer Genes

Genetics ◽  
2003 ◽  
Vol 165 (2) ◽  
pp. 695-705 ◽  
Author(s):  
Ziheng Yang ◽  
Simon Ro ◽  
Bruce Rannala
Keyword(s):  
Amino Acid ◽  
Gene Mutation ◽  
Somatic Mutation ◽  
Mutation Rates ◽  
Functional Domains ◽  
Cancer Gene ◽  
Structural Domains ◽  
Specific Amino Acid ◽  
Silent Substitution ◽  
Codon Substitution

Abstract The role of somatic mutation in cancer is well established and several genes have been identified that are frequent targets. This has enabled large-scale screening studies of the spectrum of somatic mutations in cancers of particular organs. Cancer gene mutation databases compile the results of many studies and can provide insight into the importance of specific amino acid sequences and functional domains in cancer, as well as elucidate aspects of the mutation process. Past studies of the spectrum of cancer mutations (in particular genes) have examined overall frequencies of mutation (at specific nucleotides) and of missense, nonsense, and silent substitution (at specific codons) both in the sequence as a whole and in a specific functional domain. Existing methods ignore features of the genetic code that allow some codons to mutate to missense, or stop, codons more readily than others (i.e., by one nucleotide change, vs. two or three). A new codon-based method to estimate the relative rate of substitution (fixation of a somatic mutation in a cancer cell lineage) of nonsense vs. missense mutations in different functional domains and in different tumor tissues is presented. Models that account for several potential influences on rates of somatic mutation and substitution in cancer progenitor cells and allow biases of mutation rates for particular dinucleotide sequences (CGs and dipyrimidines), transition vs. transversion bias, and variable rates of silent substitution across functional domains (useful in detecting investigator sampling bias) are considered. Likelihood-ratio tests are used to choose among models, using cancer gene mutation data. The method is applied to analyze published data on the spectrum of p53 mutations in cancers. A novel finding is that the ratio of the probability of nonsense to missense substitution is much lower in the DNA-binding and transactivation domains (ratios near 1) than in structural domains such as the linker, tetramerization (oligomerization), and proline-rich domains (ratios exceeding 100 in some tissues), implying that the specific amino acid sequence may be less critical in structural domains (e.g., amino acid changes less often lead to cancer). The transition vs. transversion bias and effect of CpG dinucleotides on mutation rates in p53 varied greatly across cancers of different organs, likely reflecting effects of different endogenous and exogenous factors influencing mutation in specific organs.

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