Results 71 to 80 of about 7,767,567 (301)

Improving prediction performance of general protein language model by domain-adaptive pretraining on DNA-binding protein

Nature Communications
DNA-protein interactions exert the fundamental structure of many pivotal biological processes, such as DNA replication, transcription, and gene regulation. However, accurate and efficient computational methods for identifying these interactions are still
Wenwu Zeng, Yutao Dou, Liangrui Pan, Liwen Xu, Shaoliang Peng   +4 more
doaj   +1 more source

Telomere DNA recognition in Saccharomycotina yeast: potential lessons for the co-evolution of ssDNA and dsDNA-binding proteins and their target sites

Frontiers in Genetics, 2015
In principle, alterations in the telomere repeat sequence would be expected to disrupt the protective nucleoprotein complexes that confer stability to chromosome ends, and hence relatively rare events in evolution.
Neal F. Lue, Olga eSteinberg-Neifach, Olga eSteinberg-Neifach   +2 more
doaj   +1 more source

e2g: an interactive web-based server for efficiently mapping large EST and cDNA sets to genomic sequences [PDF]

, 2004
Krüger J, Sczyrba A, Kurtz S, Giegerich R. e2g: an interactive web-based server for efficiently mapping large EST and cDNA sets to genomic sequences. NUCLEIC ACIDS RESEARCH.
Krüger, Jan, Sczyrba, Alexander ; https://orcid.org/, Giegerich, Robert, Kurtz, Stefan   +3 more
core   +1 more source

The Shewanella oneidensis Fic enzyme SoFic targets the switch‐I region of EF‐Tu for AMPylation

FEBS Letters, EarlyView.
Fic enzymes mediate diverse post‐translational modifications across all domains of life, including AMPylation. Prokaryotic EF‐Tu can be AMPylated and deAMPylated by the conserved Fic enzyme SoFic. Structural and biochemical approaches were used to characterize the effect of AMPylation on EF‐Tu, SoFic's enzymatic activities, and the enzyme‐target ...
Svenja Runge, Vivian Pogenberg, Alexander Baumgart, Bente Siebels, Hartmut Schlüter, Michael Hecht‐Bucher, Aymelt Itzen   +6 more
wiley   +1 more source

Why similar protein sequences encode similar three-dimensional structures? [PDF]

, 2010
Evolutionarily related proteins have similar sequences. Such similarity is called homology and can be described using substitution matrices such as Blosum 60.
Zielenkiewicz, Piotr, Kaczanowski, Szymon   +1 more
core   +1 more source

Isolation of Potato Genes That Are Induced During an Early Stage of the Hypersensitive Response to Phytophthora infestans

Molecular Plant-Microbe Interactions, 1999
Suppression subtractive hybridization (SSH) was used to generate a cDNA library enriched for sequences induced in a late-blight-resistant potato cultivar undergoing the hypersensitive response (HR).
Paul R. J. Birch, Anna O. Avrova, James M. Duncan, Gary D. Lyon, Rachel L. Toth   +4 more
doaj   +1 more source

MCALIGN: Stochastic Alignment of Noncoding DNA Sequences Based on an Evolutionary Model of Sequence Evolution [PDF]

, 2004
A method is described for performing global alignment of noncoding DNA sequences based on an evolutionary model parameterized by the frequency distribution of lengths of insertion/deletion events (indels) and their rate relative to nucleotide ...
Johnson, Toby, Keightley, Peter, Toby Johnson, Peter D. Keightley   +3 more
core   +1 more source

L‐aspartate oxidase provides new insights into fumarate reduction in anaerobic darkness in Synechocystis sp. PCC6803

FEBS Letters, EarlyView.
Synechocystis strains deficient in succinate dehydrogenase (SDH) secrete more succinate than the WT under dark anaerobic conditions, supporting that SDH then primarily acts as SDH, not as a fumarate reductase. L‐aspartate oxidase (Laspo) from Synechocystis is functional under anaerobic conditions, reducing fumarate to succinate.
Kateryna Kukil, Jeffrey A. Hawkes, Cecilia Blikstad, Pia Lindberg   +3 more
wiley   +1 more source

Modeling structure-function relationships in synthetic DNA sequences using attribute grammars [PDF]

, 2009
Recognizing that certain biological functions can be associated with specific DNA sequences has led various fields of biology to adopt the notion of the genetic part.
Cai, Yizhi; id_orcid, Peccoud, Jean, Cai Yizhi, Cai, Yizhi, Lux, Matthew W, Adam Laura, Lux Matthew W., Matthew W. Lux, Matthew W Lux, Jean Peccoud, Laura Adam, Adam, Laura, Yizhi Cai, Peccoud Jean, Lux, Matthew W.   +14 more
core   +1 more source

RNA‐related functions of BRCA2 in transcription, replication, and genome stability

FEBS Letters, EarlyView.
Beyond its role in homologous recombination, BRCA2 regulates R‐loop homeostasis, DNA–RNA hybrid resolution, RNA polymerase II dynamics, and transcriptional activation. Disruption of any of these functions can contribute to genome instability, inflammatory signaling, and tumorigenesis. BRCA2 is a central tumor suppressor protein best known for its roles
Lucia Alvaro‐Aranda, Sreerama Chaitanya Sridhara, Aura Carreira   +2 more
wiley   +1 more source