Results 31 to 40 of about 1,151,967 (219)

Predicting DNA-binding sites of proteins from amino acid sequence

BMC Bioinformatics, 2006
Background Understanding the molecular details of protein-DNA interactions is critical for deciphering the mechanisms of gene regulation. We present a machine learning approach for the identification of amino acid residues involved in protein-DNA ...
Wu Feihong, Terribilini Michael, Yan Changhui, Jernigan Robert L, Dobbs Drena, Honavar Vasant   +5 more
doaj   +1 more source

Emerging experimental and computational methods for studying redox‐regulated structural transitions

FEBS Letters, EarlyView.
Redox reactions can reshape proteins and alter how they behave in cells, with important consequences for health and disease. This review explores emerging experimental and computational approaches for discovering these redox‐sensitive protein switches, revealing their structural effects, and predicting their behavior, opening new opportunities to ...
Tasneem Rass, Dana Reichmann, Gábor Erdős   +2 more
wiley   +1 more source

Protein sequence alignment with family-specific amino acid similarity matrices

BMC Research Notes, 2011
Background Alignment of amino acid sequences by means of dynamic programming is a cornerstone sequence comparison method. The quality of alignments produced by dynamic programming critically depends on the choice of the alignment scoring function ...
Kuznetsov Igor B
doaj   +1 more source

Structural and biochemical analysis of a B12 superbinder

FEBS Letters, EarlyView.
BtuG proteins are vitamin B12 scavengers in Bacteroides thetaiotaomicron, a dominant human gut bacterium. We present crystal structures of three BtuG homologs bound to cobalamin and its precursor cobinamide, revealing picomolar binding affinities, among the highest known for any natural protein.
Jose M. Martinez Felices, Jacob J. Whittaker, Dirk J. Slotboom, Albert Guskov   +3 more
wiley   +1 more source

Amino acid impact factor. [PDF]

PLoS ONE, 2018
Amino acid mutations in proteins are random and those mutations which are beneficial or neutral survive during the course of evolution. Conservation or co-evolution analyses are performed on the multiple sequence alignment of homologous proteins to ...
C K Sruthi, Meher Prakash
doaj   +1 more source

Structures of mycobacterial 3‐methylcrotonyl‐CoA carboxylase reveal carrier‐domain translocation between catalytic sites

FEBS Letters, EarlyView.
Mycobacterial 3‐methylcrotonyl‐CoA carboxylase uses a mobile biotin‐carrying domain to shuttle a carboxyl group between two catalytic sites, enabling carboxylation of 3‐methylcrotonyl‐CoA during leucine breakdown. Cryo‐electron microscopy captures the carrier at both sites and reveals an inward loop movement that may prevent futile rebinding to the ...
Ajit Yadav, Bogdan I. Florea, Sebastian Geibel   +2 more
wiley   +1 more source

Application of amino acid occurrence for discriminating different folding types of globular proteins

BMC Bioinformatics, 2007
Background Predicting the three-dimensional structure of a protein from its amino acid sequence is a long-standing goal in computational/molecular biology.
Gromiha M Michael, Taguchi Y-h
doaj   +1 more source

From junk to function — How weak selection in eukaryotes builds new parts and drives genomic complexity

FEBS Letters, EarlyView.
How do genomes gain new functional parts? In eukaryotes, which tend to evolve under weak selection, much of the genome is junk. Palazzo and Qiu borrow the logic of Markov chains to show how non‐functional DNA becomes functional through the appearance of intermediate states, which arise due to epistasis, buffering, and biochemical messiness, allowing ...
Alexander F. Palazzo, Yi Qiu
wiley   +1 more source

Perbandingan Sekuens Konsensus Gen Hemaglutinin Virus Avian Influenza Subtipe H5N1 Asal Unggas di Indonesia dengan Subtipe H5N2 dan H5N9

Jurnal Veteriner, 2009
Consensus sequence of hemagglutinin (HA) gene of avian influenza viruses of H5N1 subtype isolatedfrom fowl in Indonesia – hereafter named as H5N1_Indonesia – is compared with that of H5N2 and H5N9viruses.
I Gusti Ngurah Kade Mahardika, I Nyoman Suartha, Ida Bagus Kade Suardana, I Gusti Ayu Yuniati Kencana, I Wayan Teguh Wibawan   +4 more
doaj  

Growth of fatty acid vesicles coupled with amino acid sequences of peptides toward evolvable protocells

Communications Chemistry
Understanding how genetic polymer sequences became coupled with the reproduction of protocellular compartments is a fundamental challenge in the study of the emergence of living systems.
Akiko Baba, Kazuki Yokoyama, Keidai Sato, Shuna Asanuma, Tomoko Kawahata, Ulf Olsson, Daisuke Unabara, Tasuku Hamaguchi, Koji Yonekura, Masayuki Imai   +9 more
doaj   +1 more source