Effect of the sarcosine residue on sequence scrambling in peptide b5ions

2014 ◽  
Vol 49 (2) ◽  
pp. 161-167 ◽  
Author(s):  
Alex G. Harrison
Keyword(s):  
Sequence Scrambling

scholarly journals Genetic variation and recombination in Aichi virus

2012 ◽  
Vol 93 (6) ◽  
pp. 1226-1235 ◽  
Author(s):  
Alexander N. Lukashev ◽  
Jan Felix Drexler ◽  
Ilya S. Belalov ◽  
Monika Eschbach-Bludau ◽  
Sigrid Baumgarte ◽  
...  
Keyword(s):  
Aichi Virus ◽  
Sequence Scrambling ◽  
The Family ◽  
Genetic Features ◽  
Cpg Dinucleotide ◽  
Effective Number Of Codons ◽  
Low Incidence ◽  
High Degree ◽  
Genome Scale ◽  
Very High

Aichi virus (AiV), a member of the genus Kobuvirus in the family Picornaviridae, causes gastroenteritis in humans. It was noted that AiV differs from other picornaviruses in its unusually high C content and a very high degree of genome-ordered RNA secondary structures. However, the genetic variability and mutational restrictions on a full-genome scale have not been studied. In addition to the available five complete AiV genomes, we determined here another five complete coding sequences of AiV sampled in Germany, 2004. Distinctive AiV genetic features included a low incidence of recombination along the genome without obvious hotspots or spared regions and very low rates of synonymous and non-synonymous variation, supporting an absence of AiV serotypes. In addition, the absence of recombination between AiV genotypes A and B suggested the existence of reproductive isolation between taxonomic units below the species level. In contrast to most other picornaviruses, AiV genomes strongly avoided the UpA dinucleotide, while there was no obvious selection against the CpG dinucleotide. AiV genomes also appeared to contain a codon usage bias (CUB) apparent as an effective number of codons of 39.5, which was amongst the most extreme among RNA viruses. A set of sequence scrambling algorithms was developed to determine the origin of CUB in AiV. While in most picornaviruses the genomic dinucleotide content contributed significantly to CUB, in AiV its extreme nucleotide content, i.e. 57 % third codon position C, was the main driving force behind the apparent CUB.

scholarly journals Aromatic interactions with membrane modulate human BK channel activation

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Mahdieh Yazdani ◽  
Guohui Zhang ◽  
Zhiguang Jia ◽  
Jingyi Shi ◽  
Jianmin Cui ◽  
...  
Keyword(s):  
Protein Function ◽  
Bk Channels ◽  
Bk Channel ◽  
Atomistic Simulations ◽  
Allosteric Coupling ◽  
Linker Sequence ◽  
Aromatic Interactions ◽  
Sequence Scrambling ◽  
Nonspecific Interactions ◽  
Potential Complex

Large-conductance potassium (BK) channels are transmembrane (TM) proteins that can be synergistically and independently activated by membrane voltage and intracellular Ca2+. The only covalent connection between the cytosolic Ca2+ sensing domain and the TM pore and voltage sensing domains is a 15-residue ‘C-linker’. To determine the linker’s role in human BK activation, we designed a series of linker sequence scrambling mutants to suppress potential complex interplay of specific interactions with the rest of the protein. The results revealed a surprising sensitivity of BK activation to the linker sequence. Combining atomistic simulations and further mutagenesis experiments, we demonstrated that nonspecific interactions of the linker with membrane alone could directly modulate BK activation. The C-linker thus plays more direct roles in mediating allosteric coupling between BK domains than previously assumed. Our results suggest that covalent linkers could directly modulate TM protein function and should be considered an integral component of the sensing apparatus.

scholarly journals Nonspecific membrane interactions can modulate BK channel activation

2020 ◽  
Author(s):  
Mahdieh Yazdani ◽  
Guohui Zhang ◽  
Zhiguang Jia ◽  
Jingyi Shi ◽  
Jianmin Cui ◽  
...  
Keyword(s):  
Protein Function ◽  
Bk Channels ◽  
Bk Channel ◽  
Atomistic Simulations ◽  
Allosteric Coupling ◽  
Linker Sequence ◽  
Sequence Scrambling ◽  
Intracellular Ca ◽  
Nonspecific Interactions ◽  
Potential Complex

Large-conductance potassium (BK) channels are transmembrane (TM) proteins that can be synergistically and independently activated by membrane voltage and intracellular Ca2+. The only covalent connection between the cytosolic Ca2+ sensing domain and the TM pore and voltage sensing domains is a 15-residue "C-linker". To determine the linker's role in BK activation, we designed a series of linker sequence scrambling mutants to suppress potential complex interplay of specific interactions with the rest of the protein. The results revealed a surprising sensitivity of BK activation to the linker sequence. Combing atomistic simulations and further mutagenesis experiments, we demonstrated that nonspecific interactions of the linker with membrane alone could directly modulate BK activation. The C-linker thus plays more direct roles in mediating allosteric coupling between BK domains than previously assumed. Our results also suggest that covalent linkers could directly modulate TM protein function and should be considered an integral component of the sensing apparatus.

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