scholarly journals Erratum to: Bridging themes: short protein segments found in different architectures

2021 ◽  
Author(s):  
Rachel Kolodny ◽  
Sergey Nepomnyachiy ◽  
Dan S Tawfik ◽  
Nir Ben-Tal
Keyword(s):  
Short Protein

Comparing short protein substructures by a method based on backbone torsion angles

1989 ◽  
Vol 6 (2) ◽  
pp. 155-167 ◽  
Author(s):  
Mary E. Karpen ◽  
Pieter L. de Haseth ◽  
Kenneth E. Neet
Keyword(s):  
Torsion Angles ◽  
Short Protein

scholarly journals SLiMFinder: a web server to find novel, significantly over-represented, short protein motifs

2010 ◽  
Vol 38 (Web Server) ◽  
pp. W534-W539 ◽  
Author(s):  
N. E. Davey ◽  
N. J. Haslam ◽  
D. C. Shields ◽  
R. J. Edwards
Keyword(s):  
Web Server ◽  
Protein Motifs ◽  
Short Protein

scholarly journals Indexing schemes for similarity search in datasets of short protein fragments

2007 ◽  
Vol 32 (8) ◽  
pp. 1145-1165 ◽  
Author(s):  
Aleksandar Stojmirović ◽  
Vladimir Pestov
Keyword(s):  
Similarity Search ◽  
Protein Fragments ◽  
Short Protein

Neuroimmunoregulatory properties of short protein fragments in rats subjected to immobilization stress

1987 ◽  
Vol 104 (2) ◽  
pp. 1095-1096
Author(s):  
V. Kluša ◽  
R. Muceniece ◽  
S. Svirskis ◽  
G. Zalitis ◽  
I. Liepa ◽  
...  
Keyword(s):  
Immobilization Stress ◽  
Protein Fragments ◽  
Short Protein

scholarly journals Thousands of protein linear motif classes may still be undiscovered

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0248841
Author(s):  
Denys Bulavka ◽  
Ariel A. Aptekmann ◽  
Nicolás A. Méndez ◽  
Teresa Krick ◽  
Ignacio E. Sánchez
Keyword(s):  
Amino Acid ◽  
Protein Interactions ◽  
Amino Acid Sequences ◽  
Linear Motif ◽  
Motif Length ◽  
Naturally Occurring ◽  
Motif Position ◽  
Linear Motifs ◽  
Short Protein ◽  
Amino Acid Alphabet

Linear motifs are short protein subsequences that mediate protein interactions. Hundreds of motif classes including thousands of motif instances are known. Our theory estimates how many motif classes remain undiscovered. As commonly done, we describe motif classes as regular expressions specifying motif length and the allowed amino acids at each motif position. We measure motif specificity for a pair of motif classes by quantifying how many motif-discriminating positions prevent a protein subsequence from matching the two classes at once. We derive theorems for the maximal number of motif classes that can simultaneously maintain a certain number of motif-discriminating positions between all pairs of classes in the motif universe, for a given amino acid alphabet. We also calculate the fraction of all protein subsequences that would belong to a motif class if all potential motif classes came into existence. Naturally occurring pairs of motif classes present most often a single motif-discriminating position. This mild specificity maximizes the potential number of coexisting motif classes, the expansion of the motif universe due to amino acid modifications and the fraction of amino acid sequences that code for a motif instance. As a result, thousands of linear motif classes may remain undiscovered.

scholarly journals Evolutionary Characterization of the Short Protein SPAAR

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1864
Author(s):  
Jiwon Lee ◽  
Aaron Wacholder ◽  
Anne-Ruxandra Carvunis
Keyword(s):  
Muscle Regeneration ◽  
Evolutionary Dynamics ◽  
De Novo ◽  
Sequence Divergence ◽  
Biological Processes ◽  
Noncoding Sequence ◽  
Homology Detection ◽  
Evolutionary Innovation ◽  
Short Protein

Microproteins (<100 amino acids) are receiving increasing recognition as important participants in numerous biological processes, but their evolutionary dynamics are poorly understood. SPAAR is a recently discovered microprotein that regulates muscle regeneration and angiogenesis through interactions with conserved signaling pathways. Interestingly, SPAAR does not belong to any known protein family and has known homologs exclusively among placental mammals. This lack of distant homology could be caused by challenges in homology detection of short sequences, or it could indicate a recent de novo emergence from a noncoding sequence. By integrating syntenic alignments and homology searches, we identify SPAAR orthologs in marsupials and monotremes, establishing that SPAAR has existed at least since the emergence of mammals. SPAAR shows substantial primary sequence divergence but retains a conserved protein structure. In primates, we infer two independent evolutionary events leading to the de novo origination of 5′ elongated isoforms of SPAAR from a noncoding sequence and find evidence of adaptive evolution in this extended region. Thus, SPAAR may be of ancient origin, but it appears to be experiencing continual evolutionary innovation in mammals.

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