scholarly journals IMAAAGINE: a webserver for searching hypothetical 3D amino acid side chain arrangements in the Protein Data Bank

2013 ◽  
Vol 41 (W1) ◽  
pp. W432-W440 ◽  
Author(s):  
Nurul Nadzirin ◽  
Peter Willett ◽  
Peter J. Artymiuk ◽  
Mohd Firdaus-Raih
Keyword(s):  
Amino Acid ◽  
Protein Data Bank ◽  
Data Bank ◽  
Side Chain ◽  
Amino Acid Side Chain

scholarly journals Characteristics of Interactions at Protein Segments External to Globular Domains in the Protein Data Bank

2018 ◽  
Author(s):  
Kota Kasahara ◽  
Shintaro Minami ◽  
Yasunori Aizawa
Keyword(s):  
Amino Acid ◽  
Protein Data Bank ◽  
Protein Function ◽  
Three Dimensional ◽  
Data Bank ◽  
Side Chain ◽  
Globular Domain ◽  
Amino Acid Residues ◽  
Structural Elements

ABSTRACTThe principle of three-dimensional protein structure formation is a long-standing conundrum in structural biology. A globular domain of a soluble protein is formed by a network of atomic contacts among amino acid residues, but regions external to globular domains, like loop and linker, often do not have intramolecular contacts with globular domains. Although these regions can play key roles for protein function as interfaces for intermolecular interactions, their nature remains unclear. Here, we termed protein segments external to globular domains as floating segments and sought for them in tens of thousands of entries in the Protein Data Bank. As a result, we found that 0.72 % of residues are in floating segments. Regarding secondary structural elements, coil structures are enriched in floating segments, especially for long segments. Interactions with polypeptides and polynucleotides, but not small compounds, are enriched in floating segments. The amino acid preferences of floating segments are similar to those of surface residues, with exceptions; the small side chain amino acids, Gly and Ala, are preferred, and some charged side chains, Arg and His, are disfavored for floating segments compared to surface residues. Our comprehensive characterization of floating segments may provide insights into understanding protein sequence-structure-function relationships.

Amino acid side-chain populations in aqueous and saline solution: Bis-penicillamine enkephalin

Biopolymers ◽  
1992 ◽  
Vol 32 (12) ◽  
pp. 1623-1629 ◽  
Author(s):  
Paul E. Smith ◽  
B. Montgomery Pettitt
Keyword(s):  
Amino Acid ◽  
Saline Solution ◽  
Side Chain ◽  
Amino Acid Side Chain

Effect of charged amino acid side chain length on lateral cross-strand interactions between carboxylate- and guanidinium-containing residues in a β-hairpin

Amino Acids ◽  
2015 ◽  
Vol 47 (5) ◽  
pp. 885-898 ◽  
Author(s):  
Hsiou-Ting Kuo ◽  
Shing-Lung Liu ◽  
Wen-Chieh Chiu ◽  
Chun-Jen Fang ◽  
Hsien-Chen Chang ◽  
...  
Keyword(s):  
Amino Acid ◽  
Chain Length ◽  
Side Chain ◽  
Amino Acid Side Chain ◽  
Side Chain Length

scholarly journals Biosynthesis of Butirosin: Transfer and Deprotection of the Unique Amino Acid Side Chain

2007 ◽  
Vol 14 (4) ◽  
pp. 379-386 ◽  
Author(s):  
Nicholas M. Llewellyn ◽  
Yanyan Li ◽  
Jonathan B. Spencer
Keyword(s):  
Amino Acid ◽  
Side Chain ◽  
Amino Acid Side Chain ◽  
Unique Amino Acid
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