Structures composing protein domains |
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Affiliation: | 1. Department of Physiology, Second Faculty of Medicine, Charles University, Plzenska 221, 150 00 Prague, Czech Republic;2. Laboratory of Cellular Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague, Czech Republic;3. Toxicogenomics Unit, National Institute of Public Health, Srobarova 48, 100 42 Prague, Czech Republic;4. Department of Biochemistry, Charles University, Hlavova 2030, 128 40 Prague, Czech Republic;1. Graduate Program in Biomedical Sciences, Faculty of Allied Health Sciences, Thammasat University, Pathumthani, Thailand;2. Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand |
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Abstract: | This review summarizes available data concerning intradomain structures (IS) such as functionally important amino acid residues, short linear motifs, conserved or disordered regions, peptide repeats, broadly occurring secondary structures or folds, etc. IS form structural features (units or elements) necessary for interactions with proteins or non-peptidic ligands, enzyme reactions and some structural properties of proteins. These features have often been related to a single structural level (e.g. primary structure) mostly requiring certain structural context of other levels (e.g. secondary structures or supersecondary folds) as follows also from some examples reported or demonstrated here. In addition, we deal with some functionally important dynamic properties of IS (e.g. flexibility and different forms of accessibility), and more special dynamic changes of IS during enzyme reactions and allosteric regulation. Selected notes concern also some experimental methods, still more necessary tools of bioinformatic processing and clinically interesting relationships. |
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Keywords: | Catalytic Disordered Fold Intradomain Motif Repeat 3D" },{" #name" :" keyword" ," $" :{" id" :" kwrd0045" }," $$" :[{" #name" :" text" ," $$" :[{" #name" :" underline" ," _" :" t" },{" #name" :" __text__" ," _" :" hree-" },{" #name" :" underline" ," _" :" d" },{" #name" :" __text__" ," _" :" imensional aa" },{" #name" :" keyword" ," $" :{" id" :" kwrd0055" }," $$" :[{" #name" :" text" ," $$" :[{" #name" :" underline" ," _" :" a" },{" #name" :" __text__" ," _" :" mino " },{" #name" :" underline" ," _" :" a" },{" #name" :" __text__" ," _" :" cid residue(s) in peptide CDR" },{" #name" :" keyword" ," $" :{" id" :" kwrd0065" }," $$" :[{" #name" :" text" ," $$" :[{" #name" :" __text__" ," _" :" hypervariable " },{" #name" :" underline" ," _" :" c" },{" #name" :" __text__" ," _" :" omplementarity " },{" #name" :" underline" ," _" :" d" },{" #name" :" __text__" ," _" :" etermining " },{" #name" :" underline" ," _" :" r" },{" #name" :" __text__" ," _" :" egion(s) of IgV FR" },{" #name" :" keyword" ," $" :{" id" :" kwrd0085" }," $$" :[{" #name" :" text" ," $$" :[{" #name" :" underline" ," _" :" f" },{" #name" :" __text__" ," _" :" ramework " },{" #name" :" underline" ," _" :" r" },{" #name" :" __text__" ," _" :" egions of IgV IS" },{" #name" :" keyword" ," $" :{" id" :" kwrd0105" }," $$" :[{" #name" :" text" ," $$" :[{" #name" :" underline" ," _" :" i" },{" #name" :" __text__" ," _" :" ntradomain " },{" #name" :" underline" ," _" :" s" },{" #name" :" __text__" ," _" :" tructure(s) Ig" },{" #name" :" keyword" ," $" :{" id" :" kwrd0115" }," $$" :[{" #name" :" text" ," _" :" immunoglobulin(s) IgV" },{" #name" :" keyword" ," $" :{" id" :" kwrd0125" }," $$" :[{" #name" :" text" ," _" :" variable domain(s) of Ig igvds" },{" #name" :" keyword" ," $" :{" id" :" kwrd0135" }," $$" :[{" #name" :" text" ," _" :" conserved variable Ig domain sequence(s) (derived by conserved domain search of BLAST) MSA" },{" #name" :" keyword" ," $" :{" id" :" kwrd0145" }," $$" :[{" #name" :" text" ," $$" :[{" #name" :" underline" ," _" :" m" },{" #name" :" __text__" ," _" :" ultiple " },{" #name" :" underline" ," _" :" s" },{" #name" :" __text__" ," _" :" equence " },{" #name" :" underline" ," _" :" a" },{" #name" :" __text__" ," _" :" lignment(s) MSA-R" },{" #name" :" keyword" ," $" :{" id" :" kwrd0155" }," $$" :[{" #name" :" text" ," $$" :[{" #name" :" underline" ," _" :" MSA" },{" #name" :" __text__" ," _" :" derived " },{" #name" :" underline" ," _" :" r" },{" #name" :" __text__" ," _" :" ecord(s) PKSI" },{" #name" :" keyword" ," $" :{" id" :" kwrd0165" }," $$" :[{" #name" :" text" ," $$" :[{" #name" :" __text__" ," _" :" peptidic " },{" #name" :" underline" ," _" :" p" },{" #name" :" __text__" ," _" :" rotein " },{" #name" :" underline" ," _" :" k" },{" #name" :" __text__" ," _" :" inase " },{" #name" :" underline" ," _" :" s" },{" #name" :" __text__" ," _" :" ubstrates and " },{" #name" :" underline" ," _" :" i" },{" #name" :" __text__" ," _" :" nhibitors SLM" },{" #name" :" keyword" ," $" :{" id" :" kwrd0175" }," $$" :[{" #name" :" text" ," $$" :[{" #name" :" underline" ," _" :" s" },{" #name" :" __text__" ," _" :" hort " },{" #name" :" underline" ," _" :" l" },{" #name" :" __text__" ," _" :" inear " },{" #name" :" underline" ," _" :" m" },{" #name" :" __text__" ," _" :" otif(s) TCR" },{" #name" :" keyword" ," $" :{" id" :" kwrd0185" }," $$" :[{" #name" :" text" ," _" :" T-cell receptor(s) TR" },{" #name" :" keyword" ," $" :{" id" :" kwrd0195" }," $$" :[{" #name" :" text" ," $$" :[{" #name" :" __text__" ," _" :" protein " },{" #name" :" underline" ," _" :" t" },{" #name" :" __text__" ," _" :" andem " },{" #name" :" underline" ," _" :" r" },{" #name" :" __text__" ," _" :" epeat(s) |
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