Understanding structural relationships proteins of unsolved three‐dimensional structure

摘要: The locations of functionally important sequences and general structural motifs have been assigned to Ile-tRNA synthetase. However, a function has not established for some segments the protein (e.g., CP1). method modeling described here cannot establish details 3 A crystal structure, and, in contrast precision model varies according extent sequence similarity or functional importance region. In synthetase, signature flanking regions are likely be similar structure proteins on which is based. For other regions, it may possible build three-dimensional by connecting well defined refining positions elements energy minimization. Structural modelling this kind must done cautiously, because order orientation motif can change subtle ways. case Tyr-tRNA beta-strand nearest N-terminus outermost strand nucleotide binding fold; Met-tRNA same innermost. Furthermore, antiparallel (Tyr-tRNA synthetase) parallel (Met-tRNA synthetase). Because multiple structures that differ their orientations possible, analogies between should naively extrapolated without independent experimental support. As above, tolerate internal deletions insertions. This provides further support practice allowing gaps computer-generated alignments. Nevertheless, more tolerant insertions than others, significance region broken alignment assessed carefully. All alignments treated equally, each evaluated within its own context. synthetases known analogy used identify elements. example, amino acid site synthetase might formed, at least part, peptide encompasses Ala50; aligns with Gly94 an example results unknown (Ile-tRNA synthetases) lead identification potential substrate