Performance of phased rotation, conformation and translation function: accurate protein model building with tripeptidic and tetrapeptidic fragments

Abstract

The automatic building of protein structures with tripeptidic and tetrapeptidic fragments was investigated. The oligopeptidic conformers were positioned in the electron-density map by a phased rotation, conformation and translation function and refined by a real-space refinement. The number of successfully located fragments lay within the interval 75-95% depending on the resolution and phase quality. The overlaps of partially located fragments were analyzed. The correctly positioned fragments were connected into chains. Chains formed in this way were extended directly into the electron density and a sequence was assigned. In the initial stage of the model building the number of located fragments was between 60% and 95%, but this number could be increased by several cycles of reciprocal-space refinement and automatic model rebuilding. A nearly complete structure can be obtained on the condition that the resolution is reasonable. Computer graphics will only be needed for a final check and small corrections.

Aggregation-Induced Emission: Together We Shine, United We Soar!

“…The conformation change of a protein is closely relevant to its activity and some physiological events, and the monitoring of conformational transitions of proteins is thereby of great significance to research regarding proteomics and pharmaceutics, etc. Specifically, protein folding and unfolding are pretty important to its secretion, membrane-bound, and cellular functions. − Study of conformation transitions of proteins is an interesting and important topic because it can provide mechanistic insights into the folding and unfolding processes of biopolymers. Despite that intermediate states have been suspected to be involved in the unfolding and refolding processes, they can hardly be detected due to the complexity of these processes as well as lack of appropriate probes.…”

Application of constrained real-space refinement of flexible molecular fragments to automatic model building of RNA structures

“…Input reflection files have been changed to better exploit the CCP4 program system and to be more compatible with the local density modification program (Pavelcik, 2012). This aspect is important also for the process called 'REFMAC recycling' (Pavelčík & Vá clavík, 2010). In favorable conditions during the model building, one can try to locate a few missing residues in a new electron density map [based on FWT/PHWT coefficients produced by the program REFMAC (Murshudov et al, 1997) or a difference map (DELFWT, PHDELFWT)].…”

“…structures: program HEL2. The connecting algorithm of the HEL program (Pavelcik, 2006b) has been improved (Pavelčík & Vá clavík, 2010) and divided into several separate steps: (i) preliminary connectivity sorting of input peaks; (ii) calculation of the distance matrix of virtual bonds and fragment overlaps; (iii) connecting well overlapped fragments into smaller chains called seeds; (iv) extending seeds.…”

“…Each fragment is refined independently of other fragments in the local electron density. An overlap (or lack of overlap) of refined fragments can detect building errors (Pavelčík & Vá clavík, 2010). This refinement, in general, considerably increases the accuracy and reliability of the model building.…”

Design and Application of Anthracene Derivative with Aggregation-Induced Emission Charateristics for Visualization and Monitoring of Erythropoietin Unfolding

“…Protein folding and unfolding are strategically important to secreted, membrane-bound, and cellular function . It is well-known that studies for the conformation change of the protein are widely applied in functional studies of proteins, which significantly promote the understanding of the mystery of life, and developments in the field of clinical diagnostics. , The conformation studies also promote understanding the role of dynamics in the function of proteins, involving motion of key residues or large-scale domain movements, which take place within the context of protein folding and unfolding. A transition between folded and unfolded structures is also required for function of some proteins .…”