About: Sequential nearest-neighbor effects on computed (13)C(α) chemical shifts

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An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Sequential nearest-neighbor effects on computed (13)C(α) chemical shifts
Creator	Serrano, Pedro Scheraga, Harold Vila, Jorge Wü, Kurt
Source	Medline; PMC
abstract	To evaluate sequential nearest-neighbor effects on quantum-chemical calculations of (13)C(α) chemical shifts, we selected the structure of the nucleic acid binding (NAB) protein from the SARS coronavirus determined by NMR in solution (PDB id 2K87). NAB is a 116-residue α/β protein, which contains 9 prolines and has 50% of its residues located in loops and turns. Overall, the results presented here show that sizeable nearest-neighbor effects are seen only for residues preceding proline, where Pro introduces an overestimation, on average, of 1.73 ppm in the computed (13)C(α) chemical shifts. A new ensemble of 20 conformers representing the NMR structure of the NAB, which was calculated with an input containing backbone torsion angle constraints derived from the theoretical (13)C(α) chemical shifts as supplementary data to the NOE distance constraints, exhibits very similar topology and comparable agreement with the NOE constraints as the published NMR structure. However, the two structures differ in the patterns of differences between observed and computed (13)C(α) chemical shifts, Δ(ca,i), for the individual residues along the sequence. This indicates that the Δ(ca,i) -values for the NAB protein are primarily a consequence of the limited sampling by the bundles of 20 conformers used, as in common practice, to represent the two NMR structures, rather than of local flaws in the structures.
has issue date	2010-07-20(xsd:dateTime)
bibo:doi	10.1007/s10858-010-9435-7
bibo:pmid	20644980
has license	no-cc
sha1sum (hex)	9817617c341787c1babe5f992ce8cc295164bb1b
schema:url	https://doi.org/10.1007/s10858-010-9435-7
resource representing a document's title	Sequential nearest-neighbor effects on computed (13)C(α) chemical shifts
has PubMed Central identifier	PMC2970923
has PubMed identifier	20644980
schema:publication	J Biomol NMR
resource representing a document's body	covid:9817617c341787c1babe5f992ce8cc295164bb1b#body_text
is schema:about of	named entity 'EFFECTS' named entity 'nearest-neighbor' named entity 'SARS coronavirus' named entity 'located' named entity 'chemical shifts' named entity 'protein' named entity 'COMPUTED' named entity 'OVERALL' named entity 'PRO' named entity 'RATHER' named entity 'TURNS' named entity '50%' named entity 'SAMPLING' named entity 'INTRODUCES' named entity 'INDIVIDUAL' named entity 'NEW' named entity 'CONTAINING' named entity 'ITS' named entity 'PUBLISHED' named entity 'STRUCTURE' named entity 'TORSION' named entity 'NEAREST' named entity 'NOE' named entity 'QUANTUM' named entity 'HERE' named entity 'PRECEDING' named entity 'NAB' named entity 'CHEMICAL' named entity 'LOCAL' named entity 'DERIVED' named entity 'NMR' named entity 'ANGLE' named entity 'LOCATED IN' named entity 'EFFECTS' named entity 'PROTEIN ' named entity 'SEQUENTIAL' named entity 'NEIGHBOR' named entity 'SHIFTS' named entity 'INPUT' named entity 'SEEN' named entity 'CALCULATED' named entity 'AGREEMENT' named entity 'SIMILAR' named entity 'PRESENTED' named entity 'RESULTS' named entity 'BACKBONE' named entity 'COMMON' named entity 'SELECTED' named entity 'COMPUTED' named entity 'DETERMINED BY' named entity 'CHEMICAL' named entity 'STRUCTURES' named entity 'SUPPLEMENTARY DATA' named entity 'RESIDUE' named entity '116' named entity 'PRACTICE' named entity 'IS A' named entity 'SARS CORONAVIRUS' named entity '2FB' named entity 'NEAREST' named entity 'CONSEQUENCE OF' named entity 'SOLUTION' named entity 'VALUES' named entity 'USED' named entity 'WHERE' named entity 'TOPOLOGY' named entity 'SEQUENTIAL' named entity 'PPM' named entity 'DISTANCE' named entity 'PROLINE' named entity 'NEIGHBOR' named entity 'REPRESENT' named entity 'EXHIBITS' named entity 'NUCLEIC ACID BINDING' named entity 'OBSERVED' named entity 'LIMITED' named entity 'SHIFTS' named entity 'LOOPS'

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