TY  - JOUR
A1  - Trautwein, Matthias
A1  - Fredriksson, Kai
A1  - Möller, Heiko Michael
A1  - Exner, Thomas E.
T1  - Automated assignment of NMR chemical shifts based on a known structure and 4D spectra
JF  - Journal of biomolecular NMR
N2  - Apart from their central role during 3D structure determination of proteins the backbone chemical shift assignment is the basis for a number of applications, like chemical shift perturbation mapping and studies on the dynamics of proteins. This assignment is not a trivial task even if a 3D protein structure is known and needs almost as much effort as the assignment for structure prediction if performed manually. We present here a new algorithm based solely on 4D [H-1, N-15]-HSQC-NOESY-[H-1, N-15]-HSQC spectra which is able to assign a large percentage of chemical shifts (73-82 %) unambiguously, demonstrated with proteins up to a size of 250 residues. For the remaining residues, a small number of possible assignments is filtered out. This is done by comparing distances in the 3D structure to restraints obtained from the peak volumes in the 4D spectrum. Using dead-end elimination, assignments are removed in which at least one of the restraints is violated. Including additional information from chemical shift predictions, a complete unambiguous assignment was obtained for Ubiquitin and 95 % of the residues were correctly assigned in the 251 residue-long N-terminal domain of enzyme I. The program including source code is available at https://github.com/thomasexner/4Dassign.
KW  - Chemical shift assignment
KW  - Protein
KW  - 3D structure
KW  - 4D NOESY
Y1  - 2016
U6  - https://doi.org/10.1007/s10858-016-0050-0
SN  - 0925-2738
SN  - 1573-5001
VL  - 65
SP  - 217
EP  - 236
PB  - Springer
CY  - Dordrecht
ER  - 
TY  - JOUR
A1  - Schudoma, Christian
A1  - Larhlimi, Abdelhalim
A1  - Walther, Dirk
T1  - The influence of the local sequence environment on RNA loop structures
JF  - RNA : a publication of the RNA Society
N2  - RNA folding is assumed to be a hierarchical process. The secondary structure of an RNA molecule, signified by base-pairing and stacking interactions between the paired bases, is formed first. Subsequently, the RNA molecule adopts an energetically favorable three-dimensional conformation in the structural space determined mainly by the rotational degrees of freedom associated with the backbone of regions of unpaired nucleotides (loops). To what extent the backbone conformation of RNA loops also results from interactions within the local sequence context or rather follows global optimization constraints alone has not been addressed yet. Because the majority of base stacking interactions are exerted locally, a critical influence of local sequence on local structure appears plausible. Thus, local loop structure ought to be predictable, at least in part, from the local sequence context alone. To test this hypothesis, we used Random Forests on a nonredundant data set of unpaired nucleotides extracted from 97 X-ray structures from the Protein Data Bank (PDB) to predict discrete backbone angle conformations given by the discretized eta/theta-pseudo-torsional space. Predictions on balanced sets with four to six conformational classes using local sequence information yielded average accuracies of up to 55%, thus significantly better than expected by chance (17%-25%). Bases close to the central nucleotide appear to be most tightly linked to its conformation. Our results suggest that RNA loop structure does not only depend on long-range base-pairing interactions; instead, it appears that local sequence context exerts a significant influence on the formation of the local loop structure.
KW  - RNA
KW  - 3D structure
KW  - structure prediction
KW  - Random Forests
KW  - machine learning
KW  - backbone conformation
Y1  - 2011
U6  - https://doi.org/10.1261/rna.2550211
SN  - 1355-8382
VL  - 17
IS  - 7
SP  - 1247
EP  - 1257
PB  - Cold Spring Harbor Laboratory Press
CY  - Cold Spring Harbor, NY
ER  -