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Fast and accurate resonance assignment of small-to-large proteins by combining automated and manual approaches.

Niklasson M, Ahlner A, Andresen C, Marsh JA, Lundström P - PLoS Comput. Biol. (2015)

Bottom Line: Unfortunately, the manual assignment of residues is tedious and time-consuming, and can represent a significant bottleneck for further characterization.Furthermore, while automated approaches have been developed, they are often limited in their accuracy, particularly for larger proteins.Here, we address this by introducing the software COMPASS, which, by combining automated resonance assignment with manual intervention, is able to achieve accuracy approaching that from manual assignments at greatly accelerated speeds.

View Article: PubMed Central - PubMed

Affiliation: Division of Biomolecular Technology, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden.

ABSTRACT
The process of resonance assignment is fundamental to most NMR studies of protein structure and dynamics. Unfortunately, the manual assignment of residues is tedious and time-consuming, and can represent a significant bottleneck for further characterization. Furthermore, while automated approaches have been developed, they are often limited in their accuracy, particularly for larger proteins. Here, we address this by introducing the software COMPASS, which, by combining automated resonance assignment with manual intervention, is able to achieve accuracy approaching that from manual assignments at greatly accelerated speeds. Moreover, by including the option to compensate for isotope shift effects in deuterated proteins, COMPASS is far more accurate for larger proteins than existing automated methods. COMPASS is an open-source project licensed under GNU General Public License and is available for download from http://www.liu.se/forskning/foass/tidigare-foass/patrik-lundstrom/software?l=en. Source code and binaries for Linux, Mac OS X and Microsoft Windows are available.

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The user interface of the ‘Label’ module.Peak lists are submitted through separate dialogs and for HNCB(i)(i-1) data there is the option to include 13Cα shifts and select which of 13Cα or 13Cβ has negative peak intensity. The deviation boxes are used to tailor the spin system labeling to the studied protein and by iteratively altering these values the overlapping resonances may be more appropriately labeled. The spin system reference box specifies which peak list that will be used as reference for labeling of the spin systems.
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pcbi-1004022-g004: The user interface of the ‘Label’ module.Peak lists are submitted through separate dialogs and for HNCB(i)(i-1) data there is the option to include 13Cα shifts and select which of 13Cα or 13Cβ has negative peak intensity. The deviation boxes are used to tailor the spin system labeling to the studied protein and by iteratively altering these values the overlapping resonances may be more appropriately labeled. The spin system reference box specifies which peak list that will be used as reference for labeling of the spin systems.

Mentions: The ‘Label’ module, Fig. 4, identifies spin systems in unassigned peak lists and labels them with arbitrary indices. The nuclei of two peaks are considered as one spin system if the chemical shifts of 15N and 1HN are equal within a user specified tolerance, termed ‘Deviation’. Using a large tolerance will ensure that all peaks in the spin system are labeled, but may cause overlapped peaks to be incorrectly assigned to the same spin system. If both (i-1) and (i)(i-1) peak lists are present, the peaks in the (i)(i-1) list are matched to the peaks in the (i-1) list to distinguish between sequential or internal correlations.


Fast and accurate resonance assignment of small-to-large proteins by combining automated and manual approaches.

Niklasson M, Ahlner A, Andresen C, Marsh JA, Lundström P - PLoS Comput. Biol. (2015)

The user interface of the ‘Label’ module.Peak lists are submitted through separate dialogs and for HNCB(i)(i-1) data there is the option to include 13Cα shifts and select which of 13Cα or 13Cβ has negative peak intensity. The deviation boxes are used to tailor the spin system labeling to the studied protein and by iteratively altering these values the overlapping resonances may be more appropriately labeled. The spin system reference box specifies which peak list that will be used as reference for labeling of the spin systems.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4288728&req=5

pcbi-1004022-g004: The user interface of the ‘Label’ module.Peak lists are submitted through separate dialogs and for HNCB(i)(i-1) data there is the option to include 13Cα shifts and select which of 13Cα or 13Cβ has negative peak intensity. The deviation boxes are used to tailor the spin system labeling to the studied protein and by iteratively altering these values the overlapping resonances may be more appropriately labeled. The spin system reference box specifies which peak list that will be used as reference for labeling of the spin systems.
Mentions: The ‘Label’ module, Fig. 4, identifies spin systems in unassigned peak lists and labels them with arbitrary indices. The nuclei of two peaks are considered as one spin system if the chemical shifts of 15N and 1HN are equal within a user specified tolerance, termed ‘Deviation’. Using a large tolerance will ensure that all peaks in the spin system are labeled, but may cause overlapped peaks to be incorrectly assigned to the same spin system. If both (i-1) and (i)(i-1) peak lists are present, the peaks in the (i)(i-1) list are matched to the peaks in the (i-1) list to distinguish between sequential or internal correlations.

Bottom Line: Unfortunately, the manual assignment of residues is tedious and time-consuming, and can represent a significant bottleneck for further characterization.Furthermore, while automated approaches have been developed, they are often limited in their accuracy, particularly for larger proteins.Here, we address this by introducing the software COMPASS, which, by combining automated resonance assignment with manual intervention, is able to achieve accuracy approaching that from manual assignments at greatly accelerated speeds.

View Article: PubMed Central - PubMed

Affiliation: Division of Biomolecular Technology, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden.

ABSTRACT
The process of resonance assignment is fundamental to most NMR studies of protein structure and dynamics. Unfortunately, the manual assignment of residues is tedious and time-consuming, and can represent a significant bottleneck for further characterization. Furthermore, while automated approaches have been developed, they are often limited in their accuracy, particularly for larger proteins. Here, we address this by introducing the software COMPASS, which, by combining automated resonance assignment with manual intervention, is able to achieve accuracy approaching that from manual assignments at greatly accelerated speeds. Moreover, by including the option to compensate for isotope shift effects in deuterated proteins, COMPASS is far more accurate for larger proteins than existing automated methods. COMPASS is an open-source project licensed under GNU General Public License and is available for download from http://www.liu.se/forskning/foass/tidigare-foass/patrik-lundstrom/software?l=en. Source code and binaries for Linux, Mac OS X and Microsoft Windows are available.

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