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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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Secondary structure for the CLD(B) domain from CDPK3 based on COMPASS assignments.Red bars represent the calculated SSP score [17] for each residue and gray areas indicate values from the submitted secondary structure file, in this case based on the crystal structure of a larger fragment of the protein [33]. Positive and negative values represent α-helix and β-strand propensity, respectively.
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pcbi-1004022-g007: Secondary structure for the CLD(B) domain from CDPK3 based on COMPASS assignments.Red bars represent the calculated SSP score [17] for each residue and gray areas indicate values from the submitted secondary structure file, in this case based on the crystal structure of a larger fragment of the protein [33]. Positive and negative values represent α-helix and β-strand propensity, respectively.

Mentions: Knowledge of protein secondary structure is both valuable on its own, and can be a very useful aid in the assignment process and for validation of resonance assignments. Since the secondary structure can be accurately predicted if backbone chemical shifts are known, it is recalculated and displayed as soon as a new fragment has been assigned using the SSP algorithm [17]. The SSP score for a residue ranges from approximately −1 for a fully developed β-strand to approximately 1 for a fully developed α-helix. It is calculated by weighted averaging over five residues so that also the chemical shifts of two residues prior to and after the analyzed residue are taken into account, which results in smoothening. The SSP scores are plotted against residue number in the GUI. If the expected secondary structure is provided, it is possible to highlight it in the SSP graph. The calculated secondary structure may be exported as an image as shown in Fig. 7.


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)

Secondary structure for the CLD(B) domain from CDPK3 based on COMPASS assignments.Red bars represent the calculated SSP score [17] for each residue and gray areas indicate values from the submitted secondary structure file, in this case based on the crystal structure of a larger fragment of the protein [33]. Positive and negative values represent α-helix and β-strand propensity, respectively.
© Copyright Policy
Related In: Results  -  Collection

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

pcbi-1004022-g007: Secondary structure for the CLD(B) domain from CDPK3 based on COMPASS assignments.Red bars represent the calculated SSP score [17] for each residue and gray areas indicate values from the submitted secondary structure file, in this case based on the crystal structure of a larger fragment of the protein [33]. Positive and negative values represent α-helix and β-strand propensity, respectively.
Mentions: Knowledge of protein secondary structure is both valuable on its own, and can be a very useful aid in the assignment process and for validation of resonance assignments. Since the secondary structure can be accurately predicted if backbone chemical shifts are known, it is recalculated and displayed as soon as a new fragment has been assigned using the SSP algorithm [17]. The SSP score for a residue ranges from approximately −1 for a fully developed β-strand to approximately 1 for a fully developed α-helix. It is calculated by weighted averaging over five residues so that also the chemical shifts of two residues prior to and after the analyzed residue are taken into account, which results in smoothening. The SSP scores are plotted against residue number in the GUI. If the expected secondary structure is provided, it is possible to highlight it in the SSP graph. The calculated secondary structure may be exported as an image as shown in Fig. 7.

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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