Faculty Opinions recommendation of Chemically accurate protein structures: validation of protein NMR structures by comparison of measured and predicted pKa values.

2006 ◽  
Author(s):  
Thorsten Dieckmann
Keyword(s):  
Protein Nmr ◽  
Protein Structures ◽  
Pka Values ◽  
Nmr Structures

scholarly journals A method for validating the accuracy of NMR protein structures

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Nicholas J. Fowler ◽  
Adnan Sljoka ◽  
Mike P. Williamson
Keyword(s):  
Secondary Structure ◽  
Crystal Structures ◽  
Protein Structures ◽  
Random Coil ◽  
Local Rigidity ◽  
Correlation Score ◽  
Nmr Structures ◽  
Explicit Solvent ◽  
Structure Ensemble ◽  
Better Than

AbstractWe present a method that measures the accuracy of NMR protein structures. It compares random coil index [RCI] against local rigidity predicted by mathematical rigidity theory, calculated from NMR structures [FIRST], using a correlation score (which assesses secondary structure), and an RMSD score (which measures overall rigidity). We test its performance using: structures refined in explicit solvent, which are much better than unrefined structures; decoy structures generated for 89 NMR structures; and conventional predictors of accuracy such as number of restraints per residue, restraint violations, energy of structure, ensemble RMSD, Ramachandran distribution, and clashscore. Restraint violations and RMSD are poor measures of accuracy. Comparisons of NMR to crystal structures show that secondary structure is equally accurate, but crystal structures are typically too rigid in loops, whereas NMR structures are typically too floppy overall. We show that the method is a useful addition to existing measures of accuracy.

PRE‐driven protein NMR structures: an alternative approach in highly paramagnetic systems

FEBS Journal ◽  
2020 ◽  
Author(s):  
Inês B. Trindade ◽  
Michele Invernici ◽  
Francesca Cantini ◽  
Ricardo O. Louro ◽  
Mario Piccioli
Keyword(s):  
Protein Nmr ◽  
Nmr Structures ◽  
Alternative Approach

scholarly journals Role of backbone strain in de novo design of complex α/β protein structures

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Nobuyasu Koga ◽  
Rie Koga ◽  
Gaohua Liu ◽  
Javier Castellanos ◽  
Gaetano T. Montelione ◽  
...  
Keyword(s):  
De Novo ◽  
Protein Structures ◽  
De Novo Design ◽  
Structure Packing ◽  
Nmr Structures ◽  
Β Protein ◽  
Wide Range ◽  
Explicit Consideration ◽  
Non Local

AbstractWe previously elucidated principles for designing ideal proteins with completely consistent local and non-local interactions which have enabled the design of a wide range of new αβ-proteins with four or fewer β-strands. The principles relate local backbone structures to supersecondary-structure packing arrangements of α-helices and β-strands. Here, we test the generality of the principles by employing them to design larger proteins with five- and six- stranded β-sheets flanked by α-helices. The initial designs were monomeric in solution with high thermal stability, and the nuclear magnetic resonance (NMR) structure of one was close to the design model, but for two others the order of strands in the β-sheet was swapped. Investigation into the origins of this strand swapping suggested that the global structures of the design models were more strained than the NMR structures. We incorporated explicit consideration of global backbone strain into the design methodology, and succeeded in designing proteins with the intended unswapped strand arrangements. These results illustrate the value of experimental structure determination in guiding improvement of de novo design, and the importance of consistency between local, supersecondary, and global tertiary interactions in determining protein topology. The augmented set of principles should inform the design of larger functional proteins.

scholarly journals Prion protein NMR structures of cats, dogs, pigs, and sheep

2005 ◽  
Vol 102 (3) ◽  
pp. 640-645 ◽  
Author(s):  
D. A. Lysek ◽  
C. Schorn ◽  
L. G. Nivon ◽  
V. Esteve-Moya ◽  
B. Christen ◽  
...  
Keyword(s):  
Prion Protein ◽  
Protein Nmr ◽  
Nmr Structures

scholarly journals Control over overall shape and size in de novo designed proteins

2015 ◽  
Vol 112 (40) ◽  
pp. E5478-E5485 ◽  
Author(s):  
Yu-Ru Lin ◽  
Nobuyasu Koga ◽  
Rie Tatsumi-Koga ◽  
Gaohua Liu ◽  
Amanda F. Clouser ◽  
...  
Keyword(s):  
Secondary Structure ◽  
De Novo ◽  
Protein Structures ◽  
Nmr Structures ◽  
Designed Proteins ◽  
Custom Design ◽  
Fine Control ◽  
Rule Set ◽  
Protein Shape ◽  
Shape And Size

We recently described general principles for designing ideal protein structures stabilized by completely consistent local and nonlocal interactions. The principles relate secondary structure patterns to tertiary packing motifs and enable design of different protein topologies. To achieve fine control over protein shape and size within a particular topology, we have extended the design rules by systematically analyzing the codependencies between the lengths and packing geometry of successive secondary structure elements and the backbone torsion angles of the loop linking them. We demonstrate the control afforded by the resulting extended rule set by designing a series of proteins with the same fold but considerable variation in secondary structure length, loop geometry, β-strand registry, and overall shape. Solution NMR structures of four designed proteins for two different folds show that protein shape and size can be precisely controlled within a given protein fold. These extended design principles provide the foundation for custom design of protein structures performing desired functions.

scholarly journals 1P084 NOESY-HSQC simulation on accuracy o protein NMR structures

2004 ◽  
Vol 44 (supplement) ◽  
pp. S50
Author(s):  
T. Ikeya ◽  
Y. Ito ◽  
K. Shimizu ◽  
T. Noguchi
Keyword(s):  
Protein Nmr ◽  
Nmr Structures
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