Theoretically, crystals with supercells exist at a unique crossroads where they can be considered as either a large unit cell with closely spaced reflections in reciprocal space or a higher dimensional superspace with a modulation that is commensurate with the supercell. In the latter case, the structure would be defined as an average structure with functions representing a modulation to determine the atomic location in 3D space. Here, a model protein structure and simulated diffraction data were used to investigate the possibility of solving a real incommensurately modulated protein crystal using a supercell approximation. In this way, the answer was known and the refinement method could be tested. Firstly, an average structure was solved by using the `main' reflections, which represent the subset of the reflections that belong to the subcell and in general are more intense than the `satellite' reflections. The average structure was then expanded to create a supercell and refined using all of the reflections. Surprisingly, the refined solution did not match the expected solution, even though the statistics were excellent. Interestingly, the corresponding superspace group had multiple 3D daughter supercell space groups as possibilities, and it was one of the alternate daughter space groups that the refinement locked in on. The lessons learned here will be applied to a real incommensurately modulated profilin-actin crystal that has the same superspace group.
- MeSH
- Actins chemistry MeSH
- Protein Conformation MeSH
- Crystallography, X-Ray methods MeSH
- Models, Molecular MeSH
- Profilins chemistry MeSH
- Publication type
- Journal Article MeSH
Three-dimensional structure models refined using low-resolution data from crystallographic or electron cryo-microscopy experiments can benefit from high-quality restraints derived from quantum-chemical methods. However, nonperiodic atom-centered quantum-chemistry codes do not inherently account for nearest-neighbor interactions of crystallographic symmetry-related copies in a satisfactory way. Here, these nearest-neighbor effects have been included in the model by expanding to a super-cell and then truncating the super-cell to only include residues from neighboring cells that are interacting with the asymmetric unit. In this way, the fragmentation approach can adequately and efficiently include nearest-neighbor effects. It has previously been shown that a moderately sized X-ray structure can be treated using quantum methods if a fragmentation approach is applied. In this study, a target protein (PDB entry 4gif) was partitioned into a number of large fragments. The use of large fragments (typically hundreds of atoms) is tractable when a GPU-based package such as TeraChem is employed or cheaper (semi-empirical) methods are used. The QM calculations were run at the HF-D3/6-31G level. The models refined using a recently developed semi-empirical method (GFN2-xTB) were compared and contrasted. To validate the refinement procedure for a non-P1 structure, a standard set of crystallographic metrics were used. The robustness of the implementation is shown by refining 13 additional protein models across multiple space groups and a summary of the refinement metrics is presented.
The paper reports the structure of the small laccase from Streptomyces coelicolor determined from a crystal soaked with potassium hexacyanoferrate [K4Fe(CN)6]. The decolorization of the natively blue crystal observed upon soaking indicates the reduction of the enzyme in the crystal. The ligand binds between laccase molecules and stabilizes the crystal. The increased diffraction limit of the diffraction data collected from this crystal enabled the refinement of the small laccase structure at 2.3 Å resolution, which is the highest resolution obtained to date.
- MeSH
- Bacterial Proteins chemistry MeSH
- Color MeSH
- Ferricyanides chemistry MeSH
- Protein Conformation MeSH
- Crystallography, X-Ray MeSH
- Laccase chemistry MeSH
- Copper chemistry MeSH
- Models, Molecular MeSH
- Molecular Sequence Data MeSH
- Enzyme Stability MeSH
- Streptomyces coelicolor enzymology MeSH
- Binding Sites MeSH
- Iron chemistry MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
... Contents -- Protein Structure -- Part 1 Basic Structural Principles -- 1. ... ... Motifs of Protein Structure -- Few general principles emerged from the first protein structure -- The ... ... -- Topology diagrams are useful for classification of protein structures -- Secondary structure elements ... ... 72 -- The hemagglutinin polypeptide chain folds into a complex structure 72 -- The subunit structure ... ... is necessary for prediction of tertiary structure 251 -- Prediction methods for secondary structure ...
xv, 302 stran : ilustrace ; 28 cm
- Conspectus
- Biochemie. Molekulární biologie. Biofyzika
- NML Fields
- biochemie
- molekulární biologie, molekulární medicína
In general, the structural requirements postulated for a high brassinolide activity are: 2alpha,3alpha-diol, 6-ketone or better 7-oxalactone in B-ring, A/B trans fused ring junction, a cis C-22,C-23-diol preferentially with RR configurations, and a C-24 methyl or ethyl substituent [Takatsuto S, Yazawa N, Ikekawa N, Takematsu T, Takeuchi Y, Koguchi M. Structure-activity relationship of brassinosteroids. Phytochemistry 1983;22:2437-41; Thompson MJ, Meudt WJ, Mandava NB, Dutky SR, Lusby WR, Spaulding DW. Synthesis of brassinosteroids and relationship of structure to plant growth-promoting effects. Steroids 1982;39:89-105]. We found that the 3alpha,4alpha-diols 4, 6 and 8 are more active than the 2alpha,3alpha-diols 3, 5 and 7 [Sisa M, Budesinsky M, Kohout L. Synthesis of 7a-homo and 7a,7b-dihomo-5alpha-cholestane analogues of brassinolide. Collect Czech Chem Commun 2003;68:2171-89]. This fact is in strong contrast with the structure requirements mentioned above. Our hypothesis suggests that the lower activity of 2alpha,3alpha-diols and/or the higher activity of 3alpha,4alpha-diols could be explained by twisting and distortion of the molecule due to the seven- or eight-membered B-ring and also by the position of a carbonyl group relative to the A-ring diol. 3D-SAR computer methodologies as alignments and overlaps of GRID maps and 3D-QSAR analysis GRID-GOLPE (CoMFA-like) were used as an effort to explain the higher bioactivity of 3alpha,4alpha-diols 4, 6 and 8 in comparison with the 2alpha,3alpha-diols 3, 5 and 7 of B-ring enlarged brassinosteroids.
- MeSH
- Principal Component Analysis MeSH
- Biological Assay methods MeSH
- Cholestanols chemistry metabolism MeSH
- Fabaceae metabolism MeSH
- Least-Squares Analysis MeSH
- Molecular Conformation MeSH
- Models, Molecular MeSH
- Polycyclic Compounds chemistry metabolism MeSH
- Steroids, Heterocyclic chemistry metabolism metabolism MeSH
- Structure-Activity Relationship MeSH
Malaria is a disease caused by protozoan parasites of the genus Plasmodium that affects millions of people worldwide. In recent years there have been parasite resistances to several drugs, including the first-line antimalarial treatment. With the aim of proposing new drugs candidates for the treatment of disease, Quantitative Structure⁻Activity Relationship (QSAR) methodology was applied to 83 N-myristoyltransferase inhibitors, synthesized by Leatherbarrow et al. The QSAR models were developed using 63 compounds, the training set, and externally validated using 20 compounds, the test set. Ten different alignments for the two test sets were tested and the models were generated by the technique that combines genetic algorithms and partial least squares. The best model shows r² = 0.757, q²adjusted = 0.634, R²pred = 0.746, R²m = 0.716, ∆R²m = 0.133, R²p = 0.609, and R²r = 0.110. This work suggested a good correlation with the experimental results and allows the design of new potent N-myristoyltransferase inhibitors.
- MeSH
- Acyltransferases antagonists & inhibitors MeSH
- Algorithms MeSH
- Antimalarials chemistry pharmacology MeSH
- Quantitative Structure-Activity Relationship MeSH
- Drug Resistance drug effects MeSH
- Humans MeSH
- Least-Squares Analysis MeSH
- Models, Molecular MeSH
- Plasmodium drug effects enzymology MeSH
- Protozoan Proteins antagonists & inhibitors MeSH
- Drug Design MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
