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Redetermined structure of ?-dl-me-thio-nine at 105?K: an example of the importance of freely refining the positions of the amino-group H atoms.

ABSTRACT: Diffraction data were taken from the contribution named '?-dl-Me-thio-nine at 105 K' by Alagar et al. [Acta Cryst. (2005 ?). E61, o1165-o1167]. Refinement of the coordinates of the three amino H atoms, previously constrained to an idealized geometry, shows that the amino group is in fact rotated 13.5° from the perfectly staggered orientation. This apparently modest change has a profound impact on the calculated hydrogen-bond geometries.

SUBMITTER: Gorbitz CH

PROVIDER: S-EPMC4257275 | biostudies-literature | 2014 Nov

REPOSITORIES: biostudies-literature

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Redetermined structure of β-dl-me-thio-nine at 105 K: an example of the importance of freely refining the positions of the amino-group H atoms.

Görbitz Carl Henrik CH

Acta crystallographica. Section E, Structure reports online 20141015 Pt 11

Diffraction data were taken from the contribution named 'β-dl-Me-thio-nine at 105 K' by Alagar et al. [Acta Cryst. (2005 ▶). E61, o1165-o1167]. Refinement of the coordinates of the three amino H atoms, previously constrained to an idealized geometry, shows that the amino group is in fact rotated 13.5° from the perfectly staggered orientation. This apparently modest change has a profound impact on the calculated hydrogen-bond geometries. ...[more]

PMID: 25484740

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Project description:Understanding of solid-to-solid phase transition mechanisms in polymorphic systems is of critical importance for rigorous control over polymorph purity in the pharmaceutical industry to achieve the desired bioavailability and efficacy of drugs. Ubiquitous defects in crystals may play an important role in the pathways of phase transitions. However, such effects remain poorly understood. Here, the effects of crystal defects on the solid-to-solid phase transformations between dl-me-thio-nine polymorphs α and β are investigated by means of experimental and computational approaches. Thermal analyses of polycrystalline powders show two endothermic peaks in the α-to-β phase transition (and two exothermic peaks for the reverse transition), in contrast with one thermal event observed for single crystals. Variable-temperature 1D and 2D Raman spectra, as well as powder X-ray diffraction patterns, reveal the appearance of two peaks that can attributed to a two-step phase transition, and the extent of the second-step phase transition increases with milling time (or defect density). Quantification of transition kinetics unveils a remarkably higher energy barrier in the second-step phase transition than in the first, proceeding by the cooperative molecular motion pathway. The good linear fitting on the kinetic data by the Jeziorny model suggests that the second-step transition follows the nucleation and growth mechanism. Molecular dynamics simulations were also conducted to understand the role of crystal defects in the solid-state phase transition by tracking the atomic distribution and hydrogen bond lifetime during the transition. It was found that the increasing defect density hinders the propagation of cooperative molecular motion, leading to a combined transition mechanism involving both cooperative motion and nucleation and growth. This study highlights the significant impact of crystal defects on solid-state phase transitions, and the two-step transition mechanism postulated may be universal given the ubiquitous presence of defects in crystalline materials.

Project description:BackgroundThe number of available structures of large multi-protein assemblies is quite small. Such structures provide phenomenal insights on the organization, mechanism of formation and functional properties of the assembly. Hence detailed analysis of such structures is highly rewarding. However, the common problem in such analyses is the low resolution of these structures. In the recent times a number of attempts that combine low resolution cryo-EM data with higher resolution structures determined using X-ray analysis or NMR or generated using comparative modeling have been reported. Even in such attempts the best result one arrives at is the very course idea about the assembly structure in terms of trace of the C(alpha) atoms which are modeled with modest accuracy.Methodology/principal findingsIn this paper first we present an objective approach to identify potentially solvent exposed and buried residues solely from the position of C(alpha) atoms and amino acid sequence using residue type-dependent thresholds for accessible surface areas of C(alpha). We extend the method further to recognize potential protein-protein interface residues. CONCLUSION/ SIGNIFICANCE: Our approach to identify buried and exposed residues solely from the positions of C(alpha) atoms resulted in an accuracy of 84%, sensitivity of 83-89% and specificity of 67-94% while recognition of interfacial residues corresponded to an accuracy of 94%, sensitivity of 70-96% and specificity of 58-94%. Interestingly, detailed analysis of cases of mismatch between recognition of interface residues from C(alpha) positions and all-atom models suggested that, recognition of interfacial residues using C(alpha) atoms only correspond better with intuitive notion of what is an interfacial residue. Our method should be useful in the objective analysis of structures of protein assemblies when positions of only (alpha) positions are available as, for example, in the cases of integration of cryo-EM data and high resolution structures of the components of the assembly.

Dataset Information

Redetermined structure of ?-dl-me-thio-nine at 105?K: an example of the importance of freely refining the positions of the amino-group H atoms.

Publications

Redetermined structure of β-dl-me-thio-nine at 105 K: an example of the importance of freely refining the positions of the amino-group H atoms.

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