scholarly journals Protein crystal lattices are dynamic assemblies: the role of conformational entropy in the protein condensed phase

IUCrJ ◽  
2018 ◽  
Vol 5 (2) ◽  
pp. 130-140 ◽  
Author(s):  
Margarita Dimova ◽  
Yancho D. Devedjiev
Keyword(s):  
Condensed Phase ◽  
Protein Structures ◽  
Van Der Waals Interactions ◽  
Protein Crystal ◽  
Crystal Formation ◽  
Conformational Entropy ◽  
Crystal Lattices ◽  
Crystal Contacts ◽  
First Time

Until recently, the occurrence of conformational entropy in protein crystal contacts was considered to be a very unlikely event. A study based on the most accurately refined protein structures demonstrated that side-chain conformational entropy and static disorder might be common in protein crystal lattices. The present investigation uses structures refined using ensemble refinement to show that although paradoxical, conformational entropy is likely to be the major factor in the emergence and integrity of the protein condensed phase. This study reveals that the role of shape entropy and local entropic forces expands beyond the onset of crystallization. For the first time, the complete pattern of intermolecular interactions by protein atoms in crystal lattices is presented, which shows that van der Waals interactions dominate in crystal formation.

scholarly journals The role of flexibility and molecular shape in the crystallization of proteins by surface mutagenesis

2015 ◽  
Vol 71 (2) ◽  
pp. 157-162 ◽  
Author(s):  
Yancho D. Devedjiev
Keyword(s):  
Protein Crystallization ◽  
Protein Structures ◽  
Physicochemical Characteristics ◽  
Molecular Shape ◽  
Side Chain ◽  
Static Disorder ◽  
Relative Contribution ◽  
Crystal Contacts ◽  
Essential Prerequisite

Proteins are dynamic systems and interact with their environment. The analysis of crystal contacts in the most accurately determined protein structures (d< 1.5 Å) reveals that in contrast to current views, static disorder and high side-chain entropy are common in the crystal contact area. These observations challenge the validity of the theory that presumes that the occurrence of well ordered patches of side chains at the surface is an essential prerequisite for a successful crystallization event. The present paper provides evidence in support of the approach for understanding protein crystallization as a process dependent on multiple factors, each with its relative contribution, rather than a phenomenon driven by a few dominant physicochemical characteristics. The role of the molecular shape as a factor in the crystallization of proteins by surface mutagenesis is discussed.

Stabilisation of Aragonite: The Role of Mg2+ and Other Impurity Ions

2019 ◽  
Author(s):  
Matthew Boon ◽  
William Rickard ◽  
Andrew Rohl ◽  
Franca Jones
Keyword(s):  
Electron Backscatter Diffraction ◽  
Crystal Formation ◽  
Sulfate Ions ◽  
Inorganic Systems ◽  
Sodium Magnesium ◽  
Stable Product ◽  
The Stability ◽  
Backscatter Diffraction ◽  
First Time

Aragonite formation and stabilisation in seawater is still an area of active investigation since the thermodynamically stable product at room temperature is calcite. In this manuscript, purely inorganic systems that were found to stabilise aragonite were analysed by various techniques. Dynamic Light Scattering was used to characterise the nucleation behaviour of the system and it was found that the presence of magnesium ions during crystal formation inhibits nucleation overall, not just calcite nucleation. In addition, it was found that sulfate is not necessary to stabilise aragonite. Microanalysis by energy dispersive X-ray spectroscopy (EDS) and electron backscatter diffraction (EBSD) revealed that the aragonite that was formed had a disordered core with, sodium, magnesium and sulfate ions incorporated into the structure. To the best of the authors’ knowledge this is the first time an ACC core in aragonite has been visualised in a completely abiotic, synthetic system (in the absence of organic molecules). Inclusion of these impurities into the structure may explain the stability of aragonite in natural seawaters.

scholarly journals Controlling Protein Crystallization by Free Energy Guided Design of Interactions at Crystal Contacts

Crystals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 588
Author(s):  
Johannes Hermann ◽  
Daniel Bischoff ◽  
Phillip Grob ◽  
Robert Janowski ◽  
Dariusch Hekmat ◽  
...  
Keyword(s):  
Free Energy ◽  
Protein Interactions ◽  
Computational Study ◽  
Protein Crystallization ◽  
Lactobacillus Brevis ◽  
Protein Crystal ◽  
Crystal Formation ◽  
Contact Stability ◽  
Crystal Contacts ◽  
Energy Simulations

Protein crystallization can function as an effective method for protein purification or formulation. Such an application requires a comprehensive understanding of the intermolecular protein–protein interactions that drive and stabilize protein crystal formation to ensure a reproducible process. Using alcohol dehydrogenase from Lactobacillus brevis (LbADH) as a model system, we probed in our combined experimental and computational study the effect of residue substitutions at the protein crystal contacts on the crystallizability and the contact stability. Increased or decreased contact stability was calculated using molecular dynamics (MD) free energy simulations and showed excellent qualitative correlation with experimentally determined increased or decreased crystallizability. The MD simulations allowed us to trace back the changes to their physical origins at the atomic level. Engineered charge–charge interactions as well as engineered hydrophobic effects could be characterized and were found to improve crystallizability. For example, the simulations revealed a redesigning of a water mediated electrostatic interaction (“wet contact”) into a water depleted hydrophobic effect (“dry contact”) and the optimization of a weak hydrogen bonding contact towards a strong one. These findings explained the experimentally found improved crystallizability. Our study emphasizes that it is difficult to derive simple rules for engineering crystallizability but that free energy simulations could be a very useful tool for understanding the contribution of crystal contacts for stability and furthermore could help guide protein engineering strategies to enhance crystallization for technical purposes.

scholarly journals Berkeley Screen: a set of 96 solutions for general macromolecular crystallization

2017 ◽  
Vol 50 (5) ◽  
pp. 1352-1358 ◽  
Author(s):  
Jose H. Pereira ◽  
Ryan P. McAndrew ◽  
Giovani P. Tomaleri ◽  
Paul D. Adams
Keyword(s):  
Crystal Packing ◽  
Protein Structures ◽  
Data Bank ◽  
Protein Crystal ◽  
Crystal Formation ◽  
Density Maps ◽  
Crystallization Experiments ◽  
Particular Solution ◽  
Crystallization Conditions ◽  
Macromolecular Crystallization

Using statistical analysis of the Biological Macromolecular Crystallization Database, combined with previous knowledge about crystallization reagents, a crystallization screen called the Berkeley Screen has been created. Correlating crystallization conditions and high-resolution protein structures, it is possible to better understand the influence that a particular solution has on protein crystal formation. Ions and small molecules such as buffers and precipitants used in crystallization experiments were identified in electron density maps, highlighting the role of these chemicals in protein crystal packing. The Berkeley Screen has been extensively used to crystallize target proteins from the Joint BioEnergy Institute and the Collaborative Crystallography program at the Berkeley Center for Structural Biology, contributing to several Protein Data Bank entries and related publications. The Berkeley Screen provides the crystallographic community with an efficient set of solutions for general macromolecular crystallization trials, offering a valuable alternative to the existing commercially available screens.

scholarly journals Crystallization of lysozyme with (R)-, (S)- and (RS)-2-methyl-2,4-pentanediol

2015 ◽  
Vol 71 (3) ◽  
pp. 427-441 ◽  
Author(s):  
Mark Stauber ◽  
Jean Jakoncic ◽  
Jacob Berger ◽  
Jerome M. Karp ◽  
Ariel Axelbaum ◽  
...  
Keyword(s):  
Small Molecule ◽  
Protein Crystallization ◽  
Protein Structures ◽  
Preferential Interaction ◽  
Crystal Contacts ◽  
Chiral Interactions

Chiral control of crystallization has ample precedent in the small-molecule world, but relatively little is known about the role of chirality in protein crystallization. In this study, lysozyme was crystallized in the presence of the chiral additive 2-methyl-2,4-pentanediol (MPD) separately using theRandSenantiomers as well as with a racemicRSmixture. Crystals grown with (R)-MPD had the most order and produced the highest resolution protein structures. This result is consistent with the observation that in the crystals grown with (R)-MPD and (RS)-MPD the crystal contacts are made by (R)-MPD, demonstrating that there is preferential interaction between lysozyme and this enantiomer. These findings suggest that chiral interactions are important in protein crystallization.

Stabilisation of Aragonite: The Role of Mg2+ and Other Impurity Ions

2019 ◽  
Author(s):  
Matthew Boon ◽  
William Rickard ◽  
Andrew Rohl ◽  
Franca Jones
Keyword(s):  
Electron Backscatter Diffraction ◽  
Crystal Formation ◽  
Sulfate Ions ◽  
Inorganic Systems ◽  
Sodium Magnesium ◽  
Stable Product ◽  
The Stability ◽  
Backscatter Diffraction ◽  
First Time

Aragonite formation and stabilisation in seawater is still an area of active investigation since the thermodynamically stable product at room temperature is calcite. In this manuscript, purely inorganic systems that were found to stabilise aragonite were analysed by various techniques. Dynamic Light Scattering was used to characterise the nucleation behaviour of the system and it was found that the presence of magnesium ions during crystal formation inhibits nucleation overall, not just calcite nucleation. In addition, it was found that sulfate is not necessary to stabilise aragonite. Microanalysis by energy dispersive X-ray spectroscopy (EDS) and electron backscatter diffraction (EBSD) revealed that the aragonite that was formed had a disordered core with, sodium, magnesium and sulfate ions incorporated into the structure. To the best of the authors’ knowledge this is the first time an ACC core in aragonite has been visualised in a completely abiotic, synthetic system (in the absence of organic molecules). Inclusion of these impurities into the structure may explain the stability of aragonite in natural seawaters.

Psychological Resilience Provides No Independent Protection From Suicidal Risk

Crisis ◽  
2016 ◽  
Vol 37 (2) ◽  
pp. 130-139 ◽  
Author(s):  
Danica W. Y. Liu ◽  
A. Kate Fairweather-Schmidt ◽  
Richard Burns ◽  
Rachel M. Roberts ◽  
Kaarin J. Anstey
Keyword(s):  
Risk Factors ◽  
Well Being ◽  
Current Status ◽  
Psychological Resilience ◽  
Cross Sectional ◽  
Life Project ◽  
Resilience Factors ◽  
First Time

Abstract. Background: Little is known about the role of resilience in the likelihood of suicidal ideation (SI) over time. Aims: We examined the association between resilience and SI in a young-adult cohort over 4 years. Our objectives were to determine whether resilience was associated with SI at follow-up or, conversely, whether SI was associated with lowered resilience at follow-up. Method: Participants were selected from the Personality and Total Health (PATH) Through Life Project from Canberra and Queanbeyan, Australia, aged 28–32 years at the first time point and 32–36 at the second. Multinomial, linear, and binary regression analyses explored the association between resilience and SI over two time points. Models were adjusted for suicidality risk factors. Results: While unadjusted analyses identified associations between resilience and SI, these effects were fully explained by the inclusion of other suicidality risk factors. Conclusion: Despite strong cross-sectional associations, resilience and SI appear to be unrelated in a longitudinal context, once risk/resilience factors are controlled for. As independent indicators of psychological well-being, suicidality and resilience are essential if current status is to be captured. However, the addition of other factors (e.g., support, mastery) makes this association tenuous. Consequently, resilience per se may not be protective of SI.

Characteristics Of The Structure Formation Of Gypsum Binder Modified With Zinc Hydrosilicates

2020 ◽  
pp. 40-46
Keyword(s):  
Synergistic Effect ◽  
Physicochemical Properties ◽  
Structure Formation ◽  
Silicic Acid ◽  
Chemical Properties ◽  
Crystal Formation ◽  
Ability To Act ◽  
Chemical Factors ◽  
Sorption Characteristics

The authors' methodic for assessing the role of chemical and physic-chemical factors during the structure formation of gypsum stone is presented in the article. The methodic is also makes it possible to reveal the synergistic effect and to determine the ranges of variation of controls factors that ensure maximum values of such effect. The effect of a micro-sized modifier based on zinc hydro-silicates on the structure formation of building gypsum is analyzed and corresponding dependencies are found. It is shown that effects of influence of modifier on the properties of gypsum compositions are determined by chemical properties of modifier. Among the mentioned properties are sorption characteristics (which depend on the amount of silicic acid and its state) and physicochemical properties - the ability to act as a substrate during crystal formation. The proposed method can also be extended to other binding substances and materials. This article contributes to the understanding of the processes that occur during the structure formation of composites, which will make it possible to control the structure formation in the future, obtaining materials with a given set of properties.

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