scholarly journals High mobility of lattice molecules and defects during the early stage of protein crystallization

Soft Matter ◽  
2020 ◽  
Vol 16 (8) ◽  
pp. 1955-1960 ◽  
Author(s):  
Tomoya Yamazaki ◽  
Alexander E. S. Van Driessche ◽  
Yuki Kimura

Dynamic behavior of defects in lysozyme protein crystals reveals that the lattice molecules are mobile throughout the crystal.

Crystals ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 620 ◽  
Author(s):  
Hévila Brognaro ◽  
Sven Falke ◽  
Celestin Nzanzu Mudogo ◽  
Christian Betzel

Protein phase separation and protein liquid cluster formation have been observed and analysed in protein crystallization experiments and, in recent years, have been reported more frequently, especially in studies related to membraneless organelles and protein cluster formation in cells. A detailed understanding about the phase separation process preceding liquid dense cluster formation will elucidate what has, so far, been poorly understood—despite intracellular crowding and phase separation being very common processes—and will also provide more insights into the early events of in vitro protein crystallization. In this context, the phase separation and crystallization kinetics of concanavalin A were analysed in detail, which applies simultaneous dynamic light scattering and depolarized dynamic light scattering to obtain insights into metastable intermediate states between the soluble phase and the crystalline form. A multi-step mechanism was identified for ConA phase separation, according to the resultant ACF decay, acquired after an increase in the concentration of the crowding agent until a metastable ConA gel intermediate between the soluble and final crystalline phases was observed. The obtained results also revealed that ConA is trapped in a macromolecular network due to short-range intermolecular protein interactions and is unable to transform back into a non-ergodic solution.


2017 ◽  
Vol 41 (3) ◽  
pp. 947-959 ◽  
Author(s):  
Yuji Kaneko ◽  
Colleen Pappas ◽  
Teresita Malapira ◽  
Fernando Ĺ. Vale ◽  
Naoki Tajiri ◽  
...  

Background/Aims: Neuroinflammatory processes have been implicated in the pathophysiology of seizure/epilepsy. High mobility group box 1 (HMGB1), a non-histone DNA binding protein, behaves like an inflammatory cytokine in response to epileptogenic insults. Kainic acid (KA) is an excitotoxic reagent commonly used to induce epilepsy in rodents. However, the molecular mechanism by which KA-induced HMGB1 affords the initiation of epilepsy, especially the role of extracellular HMGB1 in neurotransmitter expression, remains to be elucidated. Methods: Experimental early stage of epilepsy-related hyperexcitability was induced in primary rat neural cells (PRNCs) by KA administration. We measured the localization of HMGB1, cell viability, mitochondrial activity, and expression level of glutamate metabolism-associated enzymes. Results: KA induced the translocation of HMGB1 from nucleus to cytosol, and its release from the neural cells. The translocation is associated with post-translational modifications. An increase in extracellular HMGB1 decreased PRNC cell viability and mitochondrial activity, downregulated expression of glutamate decarboxylase67 (GAD67) and glutamate dehydrogenase (GLUD1/2), and increased intracellular glutamate concentration and major histocompatibility complex II (MHC II) level. Conclusions: That a surge in extracellular HMGB1 approximated seizure initiation suggests a key pathophysiological contribution of HMGB1 to the onset of epilepsy-related hyperexcitability.


2016 ◽  
Vol 21 (1) ◽  
pp. 107-114 ◽  
Author(s):  
Daniel L. Ericson ◽  
Xingyu Yin ◽  
Alexander Scalia ◽  
Yasmin N. Samara ◽  
Richard Stearns ◽  
...  

Crystals ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 78
Author(s):  
Yoshinobu Hashizume ◽  
Koji Inaka ◽  
Naoki Furubayashi ◽  
Masayuki Kamo ◽  
Sachiko Takahashi ◽  
...  

In this paper, we present a summary on how to obtain protein crystals from which better diffraction images can be produced. In particular, we describe, in detail, quality evaluation of the protein sample, the crystallization conditions and methods, flash-cooling protection of the crystal, and crystallization under a microgravity environment. Our approach to protein crystallization relies on a theoretical understanding of the mechanisms of crystal growth. They are useful not only for space experiments, but also for crystallization in the laboratory.


2020 ◽  
Vol 5 (4) ◽  
pp. 2473011420S0008
Author(s):  
Jianying Zhang ◽  
Feng Li ◽  
Kentaro Onishi ◽  
MaCalus V. Hogan ◽  
James HC Wang

Category: Basic Sciences/Biologics; Sports Introduction/Purpose: Tendinopathy is a debilitating tendon disorder that affects millions of Americans and costs billions of healthcare dollars every year. Mechanical overloading is considered to cause the development of tendinopathy, but the underlying molecular mechanisms of tendinopathy remain unclear. High mobility group box-1 (HMGB1), an upstream potent inflammatory mediator, has been identified in high levels in early stage tendinopathy patients [1]. However, whether HMGB1 mediates tendinopathy development due to mechanical overloading is completely unknown. Metformin (Met), a hypoglycemic drug commonly used for the treatment of type II diabetes, has shown to inhibit the activity of HMGB1 via binding the acidic tail of HMGB1 [2]. In this study, we tested the hypothesis that Met prevents mechanical overloading-induced tendinopathy by inhibiting HMGB1. Methods: A total of 24 mice were divided into 4 groups and treated for 24 weeks as follows: Group 1 (Cage) with cage activities; Group 2 (Met) received daily IP injection of metformin (50 mg/kg body weight); Group 3 (ITR) ran on treadmill at 15 meters/min for 3 h/ day, 5 days a week; Group 4 (ITR+Met) ran the same protocol as that of ITR group but with daily IP injection of metformin. Six mice/group were sacrificed at 24 weeks and the Achilles and patellar tendon tissues were harvested. The tendons from the left legs were used for histochemical staining and the right for immunostaining. Results: We found that mechanical overloading induced HMGB1 release into tendon matrix (Fig. 1G, K, O). Metformin inhibited HMGB1 release (Fig. 1H, L, P). ITR induced degenerative tendinopathy as evidenced by the cell morphological changes from elongated shape in normal tendon (Fig. 2A, E, I, M) to round shape (Fig. 2C, G, K, O) and the accumulation of proteoglycans (Fig. 2K, O) in ITR tendon. Metformin injection inhibited ITR effect, which is shown by less round shaped cells and low proteoglycan levels found in metformin injected ITR tendons (Fig. 2D, H, L, P). ITR promoted the expression of chondrogenic markers (collagen II and SOX-9) in tendon (Fig. 3C, G, K, O), and metformin inhibited the expression of chondrogenic makers (Fig. 3D, H, L, P). Conclusion: Our study demonstrated that mechanical overloading induced degenerative changes in mouse tendons characterized by the presence of chondrocyte-like cells, accumulation of proteoglycans, high levels of chondrogenic marker SOX-9 and Collagen II expression. Administration of metformint reduced the degenerative responses in overloaded tendon and blocked the development of tendinopathy. These findings support the notion that mechanical overloading induces tendinopathy development by initiation of tendon inflammation via HMGB1, which leads to eventual tendon degeneration. Thus, metformin, a commonly prescribed and FDA approved drug that specifically inhibits HMGB1, can be used to prevent tendinopathy development due to mechanical overloading placed on the tendon.


1999 ◽  
Vol 55 (12) ◽  
pp. 2037-2038 ◽  
Author(s):  
Jennifer A. Garlitz ◽  
Catherine A. Summers ◽  
Robert A. Flowers ◽  
Gloria E. O. Borgstahl

Ethylammonium nitrate (EAN) is a liquid organic salt that has many potential applications in protein chemistry. Because this solvent has hydrophobic and ionic character as well as the ability to hydrogen bond, it is especially well suited for broad use in protein crystallography. For example, EAN may be used as an additive, a detergent, a precipitating agent or to deliver ligands into protein crystals. A discussion of the crystallization of lysozyme using EAN as a precipitating agent is given here.


2011 ◽  
Vol 45 (1) ◽  
pp. 53-60 ◽  
Author(s):  
Yong Yu ◽  
Xuan Wang ◽  
Dominik Oberthür ◽  
Arne Meyer ◽  
Markus Perbandt ◽  
...  

A new crystallization system is described, which makes it possible to use an evaporation-based microfluidic crystallization technique for protein crystallization. The gas and water permeability of the used polydimethylsiloxane (PDMS) material enables evaporation of the protein solution in the microfluidic device. The rates of evaporation are controlled by the relative humidity conditions, which are adjusted in a precise and stable way by using saturated solutions of different reagents. The protein crystals could nucleate and grow under different relative humidity conditions. Using this method, crystal growth could be improved so that approximately 1 mm-sized lysozyme crystals were obtained more successfully than using standard methods. The largest lysozyme crystal obtained reached 1.57 mm in size. The disadvantage of the good gas permeability in PDMS microfluidic devices becomes an advantage for protein crystallization. The radius distributions of aggregrates in the solutions inside the described microfluidic devices were derived fromin situdynamic light scattering measurements. The experiments showed that the environment inside of the microfluidic device is more stable than that of conventional crystallization techniques. However, the morphological results showed that the protein crystals grown in the microfluidic device could lose their morphological stability. Air bubbles in microfluidic devices play an important role in the evaporation progress. A model was constructed to analyze the relationship of the rates of evaporation and the growth of air bubbles to the relative humidity.


2016 ◽  
Vol 186 ◽  
pp. 187-197 ◽  
Author(s):  
Praveen K. Bommineni ◽  
Sudeep N. Punnathanam

The synthesis of high quality protein crystals is essential for determining their structure. Hence the development of strategies to facilitate the nucleation of protein crystals is of prime importance. Recently, Ghatak and Ghatak [Langmuir 2013, 29, 4373] reported heterogeneous nucleation of protein crystals on nano-wrinkled surfaces. Through a series of experiments on different proteins, they were able to obtain high quality protein crystals even at low protein concentrations and sometimes without the addition of a precipitant. In this study, the mechanism of protein crystal nucleation on nano-wrinkled surfaces is studied through Monte Carlo simulations. The wrinkled surface is modeled by a sinusoidal surface. Free-energy barriers for heterogeneous crystal nucleation on flat and wrinkled surfaces are computed and compared. The study reveals that the enhancement of nucleation is closely related to the two step nucleation process seen during protein crystallization. There is an enhancement of protein concentration near the trough of the sinusoidal surface which aids in nucleation. However, the high curvature at the trough acts as a deterrent to crystal nucleus formation. Hence, significant lowering of the free-energy barrier is seen only if the increase in the protein concentration at the trough is very high.


2008 ◽  
Vol 41 (1) ◽  
pp. 1-7 ◽  
Author(s):  
Chae Un Kim ◽  
Yi-Fan Chen ◽  
Mark W. Tate ◽  
Sol M. Gruner

Crystal cryocooling has been used in X-ray protein crystallography to mitigate radiation damage during diffraction data collection. However, cryocooling typically increases crystal mosaicity and often requires a time-consuming search for cryoprotectants. A recently developed high-pressure cryocooling method reduces crystal damage relative to traditional cryocooling procedures and eases or eliminates the need to screen for cryoprotectants. It has been proposed that the formation of high-density amorphous (HDA) ice within the protein crystal is responsible for the excellent diffraction quality of the high-pressure cryocooled crystals. This paper reports X-ray data that confirm the presence of HDA ice in the high-pressure cryocooled protein crystallization solution and protein crystals analyzed at ambient pressure. Diffuse scattering with a spacing characteristic of HDA ice is seen at low temperatures. This scattering then becomes characteristic successively to low-density amorphous, cubic and hexagonal ice phases as the temperature is gradually raised from 80 to 230 K, and seems to be highly correlated with the diffraction quality of crystals.


2020 ◽  
Vol 17 (1) ◽  
Author(s):  
Shutian Zhang ◽  
Li Hu ◽  
Jialun Jiang ◽  
Hongji Li ◽  
Qin Wu ◽  
...  

Abstract Background Microglial mediated neuroinflammation in the rostral ventrolateral medulla (RVLM) plays roles in the etiology of stress-induced hypertension (SIH). It was reported that autophagy influenced inflammation via immunophenotypic switching of microglia. High-mobility group box 1 (HMGB1) acts as a regulator of autophagy and initiates the production of proinflammatory cytokines (PICs), but the underlying mechanisms remain unclear. Methods The stressed mice were subjected to intermittent electric foot shocks plus noises administered for 2 h twice daily for 15 consecutive days. In mice, blood pressure (BP) and renal sympathetic nerve activity (RSNA) were monitored by noninvasive tail-cuff method and platinum-iridium electrodes placed respectively. Microinjection of siRNA-HMGB1 (siHMGB1) into the RVLM of mice to study the effect of HMGB1 on microglia M1 activation was done. mRFP-GFP-tandem fluorescent LC3 (tf-LC3) vectors were transfected into the RVLM to evaluate the process of autolysosome formation/autophagy flux. The expression of RAB7, lysosomal-associated membrane protein 1 (LAMP1), and lysosomal pH change were used to evaluate lysosomal function in microglia. Mitophagy was identified by transmission electron microscopic observation or by checking LC3 and MitoTracker colocalization under a confocal microscope. Results We showed chronic stress increased cytoplasmic translocations of HMGB1 and upregulation of its receptor RAGE expression in microglia. The mitochondria injury, oxidative stress, and M1 polarization were attenuated in the RVLM of stressed Cre-CX3CR1/RAGEfl/fl mice. The HMGB1/RAGE axis increased at the early stage of stress-induced mitophagy flux while impairing the late stages of mitophagy flux in microglia, as revealed by decreased GFP fluorescence quenching of GFP-RFP-LC3-II puncta and decreased colocalization of lysosomes with mitochondria. The expressions of RAB7 and LAMP1 were decreased in the stressed microglia, while knockout of RAGE reversed these effects and caused an increase in acidity of lysosomes. siHMGB1 in the RVLM resulted in BP lowering and RSNA decreasing in SIH mice. When the autophagy inducer, rapamycin, is used to facilitate the mitophagy flux, this treatment results in attenuated NF-κB activation and reduced PIC release in exogenous disulfide HMGB1 (ds-HMGB1)-stimulated microglia. Conclusions Collectively, we demonstrated that inhibition of the HMGB1/RAGE axis activation led to increased stress-induced mitophagy flux, hence reducing the activity of microglia-mediated neuroinflammation and consequently reduced the sympathetic vasoconstriction drive in the RVLM.


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