scholarly journals Efficient Refolding of Aggregation-prone Citrate Synthase by Polyol Osmolytes

2005 ◽  
Vol 280 (16) ◽  
pp. 15553-15560 ◽  
Author(s):  
Rajesh Mishra ◽  
Robert Seckler ◽  
Rajiv Bhat
Keyword(s):  
Small Molecules ◽  
Molecular Chaperones ◽  
Rational Design ◽  
Protein Production ◽  
Citrate Synthase ◽  
Protein A ◽  
Complete Recovery ◽  
Hydroxyl Groups ◽  
Native State

Efficient refolding of proteins and prevention of their aggregation during folding are of vital importance in recombinant protein production and in finding cures for several diseases. We have used citrate synthase (CS) as a model to understand the mechanism of aggregation during refolding and its prevention using several known structure-stabilizing cosolvent additives of the polyol series. Interestingly, no parallel correlation between the folding effect and the general stabilizing effect exerted by polyols was observed. Although increasing concentrations of polyols increased protein stability in general, the refolding yields for CS decreased at higher polyol concentrations, with erythritol reducing the folding yields at all concentrations tested. Among the various polyols used, glycerol was the most effective in enhancing the CS refolding yield, and a complete recovery of enzymatic activity was obtained at 7mglycerol and 10 μg/ml protein, a result superior to the action of the molecular chaperones GroEL and GroESin vitro. A good correlation between the refolding yields and the suppression of protein aggregation by glycerol was observed, with no aggregation detected at 7m. The polyols prevented the aggregation of CS depending on the number of hydroxyl groups in them. Stopped-flow fluorescence kinetics experiments suggested that polyols, including glycerol, act very early in the refolding process, as no fast and slow phases were detectable. The results conclusively demonstrate that both the thermodynamic and kinetic aspects are critical in the folding process and that all structure-stabilizing molecules need not always help in productive folding to the native state. These findings are important for the rational design of small molecules for efficient refolding of various aggregation-prone proteins of commercial and medical relevance.

Function and bioenergetics in isolated perfused trained rat hearts

1997 ◽  
Vol 272 (1) ◽  
pp. H409-H417 ◽  
Author(s):  
R. G. Spencer ◽  
P. M. Buttrick ◽  
J. S. Ingwall
Keyword(s):  
Diastolic Function ◽  
Citrate Synthase ◽  
Recovery Of Function ◽  
Complete Recovery ◽  
High Energy ◽  
Left Ventricular ◽  
Female Rats ◽  
Saturation Transfer

To evaluate the resistance of physiologically hypertrophied hearts to hypoxic insult, we quantified the development of functional deficits during hypoxia and reoxygenation in hypertrophied hearts from swim-trained female rats and we correlated this with assessment of high-energy phosphate (HEP) metabolites from simultaneous 31P nuclear magnetic resonance (NMR) measurements. Furthermore, in vivo enzymatic studies were carried out with saturation transfer NMR under well-oxygenated perfusion conditions for both beating and KCl-arrested hearts. Finally, in vitro enzymatic assays were performed. During hypoxia, the trained hearts exhibited improved systolic and diastolic function compared with hearts from sedentary animals. After 16 min of hypoxia, left ventricular (LV) developed pressure fell to 9% of baseline in control hearts but to only 21% of baseline in trained hearts (P < 0.01). LV diastolic function was also improved by training, increasing during hypoxia from a baseline of 10 to 71.0 +/- 3.3 mmHg in control hearts and to 55.3 +/- 4.8 mmHg in trained hearts (P < 0.05). Trained hearts also showed more rapid and complete recovery of function during reoxygenation and greater coronary flow per gram of heart throughout the entire protocol. Functional differences were not accompanied by differences in HEP at baseline; moreover, ATP and phosphocreatine (PCr) loss during hypoxia was similar between control and trained hearts, as was the recovery of PCr during reoxygenation. Saturation transfer experiments showed an increase in the forward creatine kinase (CrK) rate constant in trained hearts of 18% while beating, whereas in vitro enzymatic analysis revealed a 16% increase in the ratio of mitochondrial CrK to citrate synthase activity in LV tissue. Thus the relative preservation of function in hearts from trained rats could not be accounted for by overall HEP levels but may reflect adaptations in the CrK system.

Rational design of small molecules targeting the C2 domain of coagulation factor VIII

Blood ◽  
2014 ◽  
Vol 123 (1) ◽  
pp. 113-120 ◽  
Author(s):  
Gerry A. F. Nicolaes ◽  
Mahesh Kulharia ◽  
Jan Voorberg ◽  
Paul H. Kaijen ◽  
Aleksandra Wroblewska ◽  
...  
Keyword(s):  
Factor Viii ◽  
Small Molecules ◽  
Rational Design ◽  
Coagulation Factor ◽  
Coagulation Factor Viii ◽  
C2 Domain ◽  
Key Points ◽  
Thrombin Formation

Key Points Novel small molecules have been identified that specifically target FVIII. These small molecules are able to reduce in vitro thrombin formation in full blood.

scholarly journals Suppression of aggregate and amyloid formation by a novel intrinsically disordered region in metazoan Hsp110 chaperones

2021 ◽  
Author(s):  
Unekwu M. Yakubu ◽  
Kevin A. Morano
Keyword(s):  
Protein Aggregation ◽  
Molecular Chaperones ◽  
Citrate Synthase ◽  
Neuronal Cell ◽  
Amyloid Formation ◽  
Nucleotide Exchange ◽  
Aggregation Assay ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Region

AbstractMolecular chaperones maintain protein homeostasis (proteostasis) by ensuring the proper folding of polypeptides. Loss of proteostasis has been linked to the onset of numerous neurodegenerative disorders including Alzheimer’s, Parkinson’s, and Huntington’s disease. Hsp110 is related to the canonical Hsp70 class of protein folding molecular chaperones and interacts with Hsp70 as a nucleotide exchange factor (NEF), promoting rapid cycling of ADP for ATP. In addition to its NEF activity, Hsp110 possesses an Hsp70-like substrate binding domain (SBD) whose biological roles remain undefined. Previous work in Drosophila melanogaster has shown that loss of the sole Hsp110 gene (Hsc70cb) accelerates the aggregation of polyglutamine (polyQ)-expanded human Huntingtin, while its overexpression protects against polyQ-mediated neuronal cell death. We hypothesize that in addition to its role as an Hsp70 NEF, Drosophila Hsp110 may function in the fly as a protective protein “holdase”, preventing the aggregation of unfolded polypeptides via the SBD-β subdomain. Using an in vitro protein aggregation assay we demonstrate for the first time that Drosophila Hsp110 effectively prevents aggregation of the model substrate citrate synthase. We also report the discovery of a redundant and heretofore unknown potent holdase capacity in a 138 amino-acid region of Hsp110 carboxyl-terminal to both SBD-β and SBD-α (henceforth called the C-terminal extension). This sequence is highly conserved in metazoan Hsp110 genes, completely absent from fungal representatives, including Saccharomyces cerevisiae SSE1, and is computationally predicted to contain an intrinsically disordered region (IDR). We demonstrate that this IDR sequence within the human Hsp110s, Apg-1 and Hsp105α, inhibits the formation of amyloid Aβ-42 and α-synuclein fibrils in vitro but cannot mediate fibril disassembly. Together these findings demonstrate the existence of a second independent, passive holdase property of metazoan Hsp110 chaperones capable of suppressing both general protein aggregation and amyloidogenesis and raise the possibility of exploitation of this IDR for therapeutic benefit in combating neurodegenerative disease.

scholarly journals Modulating protein activity using tethered ligands with mutually exclusive binding sites

2015 ◽  
Vol 6 (1) ◽  
Author(s):  
Alberto Schena ◽  
Rudolf Griss ◽  
Kai Johnsson
Keyword(s):  
Small Molecules ◽  
Binding Sites ◽  
Protein A ◽  
Living Cells ◽  
Protein Activity ◽  
Research Areas ◽  
Specific Effector ◽  
Tethered Ligands ◽  
General Method

Abstract The possibility to design proteins whose activities can be switched on and off by unrelated effector molecules would enable applications in various research areas, ranging from biosensing to synthetic biology. We describe here a general method to modulate the activity of a protein in response to the concentration of a specific effector. The approach is based on synthetic ligands that possess two mutually exclusive binding sites, one for the protein of interest and one for the effector. Tethering such a ligand to the protein of interest results in an intramolecular ligand–protein interaction that can be disrupted through the presence of the effector. Specifically, we introduce a luciferase controlled by another protein, a human carbonic anhydrase whose activity can be controlled by proteins or small molecules in vitro and on living cells, and novel fluorescent and bioluminescent biosensors.

scholarly journals Molecular chaperones maximize the native state yield on biological times by driving substrates out of equilibrium

2017 ◽  
Vol 114 (51) ◽  
pp. E10919-E10927 ◽  
Author(s):  
Shaon Chakrabarti ◽  
Changbong Hyeon ◽  
Xiang Ye ◽  
George H. Lorimer ◽  
D. Thirumalai
Keyword(s):  
Molecular Chaperones ◽  
Atp Hydrolysis ◽  
General Relation ◽  
Native State ◽  
Folding Rate ◽  
Biologically Relevant ◽  
Final Yield ◽  
Short Time

Molecular chaperones facilitate the folding of proteins and RNA in vivo. Under physiological conditions, the in vitro folding ofTetrahymenaribozyme by the RNA chaperone CYT-19 behaves paradoxically; increasing the chaperone concentration reduces the yield of native ribozymes. In contrast, the protein chaperone GroEL works as expected; the yield of the native substrate increases with chaperone concentration. The discrepant chaperone-assisted ribozyme folding thus contradicts the expectation that it operates as an efficient annealing machine. To resolve this paradox, we propose a minimal stochastic model based on the Iterative Annealing Mechanism (IAM) that offers a unified description of chaperone-mediated folding of both proteins and RNA. Our theory provides a general relation that quantitatively predicts how the yield of native states depends on chaperone concentration. Although the absolute yield of native states decreases in theTetrahymenaribozyme, the product of the folding rate and the steady-state native yield increases in both cases. By using energy from ATP hydrolysis, both CYT-19 and GroEL drive their substrate concentrations far out of equilibrium, thus maximizing the native yield in a short time. This also holds when the substrate concentration exceeds that of GroEL. Our findings satisfy the expectation that proteins and RNA be folded by chaperones on biologically relevant time scales, even if the final yield is lower than what equilibrium thermodynamics would dictate. The theory predicts that the quantity of chaperones in vivo has evolved to optimize native state production of the folded states of RNA and proteins in a given time.

scholarly journals DUK114, the Drosophila orthologue of bovine brain calpain activator protein, is a molecular chaperone

2004 ◽  
Vol 383 (1) ◽  
pp. 165-170 ◽  
Author(s):  
Attila FARKAS ◽  
Gábor NARDAI ◽  
Peter CSERMELY ◽  
Peter TOMPA ◽  
Peter FRIEDRICH
Keyword(s):  
Heat Shock ◽  
Molecular Chaperone ◽  
Molecular Chaperones ◽  
Citrate Synthase ◽  
Sequence Similarity ◽  
Heat Shock Protein 90 ◽  
Chaperone Activity ◽  
In Vitro Assays

UK114, the goat liver tumour antigen, is a member of a widely distributed family of conserved low-molecular-mass proteins (YER057c/YjgF/UK114), the function of which is ill understood. To the various orthologues diverse functions have been ascribed, such as translation inhibition, regulation of purine repressor or calpain activation. Owing to a limited sequence similarity to Hsp90 (heat-shock protein 90), they have also been proposed to be molecular chaperones; however, this has never been tested. In the present paper, we report the cloning and characterization of the Drosophila orthologue, DUK114. In brief, DUK114 had no effect that would have qualified it as a calpain activator. In contrast, it proved to be a very potent molecular chaperone in in vitro assays. In a heat-aggregation test, it significantly decelerated the formation of citrate synthase aggregates. In a reverse assay, the recovery of the enzyme from urea- and heat-induced denatured states was accelerated almost 3-fold. On a molar basis, the chaperone activity of the 15-kDa DUK114 is comparable with that of Hsp90, the almost 6-times-larger archetypal molecular chaperone. In similar assays, DUK114 was ineffective with Drosophila calpain A or calpain B. To test for its chaperone activity in vivo, DUK114 was transfected into Schneider (S2) cells; after heat shock, the number of viable non-transfected cells started to increase after a lag time; in the presence of DUK114, cell proliferation started at once. Our work is the first experimental evidence that DUK114, and possibly other members of this family, are molecular chaperones.

Structure-based identification of small molecules against influenza A virus endonuclease: an in silico and in vitro approach

2020 ◽  
Vol 78 (4) ◽  
Author(s):  
Sai Disha K. ◽  
Rashmi Puranik ◽  
Sudheesh N. ◽  
Kavitha K. ◽  
Fajeelath Fathima ◽  
...  
Keyword(s):  
Small Molecules ◽  
Influenza A Virus ◽  
Influenza A ◽  
Protein A ◽  
Antiviral Drug ◽  
Respiratory Illness ◽  
Influenza Viruses ◽  
Influenza Activity ◽  
Viral Target

ABSTRACT Influenza viruses are known to cause acute respiratory illness, sometimes leading to high mortality rates. Though there are approved influenza antivirals available, their efficacy has reduced over time, due to the drug resistance crisis. There is a perpetual need for newer and better drugs. Drug screening based on the interaction dynamics with different viral target proteins has been a preferred approach in the antiviral drug discovery process. In this study, the FDA approved drug database was virtually screened with the help of Schrödinger software, to select small molecules exhibiting best interactions with the influenza A virus endonuclease protein. A detailed cytotoxicity profiling was carried out for the two selected compounds, cefepime and dolutegravir, followed by in vitro anti-influenza screening using plaque reduction assay. Cefepime showed no cytotoxicity up to 200 μM, while dolutegravir was non-toxic up to 100 μM in Madin–Darby canine kidney cells. The compounds did not show any reduction in viral plaque numbers indicating no anti-influenza activity. An inefficiency in the translation of the molecular interactions into antiviral activity does not necessarily mean that the molecules were inactive. Nevertheless, testing the molecules for endonuclease inhibition per se can be considered a worthwhile approach.

Hypercoagulability Syndrome Due to Heparin Co-Factor Deficiency

1964 ◽  
Vol 11 (02) ◽  
pp. 485-496 ◽  
Author(s):  
B. J Koszewski ◽  
H Vahabzadeh
Keyword(s):  
Dynamic Process ◽  
Blood Clotting ◽  
Complete Recovery ◽  
Inhibition Test ◽  
Factor Deficiency ◽  
Heparin Resistance ◽  
Fever Therapy ◽  
Intensive Course ◽  
Plasma Infusions

SummaryA case of hypercoagulability syndrome in a 35 years old male is reported. An abnormal heparin resistance was found which could be defined by means of a heparin clot-inhibition test as a deficiency in heparin co-factor. The required anticoagulant doses of heparin were forty times as high as in cases with intact heparin co-factor. The factor seemed to be used up in the process of coagulation, as plasma, but not serum, was able to correct the deficiency in vitro. Plasma infusions were helpful for four days, but a complete recovery was achieved only after an intensive course of fever therapy.The phenomenon of blood clotting should be regarded as a dynamic process which is facilitated by an array of clot promoting factors and opposed by a system of natural anticoagulants.

In the Quest for a Stable Triplet State in Small Polyaromatic Hydrocarbons : An In-Silico Tool for Rational Design and Prediction

2019 ◽  
Author(s):  
Madhumita Rano ◽  
Sumanta K Ghosh ◽  
Debashree Ghosh
Keyword(s):  
Triplet State ◽  
Small Molecules ◽  
In Silico ◽  
Qualitative Agreement ◽  
Rational Design ◽  
Polyaromatic Hydrocarbons ◽  
Spin Hamiltonian ◽  
Spin Frustration ◽  
Computationally Efficient ◽  
High Level

<div>Combining the roles of spin frustration and geometry of odd and even numbered rings in polyaromatic hydrocarbons (PAHs), we design small molecules that show exceedingly small singlet-triplet gaps and stable triplet ground states. Furthermore, a computationally efficient protocol with a model spin Hamiltonian is shown to be capable of qualitative agreement with respect to high level multireference calculations and therefore, can be used for fast molecular discovery and screening.</div>

Conjugates of Classical DNA/RNA Binder with Nucleobase: Chemical, Biochemical and Biomedical Applications

2019 ◽  
Vol 26 (30) ◽  
pp. 5609-5624
Author(s):  
Dijana Saftić ◽  
Željka Ban ◽  
Josipa Matić ◽  
Lidija-Marija Tumirv ◽  
Ivo Piantanida
Keyword(s):  
Molecular Weight ◽  
Small Molecules ◽  
Biomedical Applications ◽  
Protein Targets ◽  
New Class ◽  
Rna Targets ◽  
Covalently Linked ◽  
Structural Aspects

: Among the most intensively studied classes of small molecules (molecular weight < 650) in biomedical research are small molecules that non-covalently bind to DNA/RNA, and another intensively studied class is nucleobase derivatives. Both classes have been intensively elaborated in many books and reviews. However, conjugates consisting of DNA/RNA binder covalently linked to nucleobase are much less studied and have not been reviewed in the last two decades. Therefore, this review summarized reports on the design of classical DNA/RNA binder – nucleobase conjugates, as well as data about their interactions with various DNA or RNA targets, and even in some cases protein targets are involved. According to these data, the most important structural aspects of selective or even specific recognition between small molecule and target are proposed, and where possible related biochemical and biomedical aspects were discussed. The general conclusion is that this, rather new class of molecules showed an amazing set of recognition tools for numerous DNA or RNA targets in the last two decades, as well as few intriguing in vitro and in vivo selectivities. Several lead research lines show promising advancements toward either novel, highly selective markers or bioactive, potentially druggable molecules.

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