Pressure- and temperature-induced unfolding studies: thermodynamics of core hydrophobicity and packing of ribonuclease A

2006 ◽  
Vol 387 (3) ◽  
pp. 285-296 ◽  
Author(s):  
Josep Font ◽  
Antoni Benito ◽  
Joan Torrent ◽  
Reinhard Lange ◽  
Marc Ribó ◽  
...  
Keyword(s):  
Hydrophobic Interactions ◽  
Rnase A ◽  
Van Der Waals Interactions ◽  
Hydrophobic Core ◽  
Experimental Conditions ◽  
Unfolded State ◽  
Different Temperatures ◽  
Methylene Groups ◽  
The Stability ◽  
Core Packing

Abstract In this work we demonstrate that heat and pressure induce only slightly different energetic changes in the unfolded state of RNase A. Using pressure and temperature as denaturants on a significant number of variants, and by determining the free energy of unfolding at different temperatures, we estimated the stability of variants unable to complete the unfolding transition owing to the experimental conditions required for pressure experiments. The overall set of results allowed us to map the contributions to stability of the hydrophobic core residues of RNase A, with the positions most critical for stability being V54, V57, I106 and V108. We also show that the stability differences can be attributed to both hydrophobic interactions and packing density with an equivalent energetic magnitude. The main hydrophobic core of RNase A is tightly packed, as shown by the small-to-large and isosteric substitutions. In addition, we found that large changes in the number of methylene groups have non-additive positive stability interaction energies that are consistent with exquisite tight core packing and rearrangements of van der Waals' interactions in the protein interior, even after drastic deleterious substitutions.

scholarly journals Intermolecular Interaction of Hthyni Protein with Double Methylated DNA at 5m-Cytosine Nucleotide

2020 ◽  
Vol 25 (1) ◽  
pp. 37-44
Author(s):  
Rajendra Prasad Koirala ◽  
Shyam Prakash Khanal ◽  
Sudip Shiwakoti ◽  
Narayan Prasad Adhikari
Keyword(s):  
Nuclear Protein ◽  
Hydrophobic Interactions ◽  
Md Simulations ◽  
Van Der Waals Interactions ◽  
Salt Bridges ◽  
Protein Residues ◽  
Methylated Dna ◽  
The Stability ◽  
Dna Complex ◽  
Binding Mechanisms

Human thymocyte nuclear protein 1 (hTHYN1) is one of the DNA binding proteins. It is essential for the regulation of Pax5 expression and the development of B cells in humans. Its thermodynamic and biological functions have been unclear yet. The study of the binding mechanism of hTHYN1 protein with DNA is essential to understand various biochemical functions in the human body. In this work, molecular dynamics (MD) simulations have been performed to understand the binding mechanisms of double methylated DNA (dmDNA) at cytosine nucleotide with hTHYN1 protein. Hydrogen bonding and other non-bonded (electrostatics and van der Waals) interactions among the residue-nucleotide pairs have been observed during the MD simulations and are also found responsible to form protein-DNA complex and to provide the stability of the structure. No salt bridges and hydrophobic interactions have been detected. Some of the protein residues in hTHYN1 have been found to strongly cooperate in the formation of the DNA-protein complex. Arginine residue of hTHYN1 has been observed as a major contributor in binding to the DNA. Many other residues also have significant roles in binding with DNA.

scholarly journals Atomic insights into the effects of pathological mutants through the disruption of hydrophobic core in the prion protein

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Juhwan Lee ◽  
Iksoo Chang ◽  
Wookyung Yu
Keyword(s):  
Amino Acids ◽  
Protein Folding ◽  
Prion Protein ◽  
Hydrophobic Interactions ◽  
Energy Difference ◽  
Hydrophobic Core ◽  
Free Energy Difference ◽  
The Stability ◽  
Simulation Time ◽  
Folding Free Energy

AbstractDestabilization of prion protein induces a conformational change from normal prion protein (PrPC) to abnormal prion protein (PrPSC). Hydrophobic interaction is the main driving force for protein folding, and critically affects the stability and solvability. To examine the importance of the hydrophobic core in the PrP, we chose six amino acids (V176, V180, T183, V210, I215, and Y218) that make up the hydrophobic core at the middle of the H2-H3 bundle. A few pathological mutants of these amino acids have been reported, such as V176G, V180I, T183A, V210I, I215V, and Y218N. We focused on how these pathologic mutations affect the hydrophobic core and thermostability of PrP. For this, we ran a temperature-based replica-exchange molecular dynamics (T-REMD) simulation, with a cumulative simulation time of 28 μs, for extensive ensemble sampling. From the T-REMD ensemble, we calculated the protein folding free energy difference between wild-type and mutant PrP using the thermodynamic integration (TI) method. Our results showed that pathological mutants V176G, T183A, I215V, and Y218N decrease the PrP stability. At the atomic level, we examined the change in pair-wise hydrophobic interactions from valine-valine to valine-isoleucine (and vice versa), which is induced by mutation V180I, V210I (I215V) at the 180th–210th (176th–215th) pair. Finally, we investigated the importance of the π-stacking between Y218 and F175.

scholarly journals Perplexing cooperative folding and stability of a low-sequence complexity, polyproline 2 protein lacking a hydrophobic core

2017 ◽  
Vol 114 (9) ◽  
pp. 2241-2246 ◽  
Author(s):  
Zachary P. Gates ◽  
Michael C. Baxa ◽  
Wookyung Yu ◽  
Joshua A. Riback ◽  
Hui Li ◽  
...  
Keyword(s):  
Room Temperature ◽  
Polypeptide Chain ◽  
Helical Structure ◽  
Residue Level ◽  
Hydrophobic Core ◽  
Native State ◽  
Sequence Complexity ◽  
Unfolded State ◽  
The Stability ◽  
Stabilizing Factors

The burial of hydrophobic side chains in a protein core generally is thought to be the major ingredient for stable, cooperative folding. Here, we show that, for the snow flea antifreeze protein (sfAFP), stability and cooperativity can occur without a hydrophobic core, and without α-helices or β-sheets. sfAFP has low sequence complexity with 46% glycine and an interior filled only with backbone H-bonds between six polyproline 2 (PP2) helices. However, the protein folds in a kinetically two-state manner and is moderately stable at room temperature. We believe that a major part of the stability arises from the unusual match between residue-level PP2 dihedral angle bias in the unfolded state and PP2 helical structure in the native state. Additional stabilizing factors that compensate for the dearth of hydrophobic burial include shorter and stronger H-bonds, and increased entropy in the folded state. These results extend our understanding of the origins of cooperativity and stability in protein folding, including the balance between solvent and polypeptide chain entropies.

Applicability of Instability Index for In vitro Protein Stability Prediction

2019 ◽  
Vol 26 (5) ◽  
pp. 339-347 ◽  
Author(s):  
Dilani G. Gamage ◽  
Ajith Gunaratne ◽  
Gopal R. Periyannan ◽  
Timothy G. Russell
Keyword(s):  
Protein Stability ◽  
Caulobacter Crescentus ◽  
Effect Of Temperature ◽  
Instability Index ◽  
Dipeptide Composition ◽  
Experimental Conditions ◽  
The Stability ◽  
Vitro Protein

Background: The dipeptide composition-based Instability Index (II) is one of the protein primary structure-dependent methods available for in vivo protein stability predictions. As per this method, proteins with II value below 40 are stable proteins. Intracellular protein stability principles guided the original development of the II method. However, the use of the II method for in vitro protein stability predictions raises questions about the validity of applying the II method under experimental conditions that are different from the in vivo setting. Objective: The aim of this study is to experimentally test the validity of the use of II as an in vitro protein stability predictor. Methods: A representative protein CCM (CCM - Caulobacter crescentus metalloprotein) that rapidly degrades under in vitro conditions was used to probe the dipeptide sequence-dependent degradation properties of CCM by generating CCM mutants to represent stable and unstable II values. A comparative degradation analysis was carried out under in vitro conditions using wildtype CCM, CCM mutants and two other candidate proteins: metallo-β-lactamase L1 and α -S1- casein representing stable, borderline stable/unstable, and unstable proteins as per the II predictions. The effect of temperature and a protein stabilizing agent on CCM degradation was also tested. Results: Data support the dipeptide composition-dependent protein stability/instability in wt-CCM and mutants as predicted by the II method under in vitro conditions. However, the II failed to accurately represent the stability of other tested proteins. Data indicate the influence of protein environmental factors on the autoproteolysis of proteins. Conclusion: Broader application of the II method for the prediction of protein stability under in vitro conditions is questionable as the stability of the protein may be dependent not only on the intrinsic nature of the protein but also on the conditions of the protein milieu.

scholarly journals Comprehensive modeling of bloodstain aging by multivariate Raman spectral resolution with kinetics

2019 ◽  
Vol 2 (1) ◽  
Author(s):  
Ayari Takamura ◽  
Daisuke Watanabe ◽  
Rintaro Shimada ◽  
Takeaki Ozawa
Keyword(s):  
Spectral Resolution ◽  
Aging Process ◽  
Near Infrared ◽  
Biochemical Characterization ◽  
Forensic Analysis ◽  
Chemical Mechanism ◽  
Experimental Conditions ◽  
Spectral Components ◽  
Different Temperatures ◽  
Analytical Approaches

Abstract Blood, as a cardinal biological system, is a challenging target for biochemical characterization because of sample complexity and a lack of analytical approaches. To reveal and evaluate aging process of blood compositions is an unexplored issue in forensic analysis, which is useful to elucidate the details of a crime. Here we demonstrate a spectral deconvolution model of near-infrared Raman spectra of bloodstain to comprehensively describe the aging process based on the chemical mechanism, particularly the kinetics. The bloodstain spectra monitored over several months at different temperatures are decomposed into significant spectral components by multivariate calculation. The kinetic schemes of the spectral components are explored and subsequently incorporated into the developed algorithm for the optimal spectral resolution. Consequently, the index of bloodstain aging is proposed, which can be used under different experimental conditions. This work provides a novel perspective on the chemical mechanisms in bloodstain aging and facilitates forensic applications.

scholarly journals A Superhydrophobic, Antibacterial, and Durable Surface of Poplar Wood

Nanomaterials ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1885
Author(s):  
Xinyu Wu ◽  
Feng Yang ◽  
Jian Gan ◽  
Zhangqian Kong ◽  
Yan Wu
Keyword(s):  
Stearic Acid ◽  
Antibacterial Properties ◽  
Alkali Resistance ◽  
Poplar Wood ◽  
X Ray Diffraction ◽  
X Ray ◽  
Different Temperatures ◽  
Acid And Alkali Resistance ◽  
The Stability

The silver particles were grown in situ on the surface of wood by the silver mirror method and modified with stearic acid to acquire a surface with superhydrophobic and antibacterial properties. Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), and X-ray energy spectroscopy (XPS) were used to analyze the reaction mechanism of the modification process. Scanning electron microscopy (SEM) and contact angle tests were used to characterize the wettability and surface morphology. A coating with a micro rough structure was successfully constructed by the modification of stearic acid, which imparted superhydrophobicity and antibacterial activity to poplar wood. The stability tests were performed to discuss the stability of its hydrophobic performance. The results showed that it has good mechanical properties, acid and alkali resistance, and UV stability. The durability tests demonstrated that the coating has the function of water resistance and fouling resistance and can maintain the stability of its hydrophobic properties under different temperatures of heat treatment.

scholarly journals An assessment of methanolysis and other factors used in the analysis of carbohydrate-containing materials

1971 ◽  
Vol 125 (4) ◽  
pp. 1009-1018 ◽  
Author(s):  
R. E. Chambers ◽  
J. R. Clamp
Keyword(s):  
Hydrochloric Acid ◽  
Analytical Procedure ◽  
Internal Standard ◽  
Inorganic Contaminants ◽  
Rotary Evaporation ◽  
Silver Salts ◽  
Methanolic Hydrochloric Acid ◽  
Different Temperatures ◽  
The Stability ◽  
Analytical System

The stability of monosaccharides in methanolic hydrochloric acid of different strengths and at different temperatures was determined. They are generally stable for 24h in methanolic 1m- and 2m-hydrochloric acid at both 85°C and 100°C, but undergo considerable destruction in methanolic 4m- and 6m-hydrochloric acid at 100°C. Analysis of glycopeptides and oligosaccharides of known composition showed that release of carbohydrate was complete within 3h in methanolic 1m-hydrochloric acid at 85°C. Removal of methanolic hydrochloric acid by rotary evaporation resulted in considerable losses of monosaccharides, which could be prevented by prior neutralization. Methanolysis caused extensive de-N-acetylation of acetamidohexoses, so that a re-N-acetylation step is necessary in the analytical procedure. The addition of acetic anhydride for this purpose also prevented loss of internal standard by adsorption on the insoluble silver salts used in neutralization. Several trimethylsilylating agents were studied and suitable conditions are recommended. The effects on the analytical system of water and some common organic and inorganic contaminants are assessed.

scholarly journals Effective Separation of Prime Olefins from Gas Stream Using Anion Pillared Metal Organic Frameworks: Ideal Adsorbed Solution Theory Studies, Cyclic Application and Stability

Catalysts ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 510
Author(s):  
Majeda Khraisheh ◽  
Fares. Almomani ◽  
Gavin Walker
Keyword(s):  
Breakthrough Curves ◽  
Isotherm Models ◽  
Regeneration Ability ◽  
Solution Theory ◽  
Experimental Conditions ◽  
Ideal Adsorbed Solution Theory ◽  
Adsorbed Solution ◽  
The Stability ◽  
Adsorption Desorption ◽  
Adsorbed Solution Theory

The separation of C3H4/C3H6 is one of the most energy intensive and challenging operations, requiring up to 100 theoretical stages, in traditional cryogenic distillation. In this investigation, the potential application of two MOFs (SIFSIX-3-Ni and NbOFFIVE-1-Ni) was tested by studying the adsorption–desorption behaviors at a range of operational temperatures (300–360 K) and pressures (1–100 kPa). Dynamic adsorption breakthrough tests were conducted and the stability and regeneration ability of the MOFs were established after eight consecutive cycles. In order to establish the engineering key parameters, the experimental data were fitted to four isotherm models (Langmuir, Freundlich, Sips and Toth) in addition to the estimation of the thermodynamic properties such as the isosteric heats of adsorption. The selectivity of the separation was tested by applying ideal adsorbed solution theory (IAST). The results revealed that SIFSIX-3-Ni is an effective adsorbent for the separation of 10/90 v/v C3H4/C3H6 under the range of experimental conditions used in this study. The maximum adsorption reported for the same combination was 3.2 mmolg−1. Breakthrough curves confirmed the suitability of this material for the separation with a 10-min gab before the lighter C3H4 is eluted from the column. The separated C3H6 was obtained with a 99.98% purity.

scholarly journals Influence of study model, baseline catalytic concentrations and analytical system on the stability of serum alanine aminotransferase

2020 ◽  
Vol 1 (2) ◽  
Author(s):  
Josep Miquel Bauça ◽  
Andrea Caballero ◽  
Carolina Gómez ◽  
Débora Martínez-Espartosa ◽  
Isabel García del Pino ◽  
...  
Keyword(s):  
Alanine Aminotransferase ◽  
Experimental Models ◽  
Individual Variability ◽  
Serum Samples ◽  
Multicentric Study ◽  
Different Temperatures ◽  
The Stability ◽  
Analytical System ◽  
Definition Of ◽  
Analytical Platforms

AbstractObjectivesThe stability of the analytes most commonly used in routine clinical practice has been the subject of intensive research, with varying and even conflicting results. Such is the case of alanine aminotransferase (ALT). The purpose of this study was to determine the stability of serum ALT according to different variables.MethodsA multicentric study was conducted in eight laboratories using serum samples with known initial catalytic concentrations of ALT within four different ranges, namely: <50 U/L (<0.83 μkat/L), 50–200 U/L (0.83–3.33 μkat/L), 200–400 U/L (3.33–6.67 μkat/L) and >400 U/L (>6.67 μkat/L). Samples were stored for seven days at two different temperatures using four experimental models and four laboratory analytical platforms. The respective stability equations were calculated by linear regression. A multivariate model was used to assess the influence of different variables.ResultsCatalytic concentrations of ALT decreased gradually over time. Temperature (−4%/day at room temperature vs. −1%/day under refrigeration) and the analytical platform had a significant impact, with Architect (Abbott) showing the greatest instability. Initial catalytic concentrations of ALT only had a slight impact on stability, whereas the experimental model had no impact at all.ConclusionsThe constant decrease in serum ALT is reduced when refrigerated. Scarcely studied variables were found to have a significant impact on ALT stability. This observation, added to a considerable inter-individual variability, makes larger studies necessary for the definition of stability equations.

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