Secondary Structure Composition and pH-dependent Conformational Changes of Soluble Recombinant HLA-DM

Background:pH is one of the decisive macromolecular properties of proteins that significantly affects enzyme structure, stability and reaction rate. Change in pH may protonate or deprotonate the side group of aminoacid residues in the protein, thereby resulting in changes in chemical and structural features. Hence studies on the kinetics of enzyme deactivation by pH are important for assessing the bio-functionality of industrial enzymes. L-asparaginase is one such important enzyme that has potent applications in cancer therapy and food industry.Objective:The objective of the study is to understand and analyze the influence of pH on deactivation and stability of Vibrio cholerae L-asparaginase.Methods:Kinetic studies were conducted to analyze the effect of pH on stability and deactivation of Vibrio cholerae L-asparaginase. Circular Dichroism (CD) and Differential Scanning Calorimetry (DSC) studies have been carried out to understand the pH-dependent conformational changes in the secondary structure of V. cholerae L-asparaginase.Results:The enzyme was found to be least stable at extreme acidic conditions (pH< 4.5) and exhibited a gradual increase in melting temperature from 40 to 81 °C within pH range of 4.0 to 7.0. Thermodynamic properties of protein were estimated and at pH 7.0 the protein exhibited ΔG37of 26.31 kcal mole-1, ΔH of 204.27 kcal mole-1 and ΔS of 574.06 cal mole-1 K-1.Conclusion:The stability and thermodynamic analysis revealed that V. cholerae L-asparaginase was highly stable over a wide range of pH, with the highest stability in the pH range of 5.0–7.0.

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Correlation of membrane protein conformational and functional dynamics

Nature Communications ◽

10.1038/s41467-021-24660-1 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Raghavendar Reddy Sanganna Gari ◽

Joel José Montalvo‐Acosta ◽

George R. Heath ◽

Yining Jiang ◽

Xiaolong Gao ◽

...

Keyword(s):

Membrane Protein ◽

Conformational Changes ◽

Single Channel ◽

Conformational Dynamics ◽

Md Simulations ◽

High Temporal Resolution ◽

Dependent Manner ◽

Functional Dynamics ◽

Ph Dependent ◽

Open States

AbstractConformational changes in ion channels lead to gating of an ion-conductive pore. Ion flux has been measured with high temporal resolution by single-channel electrophysiology for decades. However, correlation between functional and conformational dynamics remained difficult, lacking experimental techniques to monitor sub-millisecond conformational changes. Here, we use the outer membrane protein G (OmpG) as a model system where loop-6 opens and closes the β-barrel pore like a lid in a pH-dependent manner. Functionally, single-channel electrophysiology shows that while closed states are favored at acidic pH and open states are favored at physiological pH, both states coexist and rapidly interchange in all conditions. Using HS-AFM height spectroscopy (HS-AFM-HS), we monitor sub-millisecond loop-6 conformational dynamics, and compare them to the functional dynamics from single-channel recordings, while MD simulations provide atomistic details and energy landscapes of the pH-dependent loop-6 fluctuations. HS-AFM-HS offers new opportunities to analyze conformational dynamics at timescales of domain and loop fluctuations.

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Conformational Changes in Wheat Gluten After using Ag-nanoparticles

International Agrophysics ◽

10.2478/intag-2014-0021 ◽

2014 ◽

Vol 28 (3) ◽

pp. 311-317 ◽

Cited By ~ 1

Author(s):

Agnieszka Nawrocka

Keyword(s):

Aqueous Solution ◽

Silver Nanoparticles ◽

Secondary Structure ◽

Conformational Changes ◽

Fungal Infections ◽

Wheat Gluten ◽

Control Sample ◽

Antimicrobial Properties ◽

Protective Layer ◽

Trisodium Citrate

Abstract Silver nanoparticles have antimicrobial properties since they can be regarded as an efficient protector against pathogenic microorganisms. Fourier transform infrared spectroscopy was used to examine conformational changes in the secondary structure of wheat gluten washed out from grain treated with an aqueous solution of silver nanoparticles stabilized by tri-sodium citrate. Silver nanoparticles were used as a protective layer on the grain surface against bacterial and fungal infections (antimicrobial agent). Analysis of the amide I band revealed significant changes in the secondary structure after using silver nanoparticles. An increase in the β-sheet content (from 36.2 to 39.2%) was observed at the expense of the α-helix and β-turn content. To find factors causing these changes, the wheat grains were treated by an aqueous solution of trisodium citrate and water. The results obtained indicate that the changes in the gluten structure were connected mainly with the trisodium citrate action due to presence of a small number of free molecules of the stabilizer in the solution of silver nanoparticles. Additionally, the conformational changes in gluten pointed out that gluten flexibility increased (decrease in the αH/βS ratio from 1.40 for the control sample to 1.26 for the silver nanoparticle-treated samples) as well as the solubility of gluten decreased (decrease in the β-turn content from 13.1 to 11.4%).

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Processing of RNA Containing 8-Oxo-7,8-Dihydroguanosine (8-oxoG) by the Exoribonuclease Xrn-1

Frontiers in Molecular Biosciences ◽

10.3389/fmolb.2021.780315 ◽

2021 ◽

Vol 8 ◽

Author(s):

Cheyenne N. Phillips ◽

Shawn Schowe ◽

Conner J. Langeberg ◽

Namoos Siddique ◽

Erich G. Chapman ◽

...

Keyword(s):

Secondary Structure ◽

Conformational Changes ◽

Solid Phase Synthesis ◽

Solid Phase ◽

Spatial Constraints ◽

Phase Synthesis ◽

Naturally Occurring ◽

Processive Enzyme ◽

Moving Band ◽

Hydrolysis Of

Understanding how oxidatively damaged RNA is handled intracellularly is of relevance due to the link between oxidized RNA and the progression/development of some diseases as well as aging. Among the ribonucleases responsible for the decay of modified (chemically or naturally) RNA is the exonuclease Xrn-1, a processive enzyme that catalyzes the hydrolysis of 5′-phosphorylated RNA in a 5′→3′ direction. We set out to explore the reactivity of this exonuclease towards oligonucleotides (ONs, 20-nt to 30-nt long) of RNA containing 8-oxo-7,8-dihydroguanosine (8-oxoG), obtained via solid-phase synthesis. The results show that Xrn-1 stalled at sites containing 8-oxoG, evidenced by the presence of a slower moving band (via electrophoretic analyses) than that observed for the canonical analogue. The observed fragment(s) were characterized via PAGE and MALDI-TOF to confirm that the oligonucleotide fragment(s) contained a 5′-phosphorylated 8-oxoG. Furthermore, the yields for this stalling varied from app. 5–30% with 8-oxoG located at different positions and in different sequences. To gain a better understanding of the decreased nuclease efficiency, we probed: 1) H-bonding and spatial constraints; 2) anti-syn conformational changes; 3) concentration of divalent cation; and 4) secondary structure. This was carried out by introducing methylated or brominated purines (m1G, m6,6A, or 8-BrG), probing varying [Mg2+], and using circular dichroism (CD) to explore the formation of structured RNA. It was determined that spatial constraints imposed by conformational changes around the glycosidic bond may be partially responsible for stalling, however, the results do not fully explain some of the observed higher stalling yields. We hypothesize that altered π-π stacking along with induced H-bonding interactions between 8-oxoG and residues within the binding site may also play a role in the decreased Xrn-1 efficiency. Overall, these observations suggest that other factors, yet to be discovered/established, are likely to contribute to the decay of oxidized RNA. In addition, Xrn-1 degraded RNA containing m1G, and stalled mildly at sites where it encountered m6,6A, or 8-BrG, which is of particular interest given that the former two are naturally occurring modifications.

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pH-Dependent Conformational Changes in Proteins and Their Effect on Experimental pKas: The Case of Nitrophorin 4

PLoS Computational Biology ◽

10.1371/journal.pcbi.1002761 ◽

2012 ◽

Vol 8 (11) ◽

pp. e1002761 ◽

Cited By ~ 71

Author(s):

Natali V. Di Russo ◽

Dario A. Estrin ◽

Marcelo A. Martí ◽

Adrian E. Roitberg

Keyword(s):

Conformational Changes ◽

Nitrophorin 4 ◽

Ph Dependent

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Circular Dichroism of C-Phycoerythrin: A Conformational Analysis

Zeitschrift für Naturforschung C ◽

10.1515/znc-1980-5-603 ◽

1980 ◽

Vol 35 (5-6) ◽

pp. 367-375 ◽

Cited By ~ 20

Author(s):

Elisabeth Langer ◽

Harald Lehner ◽

Wolfhart Rüdiger ◽

Barbara Zickendraht-Wendelstadt

Keyword(s):

Circular Dichroism ◽

Secondary Structure ◽

Conformational Changes ◽

Spectral Region ◽

Protein Unfolding ◽

Extensive Study ◽

Random Coil ◽

Linear Superposition ◽

Thermally Induced ◽

Circular Dichroïsm

Abstract An extensive study of the chiroptical properties of C-phycoerythrin and the α-and β-subunits in the spectral region from 700 -200 nm is presented. Based on the VIS-circular dichroism inherently chiral conform ations are proposed for the co valently linked chromophores. By means of mean residue ellipticities and the experimental circular dichroism spectra in the region of the n → π* peptide transition the a-helix contents of the apoproteins of the ac-and ß-subunits are estimated to amount to 60% and 40%, respectively. The circular dichroism spectrum of native C-phycoerythrin is congruent with a linear superposition of the α-and β-subspectra, in the whole spectral region studied. Since a-and β-subunits are associated in native C-phycoery-thrin as revealed by sedim entation analysis the interactions between the subunits in the native chromoprotein are not accom panied by substantial conform ational changes. In the temperature range 0°-40°C the thermally induced changes of the chrom ophores in native C-phycoerythrin are not associated with changes of the secondary structure of the apoprotein. Unfolding occurs at 60°-70°C but slowly leads to irreversible denaturation. Protein unfolding starts at 3 M urea. The random coil secondary structure of the apoproteins is reached at 8 M urea. At this concentration the absorbance and the optical activity of the chrom o phores are reduced by a factor 3 and 10, respectively. The conformational changes in the peptide with increasing denaturant concentration are not synchronous with those induced in the Chromo phore indicating that a m ultistep process is operative during unfolding. The C D results on dena turation are supplem ented by absorption and em ission spectroscopy.

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Relationship of Secondary Structures and Wear Resistance of Antifriction Aluminum Alloys for Journal Bearings from the Point of View of Self-Organization During Friction

Entropy ◽

10.3390/e21111048 ◽

2019 ◽

Vol 21 (11) ◽

pp. 1048 ◽

Cited By ~ 2

Author(s):

Gershman ◽

Mironov ◽

Podrabinnik ◽

Kuznetsova ◽

Gershman ◽

...

Keyword(s):

Secondary Structure ◽

Organization Theory ◽

Secondary Structures ◽

Point Of View ◽

Self Organization ◽

Friction Surfaces ◽

Relationship Of ◽

The Relationship ◽

Secondary Structure Composition ◽

Antifriction Alloys

The paper investigates the relationship between the tribological properties/compositions of new aluminum antifriction alloys and compositions of the secondary structures formed on their friction surfaces. Eight alloys with various compositions have been analyzed. The elemental compositions of the secondary structures on their friction surfaces have been determined. The relationship between the alloy secondary structure compositions with wear rate has been found. An attempt has been made to determine the secondary structure composition patterns based on the non-equilibrium thermodynamics and self-organization theory.

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pH-Dependent Conformational Changes of Concanavalin A

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.68.9.2173 ◽

1971 ◽

Vol 68 (9) ◽

pp. 2173-2176 ◽

Cited By ~ 34

Author(s):

R. Zand ◽

B. B. L. Agrawal ◽

I. J. Goldstein

Keyword(s):

Conformational Changes ◽

Concanavalin A ◽

Ph Dependent

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Systematic FTIR Spectroscopy Study of the Secondary Structure Changes in Human Serum Albumin under Various Denaturation Conditions

Biomolecules ◽

10.3390/biom9080359 ◽

2019 ◽

Vol 9 (8) ◽

pp. 359 ◽

Cited By ~ 22

Author(s):

Usoltsev ◽

Sitnikova ◽

Kajava ◽

Uspenskaya

Keyword(s):

Secondary Structure ◽

Human Serum Albumin ◽

Serum Albumin ◽

Human Serum ◽

Ftir Spectroscopy ◽

Conformational Changes ◽

Data Interpretation ◽

Random Coil ◽

Helical Conformation ◽

Structure Changes

Human serum albumin (HSA) is the most abundant protein in blood plasma. HSA is involved in the transport of hormones, fatty acids, and some other compounds, maintenance of blood pH, osmotic pressure, and many other functions. Although this protein is well studied, data about its conformational changes upon different denaturation factors are fragmentary and sometimes contradictory. This is especially true for FTIR spectroscopy data interpretation. Here, the effect of various denaturing agents on the structural state of HSA by using FTIR spectroscopy in the aqueous solutions was systematically studied. Our data suggest that the second derivative deconvolution method provides the most consistent interpretation of the obtained IR spectra. The secondary structure changes of HSA were studied depending on the concentration of the denaturing agent during acid, alkaline, and thermal denaturation. In general, the denaturation of HSA in different conditions is accompanied by a decrease in α-helical conformation and an increase in random coil conformation and the intermolecular β-strands. Meantime, some variation in the conformational changes depending on the type of the denaturation agent were also observed. The increase of β-structural conformation suggests that HSA may form amyloid-like aggregates upon the denaturation.

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