Surface-induced effects in fluctuation-based measurements of single-polymer elasticity: A direct probe of the radius of gyration

Success in protein-free deposition of native nucleic acid molecules from solutions of selected ionic conditions prompted attempts for high resolution imaging of nucleic acid interactions with proteins, not attainable by conventional EM. Since the nucleic acid molecules can be visualized in the dark-field STEM mode without contrasting by heavy atoms, the established linearity between scattering cross-section and molecular weight can be applied to the determination of their molecular mass (M) linear density (M/L), mass distribution and radius of gyration (RG). Determination of these parameters promotes electron microscopic imaging of biological macromolecules by STEM to a quantitative analytical level. This technique is applied to study the mechanism of 16S rRNA folding during the assembly process of the 30S ribosomal subunit of E. coli. The sequential addition of protein S4 which binds to the 5'end of the 16S rRNA and S8 and S15 which bind to the central domain of the molecule leads to a corresponding increase of mass and increased coiling of the 16S rRNA in the core particles. This increased compactness is evident from the decrease in RG values from 114Å to 91Å (in “ribosomal” buffer consisting of 10 mM Hepes pH 7.6, 60 mM KCl, 2 m Mg(OAc)2, 1 mM DTT). The binding of S20, S17 and S7 which interact with the 5'domain, the central domain and the 3'domain, respectively, continues the trend of mass increase. However, the RG values of the core particles exhibit a reverse trend, an increase to 108Å. In addition, the binding of S7 leads to the formation of a globular mass cluster with a diameter of about 115Å and a mass of ∽300 kDa. The rest of the mass, about 330 kDa, remains loosely coiled giving the particle a “medusa-like” appearance. These results provide direct evidence that 16S RNA undergoes significant structural reorganization during the 30S subunit assembly and show that its interactions with the six primary binding proteins are not sufficient for 16S rRNA coiling into particles resembling the native 30S subunit, contrary to what has been reported in the literature.

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Radius of gyration

AccessScience ◽

10.1036/1097-8542.571400 ◽

2015 ◽

Keyword(s):

Radius Of Gyration

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The Reactive Formation of Diblock Copolymer at a Polymer/Polymer Interface and its Effect on Interfacial Structure

MRS Proceedings ◽

10.1557/proc-629-ff2.2 ◽

2000 ◽

Vol 629 ◽

Cited By ~ 1

Author(s):

Jonathan S. Schulze ◽

Timothy P. Lodge ◽

Christopher W. Macosko

Keyword(s):

Molecular Weight ◽

Interfacial Structure ◽

Root Mean Square Roughness ◽

Radius Of Gyration ◽

Interfacial Region ◽

Force Microscopy ◽

Amino Terminal ◽

Polymer Interface ◽

Atomic Force ◽

Time Required

ABSTRACTThe reaction of perdeuterated amino-terminal polystyrene (dPS-NH2) with anhydrideterminal poly(methyl methacrylate) (PMMA-anh) at a PS/PMMA interface has been observed with forward recoil spectrometry (FRES). Bilayer samples were constructed by placing thin films of PS containing ∼8.5 wt % dPS-NH2 on a PMMA-anh layer. Significant reaction was observed only after annealing the samples at 174°C for several hours, a time scale at least two orders of magnitude greater than the time required for the dPS-NH2 chains to diffuse through the bulk PS layer. The topography of the interfacial region as copolymer formed was measured using atomic force microscopy (AFM). Roughening of the PS/PMMA interface was observed to varying degrees in all annealed samples. Furthermore, the extent of this roughening was found to depend on the PS matrix molecular weight. Reaction in the samples with a high molecular weight PS matrix resulted in a root mean square roughness approximately equal to the radius of gyration Rg of the copolymer. However, approximately twice as much roughening was observed in the low molecular weight PS matrix. This study reveals how the molecular weight of one of the phases can affect the rate of reaction at a polymer/polymer interface.

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Effect of Ionic Strength on the Aggregation Propensity of Aβ1-42 Peptide: An In-silico Study

Current Chemical Biology ◽

10.2174/2212796814999200818103157 ◽

2020 ◽

Vol 14 (3) ◽

pp. 216-226

Author(s):

Priyanka Borah ◽

Venkata S.K. Mattaparthi

Keyword(s):

Diffusion Coefficient ◽

Ionic Strength ◽

Marked Effect ◽

Computational Study ◽

Conformational Dynamics ◽

Rapid Change ◽

Md Simulations ◽

Radius Of Gyration ◽

Aggregation Propensity ◽

In Silico Study

Background: Aggregation of misfolded proteins under stress conditions in the cell might lead to several neurodegenerative disorders. Amyloid-beta (Aβ1-42) peptide, the causative agent of Alzheimer’s disease, has the propensity to fold into β-sheets under stress, forming aggregated amyloid plaques. This is influenced by factors such as pH, temperature, metal ions, mutation of residues, and ionic strength of the solution. There are several studies that have highlighted the importance of ionic strength in affecting the folding and aggregation propensity of Aβ1-42 peptide. Objective: To understand the effect of ionic strength of the solution on the aggregation propensity of Aβ1-42 peptide, using computational approaches. Materials and Methods: In this study, Molecular Dynamics (MD) simulations were performed on Aβ1-42 peptide monomer placed in (i) 0 M, (ii) 0.15 M, and (iii) 0.30 M concentration of NaCl solution. To prepare the input files for the MD simulations, we have used the Amberff99SB force field. The conformational dynamics of Aβ1-42 peptide monomer in different ionic strengths of the solutions were illustrated from the analysis of the corresponding MD trajectory using the CPPtraj tool. Results: From the MD trajectory analysis, we observe that with an increase in the ionic strength of the solution, Aβ1-42 peptide monomer shows a lesser tendency to undergo aggregation. From RMSD and SASA analysis, we noticed that Aβ1-42 peptide monomer undergoes a rapid change in conformation with an increase in the ionic strength of the solution. In addition, from the radius of gyration (Rg) analysis, we observed Aβ1-42 peptide monomer to be more compact at moderate ionic strength of the solution. Aβ1-42 peptide was also found to hold its helical secondary structure at moderate and higher ionic strengths of the solution. The diffusion coefficient of Aβ1-42 peptide monomer was also found to vary with the ionic strength of the solution. We observed a relatively higher diffusion coefficient value for Aβ1-42 peptide at moderate ionic strength of the solution. Conclusion: Our findings from this computational study highlight the marked effect of ionic strength of the solution on the conformational dynamics and aggregation propensity of Aβ1-42 peptide monomer.

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Quantities Directly Measurable by Scattering

10.1093/oso/9780199670871.003.0003 ◽

2018 ◽

Author(s):

Eaton E. Lattman ◽

Thomas D. Grant ◽

Edward H. Snell

Keyword(s):

Molecular Weight ◽

Particle Shape ◽

Particle Surface ◽

Scattering Data ◽

Radius Of Gyration ◽

Particle Volume ◽

Particle Surface Area ◽

Scattering Angle ◽

Particle Dimension ◽

Maximum Particle

In this chapter we note that solution scattering data can be divided into four regions. At zero scattering angle, the scattering provides information on molecular weight of the particle in solution. Beyond that, the scattering is influenced by the radius of gyration. As the scattering angle increases, the scattering is influenced by the particle shape, and finally by the interface with the particle and the solution. There are a number of important invariants that can be calculated directly from the data including molecular mass, radius of gyration, Porod invariant, particle volume, maximum particle dimension, particle surface area, correlation length, and volume of correlation. The meaning of these is described in turn along with their mathematical derivations.

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Evaluating the Effect of the Financial Status to the Mobility Customs

ISPRS International Journal of Geo-Information ◽

10.3390/ijgi10050328 ◽

2021 ◽

Vol 10 (5) ◽

pp. 328

Author(s):

Gergo Pintér ◽

Imre Felde

Keyword(s):

Socioeconomic Status ◽

Economic Status ◽

Housing Prices ◽

Principal Component ◽

Cellular Phone ◽

Radius Of Gyration ◽

Financial Status ◽

Property Price ◽

Statistical Relationships ◽

Commuting Patterns

In this article, we explore the relationship between cellular phone data and housing prices in Budapest, Hungary. We determine mobility indicators from one months of Call Detail Records (CDR) data, while the property price data are used to characterize the socioeconomic status at the Capital of Hungary. First, we validated the proposed methodology by comparing the Home and Work locations estimation and the commuting patterns derived from the cellular network dataset with reports of the national mini census. We investigated the statistical relationships between mobile phone indicators, such as Radius of Gyration, the distance between Home and Work locations or the Entropy of visited cells, and measures of economic status based on housing prices. Our findings show that the mobility correlates significantly with the socioeconomic status. We performed Principal Component Analysis (PCA) on combined vectors of mobility indicators in order to characterize the dependence of mobility habits on socioeconomic status. The results of the PCA investigation showed remarkable correlation of housing prices and mobility customs.

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Conformational Ensembles by NMR and MD Simulations in Model Heptapeptides with Select Tri-Peptide Motifs

International Journal of Molecular Sciences ◽

10.3390/ijms22031364 ◽

2021 ◽

Vol 22 (3) ◽

pp. 1364

Author(s):

V. V. Krishnan ◽

Timothy Bentley ◽

Alina Xiong ◽

Kalyani Maitra

Keyword(s):

Principal Component ◽

Md Simulations ◽

Conformational Space ◽

Random Coil ◽

Radius Of Gyration ◽

Small Peptides ◽

Conformational Ensembles ◽

Solution State ◽

Peptide Motifs ◽

Explicit Solvent

Both nuclear magnetic resonance (NMR) and molecular dynamics (MD) simulations are routinely used in understanding the conformational space sampled by peptides in the solution state. To investigate the role of single-residue change in the ensemble of conformations sampled by a set of heptapeptides, AEVXEVG with X = L, F, A, or G, comprehensive NMR, and MD simulations were performed. The rationale for selecting the particular model peptides is based on the high variability in the occurrence of tri-peptide E*L between the transmembrane β-barrel (TMB) than in globular proteins. The ensemble of conformations sampled by E*L was compared between the three sets of ensembles derived from NMR spectroscopy, MD simulations with explicit solvent, and the random coil conformations. In addition to the estimation of global determinants such as the radius of gyration of a large sample of structures, the ensembles were analyzed using principal component analysis (PCA). In general, the results suggest that the -EVL- peptide indeed adopts a conformational preference that is distinctly different not only from a random distribution but also from other peptides studied here. The relatively straightforward approach presented herein could help understand the conformational preferences of small peptides in the solution state.

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Self-Stable Precipitation Polymerization Molecular Entanglement Effect and Molecular Weight Simulations and Experiments

Polymers ◽

10.3390/polym13142243 ◽

2021 ◽

Vol 13 (14) ◽

pp. 2243

Author(s):

Jiali Qu ◽

Yi Gao ◽

Wantai Yang

Keyword(s):

Molecular Weight ◽

Maleic Anhydride ◽

Molecular Conformation ◽

Average Molecular Weight ◽

Precipitation Polymerization ◽

Radius Of Gyration ◽

Propagation Mechanism ◽

Reactive Molecular Dynamics ◽

End Distance ◽

Good Agreement

In this paper, we developed a reactive molecular dynamics (RMD) scheme to simulate the Self-Stable Precipitation (SP) polymerization of 1-pentene and cyclopentene (C5) with maleic anhydride (MAn) in an all-atom resolution. We studied the chain propagation mechanism by tracking the changes in molecular conformation and analyzing end-to-end distance and radius of gyration. The results show that the main reason of chain termination in the reaction process was due to intramolecular cyclic entanglement, which made the active center wrapped in the center of the globular chain. After conducting the experiment in the same condition with the simulation, we found that the distribution trend and peak value of the molecular-weight-distribution curve in the simulation were consistent with experimental results. The simulated number average molecular weight (Mn) and weight average molecular weight (Mw) were in good agreement with the experiment. Moreover, the simulated molecular polydispersity index (PDI) for cyclopentene reaction with maleic anhydride was accurate, differing by 0.04 from the experimental value. These show that this model is suitable for C5–maleic anhydride self-stable precipitation polymerization and is expected to be used as a molecular weight prediction tool for other maleic anhydride self-stable precipitation polymerization system.

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