Empirical power laws for the radii of gyration of protein oligomers

Tanner, John J.

doi:10.1107/s2059798316013218

Cited by 28 publications

(26 citation statements)

References 76 publications

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“…0.4. The power-law exponents for oligomers span a narrow range of 0.38-0.41, which is close to the value of 0.40 obtained for monomers [25][26][27]. Detailed values for two time windows are presented in Table 13.…”

Section: Temperature Of the Referencesupporting

confidence: 74%

Changes of Conformation in Albumin with Temperature by Molecular Dynamics Simulations

Weber

Bełdowski

Domino

et al. 2020

Entropy

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This work presents the analysis of the conformation of albumin in the temperature range of 300 K – 312 K , i.e., in the physiological range. Using molecular dynamics simulations, we calculate values of the backbone and dihedral angles for this molecule. We analyze the global dynamic properties of albumin treated as a chain. In this range of temperature, we study parameters of the molecule and the conformational entropy derived from two angles that reflect global dynamics in the conformational space. A thorough rationalization, based on the scaling theory, for the subdiffusion Flory–De Gennes type exponent of 0 . 4 unfolds in conjunction with picking up the most appreciable fluctuations of the corresponding statistical-test parameter. These fluctuations coincide adequately with entropy fluctuations, namely the oscillations out of thermodynamic equilibrium. Using Fisher’s test, we investigate the conformational entropy over time and suggest its oscillatory properties in the corresponding time domain. Using the Kruscal–Wallis test, we also analyze differences between the mean root mean square displacement of a molecule at various temperatures. Here we show that its values in the range of 306 K – 309 K are different than in another temperature. Using the Kullback–Leibler theory, we investigate differences between the distribution of the mean root mean square displacement for each temperature and time window.

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Section: Temperature Of the Referencesupporting

confidence: 74%

Changes of Conformation in Albumin with Temperature by Molecular Dynamics Simulations

Weber

Bełdowski

Domino

et al. 2020

Entropy

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“…where N is the number of residues in the oligomer. 22 Rearrangement of Eq. (3), along with appropriate units conversion and assuming 110 Da/residue, yields the following:…”

Section: Empirical Methods For Estimating M R From Saxsmentioning

confidence: 99%

“…where I(0) has units of cm 21 , N A is Avogadro's number, C is the protein concentration in g/cm 3 , Dq is the mean difference between the particle and solvent scattering density ("contrast", in units of cm 22 ), and m is the partial specific volume in cm 3 /g. Jacques and Trewhella 7 and Mylonas and Svergun 26 describe how to estimate the contrast.…”

Section: I(0)-based Methodsmentioning

confidence: 99%

“…Because R g reports on the size of the protein, it is reasonable to think that R g contains information about the in‐solution M r . A survey of 23,699 protein structures from the PDB showed that the R g of protein monomers and oligomers exhibits power law behavior:

R_{normalg} true(in Å true) = 2.0 N^{0.4},

where N is the number of residues in the oligomer . Rearrangement of Eq.…”

Section: Determination Of the Molecular Mass In Solution From Saxsmentioning

confidence: 99%

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Determination of protein oligomeric structure from small‐angle X‐ray scattering

Korasick

Tanner

2018

Protein Science

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Small-angle X-ray scattering (SAXS) is useful for determining the oligomeric states and quaternary structures of proteins in solution. The average molecular mass in solution can be calculated directly from a single SAXS curve collected on an arbitrary scale from a sample of unknown protein concentration without the need for beamline calibration or protein standards. The quaternary structure in solution can be deduced by comparing the experimental SAXS curve to theoretical curves calculated from proposed models of the oligomer. This approach is especially robust when the crystal structure of the target protein is known, and the candidate oligomer models are derived from the crystal lattice. When SAXS data are obtained at multiple protein concentrations, this analysis can provide insight into dynamic self-association equilibria. Herein, we summarize the computational methods that are used to determine protein molecular mass and quaternary structure from SAXS data. These methods are organized into a workflow and demonstrated with four case studies using experimental SAXS data from the published literature.

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“…The radius of gyration is the determinant of the compactness of the apo or holo protein during molecular dynamics simulation. It is a measure of the mass of atoms in relations with the protein complex centre of mass [71]. In terms of RoG along the trajectory, Isopteropodin induced the least compactness on the target (Figure 11, Table 6)…”

Section: Analyses Of Time-resolved Trajectoriesmentioning

confidence: 99%

Identifying potential natural inhibitors of Brucella melitensis Methionyl-tRNA synthetase through an in-silico approach

Rowaiye

Ogugua

Ibeanu³

et al. 2021

Preprint

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Background: Brucellosis is an infectious disease caused by bacteria of the genus Brucella. Although it is the most common zoonosis worldwide, there are increasing reports of drug resistance and cases of relapse after long term treatment with the existing drugs of choice. This study therefore aims at identifying possible natural inhibitors of Brucella melitensis Methionyl-tRNA synthetase through an in-silico approach. Methods: Using PyRx 0.8 virtual screening software, the target was docked against a library of natural compounds obtained from edible African plants. The compound, 2-({3-[(3,5-dichlorobenzyl) amino] propyl} amino) quinolin-4(1H)-one (OOU) which is a co-crystallized ligand with the target was used as the reference compound. Screening of the molecular descriptors of the compounds for bioavailability, pharmacokinetic properties, and bioactivity was performed using the SWISSADME, pkCSM, and Molinspiration web servers respectively. The Fpocket and PLIP webservers were used to perform the analyses of the binding pockets and the protein ligand interactions. Analysis of the time-resolved trajectories of the Apo and Holo forms of the target was performed using the Galaxy and MDWeb servers. The lead compounds, Strophanthidin and Isopteropodin are present in Corchorus olitorius and Uncaria tomentosa (cat-claw) plants respectively. Results: Isopteropodin had a binding affinity score of -8.9 kcal / ml with the target and had 17 anti-correlating residues in pocket 1 after molecular dynamics simulation. The complex formed by Isopteropodin and the target had a total RMSD of 4.408 and a total RMSF of 9.8067. However, Strophanthidin formed 3 hydrogen bonds with the target at ILE21, GLY262 and LEU294, and induced a total RMSF of 5.4541 at Pocket 1. Conclusion: Overall, Isopteropodin and Strophanthidin were found to be better drug candidates than OOU and they showed potentials to inhibit the Brucella melitensis Methionyl-tRNA synthetase at Pocket 1, hence abilities to treat brucellosis. In vivo and in vitro investigations are needed to further evaluate the efficacy and toxicity of the lead compounds.

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Empirical power laws for the radii of gyration of protein oligomers

Cited by 28 publications

References 76 publications

Changes of Conformation in Albumin with Temperature by Molecular Dynamics Simulations

Changes of Conformation in Albumin with Temperature by Molecular Dynamics Simulations

Determination of protein oligomeric structure from small‐angle X‐ray scattering

Identifying potential natural inhibitors of Brucella melitensis Methionyl-tRNA synthetase through an in-silico approach

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