The <scp>Bio3D</scp> packages for structural bioinformatics

Grant, Barry J.; Skjærven, Lars; Yao, Xin‐Qiu

doi:10.1002/pro.3923

Cited by 309 publications

(200 citation statements)

References 46 publications

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“…ΔRMSF was determined for each condition with respect to the averaged apo RMSF and shaded regions correspond to the average standard deviation difference. Principal component analysis (PCA) and network analysis were both performed in R with the bio3D package on one representative trajectory and have been extensively described elsewhere [59][60][61] . Briefly PCA involves the diagonalization of the covariance matrix into their component eigenvalues and eigenvectors.…”

Section: Rmsd Rmsf Pca and Network Analysismentioning

confidence: 99%

Ligand Induced Conformational and Dynamical Changes in a GT-B Glycosyltransferase: Molecular Dynamic Simulations of Heptosyltransferase I Apo, Binary and Ternary Complexes

Hassan

Milicaj

et al. 2021

Preprint

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Understanding the dynamical motions and ligand recognition motifs of specific glycosyltransferase enzymes, like Heptosyltransferase I (HepI), is critical to discerning the behavior of other carbohydrate binding enzymes. Prior studies in our lab demonstrated that glycosyltransferases in the GT-B structural class, which are characterized by their connection of two Rossman-like domains by a linker region, have conservation of both structure and dynamical motions, despite low sequence conservation, therefore making discoveries found in HepI transferable to other GT-B enzymes. Through a series of 100 nanosecond Molecular Dynamics simulations of HepI in apo enzyme state, and also in the binary and ternary complexes with the native substrates/products. Ligand free energy analysis allowed determination of an anticipated enzymatic path for ligand binding and release. Principle component, dynamic cross correlation and network analyses of the simulation trajectories revealed that there are not only correlated motions between the N- and C-termini, but also that residues within the N-terminal domain communicate via a path that includes substrate proximal residues of the C-terminal domain. Analysis of structural changes, energetics of substrate/products binding and changes in pKa have elucidated a variety of inter- and intradomain interactions that are critical for catalysis. These data corroborate and allow visualization of previous experimental observations of protein conformational changes of HepI. This study has provided valuable insights into the regions involved in HepI conformational rearrangement upon ligand binding, and are likely to enhance efforts to develop new dynamics disrupting enzyme inhibitors for GT-B structural enzymes in the future.

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Section: Rmsd Rmsf Pca and Network Analysismentioning

confidence: 99%

Ligand Induced Conformational and Dynamical Changes in a GT-B Glycosyltransferase: Molecular Dynamic Simulations of Heptosyltransferase I Apo, Binary and Ternary Complexes

Hassan

Milicaj

et al. 2021

Preprint

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“…Initial validation of the MD results was performed using the ‘simulation analysis’ tools within Desmond. Additional detailed analyses were performed using the Bio3D developed by Grant et al [ 23 , 24 ].…”

Section: Methodsmentioning

confidence: 99%

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

Krishnan

Bentley

Xiong

et al. 2021

IJMS

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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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“…Here, r i and r j were Cartesian coordinates of i th and j th Cα atoms, 〈r i 〉 and 〈r j 〉 stood for the time average over all the configurations derived from the molecular dynamics simulation. This analysis was performed using the Bio3D library as implemented in R (42) (43) (44) (45).…”

Section: Methodsmentioning

confidence: 99%

“…The positive value means positively correlated motion (moving in the same direction) indicated in cyan and the negative value represents negatively correlated motion (moving in the opposite direction) indicated in magenta. The DCCM analysis is carried out using the Bio3D packages of R (42) (43) (44) (45).…”

Section: Methodsmentioning

confidence: 99%

In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and HNRNP-1

Chaudhari

Mahera

et al. 2020

Preprint

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Novel severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has claimed more than 1.5 million lives worldwide and counting. As per the GISAID database, the genomics of SARS-CoV2 is extensively studied with more than 500 genome submissions per day. Out of several hotspot mutations within the SARS-CoV-2 genome, researchers have focused a lot on missense variants but the least work is done on the UTRs. One of the most frequent 5’ UTR variants in the SARS-CoV-2 genome is the C241T with a global frequency of more than 0.9. In the present study, the effect of the C241T mutation has been studied with respect to change in RNA structure and its interaction with the host replication factors MADP1 Zinc finger CCHC-type and RNA-binding motif 1 (hnRNP1). The results obtained from molecular docking and molecular dynamics simulation indicated weaker interaction of C241T mutant stem loops with host transcription factor MADP1 indicating reduced replication efficiency. The results are also correlated with increased recovery rates and decreased death rates of global SARS-CoV-2 cases.

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The Bio3D packages for structural bioinformatics

Cited by 309 publications

References 46 publications

Ligand Induced Conformational and Dynamical Changes in a GT-B Glycosyltransferase: Molecular Dynamic Simulations of Heptosyltransferase I Apo, Binary and Ternary Complexes

Ligand Induced Conformational and Dynamical Changes in a GT-B Glycosyltransferase: Molecular Dynamic Simulations of Heptosyltransferase I Apo, Binary and Ternary Complexes

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

In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and HNRNP-1

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