scholarly journals Computational Investigation of APOBEC3H Substrate Orientation and Selectivity

2020 ◽  
Author(s):  
Mark A. Hix ◽  
G. Andres Cisneros
Keyword(s):  
Crystal Structures ◽  
Theoretical Investigation ◽  
Md Simulations ◽  
Computational Investigation ◽  
Substrate Orientation ◽  
Sequence Selectivity ◽  
Binding Orientation

There are several available crystal structures for APOBEC3H, however, none with bound substrate. Our manuscript presents a theoretical investigation of the binding orientation of the ssDNA substrate for the DNA deaminase APOBEC3H. Here, we have used classical MD simulations to explore the possible<br>binding orientation of a dsDNA substrate, as well as the possible factors leading to the observed substrate sequence selectivity.

scholarly journals Computational Investigation of APOBEC3H Substrate Orientation and Selectivity

2020 ◽  
Author(s):  
Mark A. Hix ◽  
G. Andres Cisneros
Keyword(s):  
Crystal Structures ◽  
Theoretical Investigation ◽  
Md Simulations ◽  
Computational Investigation ◽  
Substrate Orientation ◽  
Sequence Selectivity ◽  
Binding Orientation

There are several available crystal structures for APOBEC3H, however, none with bound substrate. Our manuscript presents a theoretical investigation of the binding orientation of the ssDNA substrate for the DNA deaminase APOBEC3H. Here, we have used classical MD simulations to explore the possible<br>binding orientation of a dsDNA substrate, as well as the possible factors leading to the observed substrate sequence selectivity.

scholarly journals Computational Investigation of APOBEC3H Substrate Orientation and Selectivity

2020 ◽  
Author(s):  
Mark A. Hix ◽  
G. Andres Cisneros
Keyword(s):  
Crystal Structures ◽  
Theoretical Investigation ◽  
Md Simulations ◽  
Computational Investigation ◽  
Substrate Orientation ◽  
Sequence Selectivity ◽  
Binding Orientation

There are several available crystal structures for APOBEC3H, however, none with bound substrate. Our manuscript presents a theoretical investigation of the binding orientation of the ssDNA substrate for the DNA deaminase APOBEC3H. Here, we have used classical MD simulations to explore the possible<br>binding orientation of a dsDNA substrate, as well as the possible factors leading to the observed substrate sequence selectivity.

Investigating the dynamic nature of the ABC transporters: ABCB1 and MsbA as examples for the potential synergies of MD theory and EPR applications

2015 ◽  
Vol 43 (5) ◽  
pp. 1023-1032 ◽  
Author(s):  
Thomas Stockner ◽  
Anna Mullen ◽  
Fraser MacMillan
Keyword(s):  
Crystal Structures ◽  
Conformational Changes ◽  
Abc Transporters ◽  
Epr Spectroscopy ◽  
Structural Information ◽  
Dynamic Properties ◽  
Molecular System ◽  
Synergistic Effects ◽  
Md Simulations ◽  
Substrate Spectrum

ABC transporters are primary active transporters found in all kingdoms of life. Human multidrug resistance transporter ABCB1, or P-glycoprotein, has an extremely broad substrate spectrum and confers resistance against chemotherapy drug treatment in cancer cells. The bacterial ABC transporter MsbA is a lipid A flippase and a homolog to the human ABCB1 transporter, with which it partially shares its substrate spectrum. Crystal structures of MsbA and ABCB1 have been solved in multiple conformations, providing a glimpse into the possible conformational changes the transporter could be going through during the transport cycle. Crystal structures are inherently static, while a dynamic picture of the transporter in motion is needed for a complete understanding of transporter function. Molecular dynamics (MD) simulations and electron paramagnetic resonance (EPR) spectroscopy can provide structural information on ABC transporters, but the strength of these two methods lies in the potential to characterise the dynamic regime of these transporters. Information from the two methods is quite complementary. MD simulations provide an all atom dynamic picture of the time evolution of the molecular system, though with a narrow time window. EPR spectroscopy can probe structural, environmental and dynamic properties of the transporter in several time regimes, but only through the attachment sites of an exogenous spin label. In this review the synergistic effects that can be achieved by combining the two methods are highlighted, and a brief methodological background is also presented.

scholarly journals The role of BamA in the biogenesis of beta-barrel membrane proteins

2014 ◽  
Vol 70 (a1) ◽  
pp. C578-C578
Author(s):  
Nicholas Noinaj ◽  
Adam Kuszak ◽  
Curtis Balusek ◽  
JC Gumbart ◽  
Petra Lukacik ◽  
...  
Keyword(s):  
Membrane Proteins ◽  
Outer Membrane ◽  
Crystal Structures ◽  
Outer Membrane Proteins ◽  
Hydrophobic Surface ◽  
Md Simulations ◽  
Structural Features ◽  
Bam Complex ◽  
Beta Barrel

Beta-barrel membrane proteins are essential for nutrient import, signaling, motility, and survival. In Gram-negative bacteria, the beta-barrel assembly machinery (BAM) complex is responsible for the biogenesis of beta-barrel outer membrane proteins (OMPs), with homologous complexes found in mitochondria and chloroplasts. Despite their essential roles, exactly how these OMPs are formed remains unknown. The BAM complex consists of a central and essential component called BamA (an OMP itself) and four lipoproteins called BamB-E. While the structure of the lipoproteins have been reported, the structure of full length BamA has been elusive. Recently though, we described the structure of BamA from two species of bacteria: Neisseria gonorrhoeae and Haemophilus ducreyi. BamA consists of a large periplasmic domain attached to a 16-strand transmembrane beta-barrel domain. Together, our crystal structures and molecule dynamics (MD) simulations revealed several structural features which gave clues to the mechanism by which BamA catalyzes beta-barrel assembly. The first is that the interior cavity is accessible in one BamA structure and conformationally closed in the other. Second, an exterior rim of the beta-barrel has a distinctly narrowed hydrophobic surface, locally destabilizing the outer membrane. Third, the beta-barrel can undergo lateral opening, suggesting a route from the interior cavity in BamA into the outer membrane. And fourth, a surface exposed exit pore positioned above the lateral opening site which may play a role in the biogenesis of extracellular loops. In this presentation, the crystal structures and MD simulations of BamA will be presented along with our work looking at the role of these four structural features in the role of BamA within the BAM complex.

scholarly journals Resistance from Afar: Distal Mutation V36M Allosterically Modulates the Active Site to Accentuate Drug Resistance in HCV NS3/4A Protease

2018 ◽  
Author(s):  
Ayşegül Özen ◽  
Kuan-Hung Lin ◽  
Keith P Romano ◽  
Davide Tavella ◽  
Alicia Newton ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Conformational Changes ◽  
Active Site ◽  
Md Simulations ◽  
Drug Susceptibility ◽  
Active Site Residues ◽  
Allosteric Coupling ◽  
Direct Acting ◽  
Distal Mutation ◽  
Active Site Mutations

AbstractHepatitis C virus rapidly evolves, conferring resistance to direct acting antivirals. While resistance via active site mutations in the viral NS3/4A protease has been well characterized, the mechanism for resistance of non-active site mutations is unclear. R155K and V36M often co-evolve and while R155K alters the electrostatic network at the binding site, V36M is more than 13 Å away. In this study the mechanism by which V36M confers resistance, in the context of R155K, is elucidated with drug susceptibility assays, crystal structures, and molecular dynamics (MD) simulations for three protease inhibitors: telaprevir, boceprevir and danoprevir. The R155K and R155K/V36M crystal structures differ in the α-2 helix and E2 strand near the active site, with alternative conformations at M36 and side chains of active site residues D168 and R123, revealing an allosteric coupling, which persists dynamically in MD simulations, between the distal mutation and the active site. This allosteric modulation validates the network hypothesis and elucidates how distal mutations confer resistance through propagation of conformational changes to the active site.

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