Search Results - "Gumbart, James"

Membrane thinning and lateral gating are consistent features of BamA across multiple species by Liu, Jinchan, Gumbart, James C

“…In Gram-negative bacteria, the folding and insertion of β-barrel outer membrane proteins (OMPs) to the outer membrane are mediated by the β-barrel assembly…”
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The β-barrel assembly machinery in motion by Noinaj, Nicholas, Gumbart, James C., Buchanan, Susan K.

“…In this Progress article, Buchanan and colleagues discuss recent studies that have advanced our understanding of the structure of the fully assembled β-barrel…”
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Thicket and Mesh: How the Outer Membrane Can Resist Tension Imposed by the Cell Wall by Ryoo, David, Hwang, Hyea, Gumbart, James C.

“…The cell envelope of Gram-negative bacteria is composed of an outer membrane (OM) and an inner membrane (IM) and a peptidoglycan cell wall (CW) between them…”
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Seeing is believing: Illuminating the Gram-negative outer membrane with molecular dynamics simulations by Gutishvili, Gvantsa, Yang, Lixinhao, Gumbart, James C.

“…Recent advances in molecular dynamics (MD) simulations have led to rapid improvement in our understanding of the molecular details of the outer membranes (OMs)…”
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A Novel Approach to Simulating the Gating Transitions of Mechanosensitive Channels by Gumbart, James C.

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Rapid parameterization of small molecules using the force field toolkit by Mayne, Christopher G., Saam, Jan, Schulten, Klaus, Tajkhorshid, Emad, Gumbart, James C.

“…The inability to rapidly generate accurate and robust parameters for novel chemical matter continues to severely limit the application of molecular dynamics…”
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Role of the Native Outer-Membrane Environment on the Transporter BtuB by Balusek, Curtis, Gumbart, James C.

“…BtuB is a TonB-dependent transporter that permits the high-affinity binding and transport of cobalamin (CBL), or vitamin B12, across the asymmetric outer…”
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The Adaptive Biasing Force Method: Everything You Always Wanted To Know but Were Afraid To Ask by Comer, Jeffrey, Gumbart, James C, Hénin, Jérôme, Lelièvre, Tony, Pohorille, Andrew, Chipot, Christophe

“…In the host of numerical schemes devised to calculate free energy differences by way of geometric transformations, the adaptive biasing force algorithm has…”
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Thicket and mesh: Understanding turgor pressure resistance of outer membrane-cell wall system by Ryoo, David, Hwang, Hyea, Gumbart, James C.

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Inward-facing glycine residues create sharp turns in β-barrel membrane proteins by Zhang, Zijian, Ryoo, David, Gumbart, James C.

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Escherichia coli peptidoglycan structure and mechanics as predicted by atomic-scale simulations by Gumbart, James C, Beeby, Morgan, Jensen, Grant J, Roux, Benoît

“…Bacteria face the challenging requirement to maintain their shape and avoid rupture due to the high internal turgor pressure, but simultaneously permit the…”
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Lateral Opening and Exit Pore Formation Are Required for BamA Function by Noinaj, Nicholas, Kuszak, Adam J., Balusek, Curtis, Gumbart, James C., Buchanan, Susan K.

“…The outer membrane of Gram-negative bacteria is replete with a host of β-barrel outer membrane proteins (OMPs). Despite serving a variety of essential…”
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Preparing Membrane Proteins for Simulation Using CHARMM-GUI by Li, Yupeng, Liu, Jinchan, Gumbart, James C

“…Molecular dynamics simulations of membrane proteins have grown dramatically in the last 20 years. Running these simulations first requires embedding the…”
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Efficient Determination of Protein–Protein Standard Binding Free Energies from First Principles by Gumbart, James C, Roux, Benoît, Chipot, Christophe

“…Characterizing protein–protein association quantitatively has been a long standing challenge for computer simulations. Here, a theoretical framework is put…”
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Understanding Virus Structure and Dynamics through Molecular Simulations by Lynch, Diane L., Pavlova, Anna, Fan, Zixing, Gumbart, James C.

“…Viral outbreaks remain a serious threat to human and animal populations and motivate the continued development of antiviral drugs and vaccines, which in turn…”
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Stepwise gating of the Sec61 protein-conducting channel by Sec63 and Sec62 by Itskanov, Samuel, Kuo, Katie M., Gumbart, James C., Park, Eunyong

“…Many proteins are transported into the endoplasmic reticulum by the universally conserved Sec61 channel. Post-translational transport requires two additional…”
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Structural and Functional Characterization of the LPS Transporter LptDE from Gram-Negative Pathogens by Botos, Istvan, Majdalani, Nadim, Mayclin, Stephen J., McCarthy, Jennifer Gehret, Lundquist, Karl, Wojtowicz, Damian, Barnard, Travis J., Gumbart, James C., Buchanan, Susan K.

“…Incorporation of lipopolysaccharide (LPS) into the outer membrane of Gram-negative bacteria is essential for viability, and is accomplished by a two-protein…”
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BFEE: A User-Friendly Graphical Interface Facilitating Absolute Binding Free-Energy Calculations by Fu, Haohao, Gumbart, James C, Chen, Haochuan, Shao, Xueguang, Cai, Wensheng, Chipot, Christophe

“…Quantifying protein–ligand binding has attracted the attention of both theorists and experimentalists for decades. Many methods for estimating binding free…”
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Uncovering the folding mechanism of pertactin: A comparative study of isolated and vectorial folding by Pang, Yui Tik, Hazel, Anthony J., Gumbart, James C.

“…Autotransporters are a large family of virulence factors found in Gram-negative bacteria that play important roles in their pathogenesis. The passenger domain…”
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Structural insight into the biogenesis of β-barrel membrane proteins by Noinaj, Nicholas, Kuszak, Adam J., Gumbart, James C., Lukacik, Petra, Chang, Hoshing, Easley, Nicole C., Lithgow, Trevor, Buchanan, Susan K.

“…β-barrel membrane proteins are essential for nutrient import, signalling, motility and survival. In Gram-negative bacteria, the β-barrel assembly machinery…”
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