The Experts below are selected from a list of 24141 Experts worldwide ranked by ideXlab platform
Thomas F. Miller - One of the best experts on this subject based on the ideXlab platform.
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Structurally detailed coarse-grained model for Sec-facilitated co-translational protein translocation and membrane integration.
PLoS computational biology, 2017Co-Authors: Michiel J. M. Niesen, Connie Wang, Reid C. Van Lehn, Thomas F. MillerAbstract:We present a coarse-grained simulation model that is capable of simulating the minute-Timescale Dynamics of protein translocation and membrane integration via the Sec translocon, while retaining sufficient chemical and structural detail to capture many of the sequence-specific interactions that drive these processes. The model includes accurate geometric representations of the ribosome and Sec translocon, obtained directly from experimental structures, and interactions parameterized from nearly 200 μs of residue-based coarse-grained molecular Dynamics simulations. A protocol for mapping amino-acid sequences to coarse-grained beads enables the direct simulation of trajectories for the co-translational insertion of arbitrary polypeptide sequences into the Sec translocon. The model reproduces experimentally observed features of membrane protein integration, including the efficiency with which polypeptide domains integrate into the membrane, the variation in integration efficiency upon single amino-acid mutations, and the orientation of transmembrane domains. The central advantage of the model is that it connects sequence-level protein features to biological observables and Timescales, enabling direct simulation for the mechanistic analysis of co-translational integration and for the engineering of membrane proteins with enhanced membrane integration efficiency.
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Regulation of Sec-Facilitated Protein Translocation and Membrane Integration
Biophysical Journal, 2016Co-Authors: Thomas F. MillerAbstract:A critical step in the biosynthesis of many proteins involves either translocation across a cellular membrane or integration into a cellular membrane. Both processes proceed via the Sec translocon - a ubiquitous and highly conserved transmembrane channel. Recent structural studies offer high-resolution snapshots of the translocon, and a wealth of biochemical and genetic data indicate important residues within the translocon; but many fundamental aspects of its mechanism and regulation remain unclear. Using both atomistic simulations and coarse-grained modeling, we investigate the conformational landscape and long-Timescale Dynamics of the translocon, and we explore the role of peptide substrates in the regulation of the translocation and integration pathways. Implications of these results for the regulation of Sec-mediated pathways for protein translocation, membrane integration, and integral membrane protein expression are discussed.
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Chemically Specific Dynamic Bond Percolation Model for Ion Transport in Polymer Electrolytes
Macromolecules, 2015Co-Authors: Michael A. Webb, Brett M. Savoie, Zhen-gang Wang, Thomas F. MillerAbstract:We introduce a coarse-grained approach for characterizing the long-Timescale Dynamics of ion diffusion in general polymer electrolytes using input from short molecular Dynamics trajectories. The approach includes aspects of the dynamic bond percolation model [J. Chem. Phys. 1983, 79, 3133−3142] by treating ion diffusion in terms of hopping transitions on a fluctuating lattice. We extend this well-known approach by using short (i.e., 10 ns) molecular Dynamics (MD) trajectories to predict the distribution of ion solvation sites that comprise the lattice and to predict the rate of hopping among the lattice sites. This yields a chemically specific dynamic bond percolation (CS-DBP) model that enables the description of long-Timescale ion diffusion in polymer electrolytes at a computational cost that makes feasible the screening of candidate materials. We employ the new model to characterize lithium-ion diffusion properties in six polyethers that differ by oxygen content and backbone stiffness: poly(trimethylen...
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Multi-scale simulation of electrode interfaces
2014Co-Authors: Thomas F. MillerAbstract:The computational modeling of chem. reactions at electrode interfaces presents extraordinary challenges from the perspective of electronic structure theory. Target applications include electrolyte redn. in formation of the solid-electrolyte interphase (SEI) and the nucleation and growth of metal dendrites. These problems combine large system sizes with subtle interactions, multiple dynamical Timescales, and electronically non-adiabatic eects. The development of new methods to perform reliable, on-the-fly electronic structure calcns. at a computational cost that makes feasible the simulation of long-Timescale Dynamics in large systems remains a central theor. challenge. We describe recent progress towards the development of accurate, scalable treatments for describing battery interfaces. In particular, we will focus on the recent coarse-graining strategies to enable the direct simulation of dendrite formation in lithium metal batteries [1], and we will describe the d. functional theory embedding methods [2, 3] that allow for the accurate description of electrolyte decompn. at metal electrodes.
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Long-Timescale Dynamics and regulation of Sec-facilitated protein translocation
Cell reports, 2012Co-Authors: Bin Zhang, Thomas F. MillerAbstract:We present a coarse-grained modeling approach that spans the nanosecond- to minute-Timescale Dynamics of cotranslational protein translocation. The method enables direct simulation of both integral membrane protein topogenesis and transmembrane domain (TM) stop-transfer efficiency. Simulations reveal multiple kinetic pathways for protein integration, including a mechanism in which the nascent protein undergoes slow-Timescale reorientation, or flipping, in the confined environment of the translocon channel. Competition among these pathways gives rise to the experimentally observed dependence of protein topology on ribosomal translation rate and protein length. We further demonstrate that sigmoidal dependence of stop-transfer efficiency on TM hydrophobicity arises from local equilibration of the TM across the translocon lateral gate, and it is predicted that slowing ribosomal translation yields decreased stop-transfer efficiency in long proteins. This work reveals the balance between equilibrium and nonequilibrium processes in protein targeting, and it provides insight into the molecular regulation of the Sec translocon.
Lewis E. Kay - One of the best experts on this subject based on the ideXlab platform.
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Probing slow Timescale Dynamics in proteins using methyl ^1H CEST
Journal of Biomolecular NMR, 2017Co-Authors: Tairan Yuwen, Rui Huang, Lewis E. KayAbstract:Although ^15N- and ^13C-based chemical exchange saturation transfer (CEST) experiments have assumed an important role in studies of biomolecular conformational exchange, ^1H CEST experiments are only beginning to emerge. We present a methyl-TROSY ^1H CEST experiment that eliminates deleterious ^1H–^1H NOE dips so that CEST profiles can be analyzed robustly to extract methyl proton chemical shifts of rare protein conformers. The utility of the experiment, along with a version that is optimized for ^13CHD_2 labeled proteins, is established through studies of exchanging protein systems. A comparison between methyl ^1H CEST and methyl ^1H CPMG approaches is presented to highlight the complementarity of the two experiments.
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Triple resonance-based ^13C^α and ^13C^β CEST experiments for studies of ms Timescale Dynamics in proteins
Journal of Biomolecular NMR, 2014Co-Authors: Dong Long, Ashok Sekhar, Lewis E. KayAbstract:A pair of triple resonance based CEST pulse schemes are presented for measuring ^13C^α and ^13C^β chemical shifts of sparsely populated and transiently formed conformers that are invisible to traditional NMR experiments. CEST profiles containing dips at resonance positions of ^13C^α or ^13C^β spins of major (ground) and minor (excited) conformers are obtained in a pseudo 3rd dimension that is generated by quantifying modulations of cross peaks in ^15N, ^1H^N correlation spectra. An application to the folding reaction of a G48A mutant of the Fyn SH3 domain is presented, illustrating and validating the methodology.
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Complementarity of ensemble and single-molecule measures of protein motion: a relaxation dispersion NMR study of an enzyme complex.
Proceedings of the National Academy of Sciences of the United States of America, 2006Co-Authors: Pramodh Vallurupalli, Lewis E. KayAbstract:Single-molecule fluorescence experiments have shown that the conformation of the complex between Escherichia coli general NAD(P)H:flavin oxidoreductase (FRE) and flavin adenine dinucleotide (FAD) fluctuates over a range of Timescales between 10(-4) and 1 s. Here we use (15)N and (13)C relaxation dispersion NMR methods to study millisecond-Timescale Dynamics in the complex. In this time regime, the protein is extremely flexible, with residues that undergo conformational exchange located throughout the molecule. Three distinct regions of Dynamics are quantified, with two of them involving residues making contact to the donor (Tyr-35) and acceptor (FAD) sites that participate in the electron transfer reaction monitored in single-molecule experiments. Modulation of the donor-acceptor distance through these conformational exchange processes, occurring with rates of approximately 400 and 1,200 s(-1) (22 degrees C), affects the rate of electron transfer and partially accounts for the range of the observed Dynamics monitored in the fluorescence experiments.
Pramodh Vallurupalli - One of the best experts on this subject based on the ideXlab platform.
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complementarity of ensemble and single molecule measures of protein motion a relaxation dispersion nmr study of an enzyme complex
Proceedings of the National Academy of Sciences of the United States of America, 2006Co-Authors: Pramodh VallurupalliAbstract:Single-molecule fluorescence experiments have shown that the conformation of the complex between Escherichia coli general NAD(P)H:flavin oxidoreductase (FRE) and flavin adenine dinucleotide (FAD) fluctuates over a range of Timescales between 10−4 and 1 s. Here we use 15N and 13C relaxation dispersion NMR methods to study millisecond-Timescale Dynamics in the complex. In this time regime, the protein is extremely flexible, with residues that undergo conformational exchange located throughout the molecule. Three distinct regions of Dynamics are quantified, with two of them involving residues making contact to the donor (Tyr-35) and acceptor (FAD) sites that participate in the electron transfer reaction monitored in single-molecule experiments. Modulation of the donor–acceptor distance through these conformational exchange processes, occurring with rates of ≈400 and 1,200 s−1 (22°C), affects the rate of electron transfer and partially accounts for the range of the observed Dynamics monitored in the fluorescence experiments.
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Complementarity of ensemble and single-molecule measures of protein motion: a relaxation dispersion NMR study of an enzyme complex.
Proceedings of the National Academy of Sciences of the United States of America, 2006Co-Authors: Pramodh Vallurupalli, Lewis E. KayAbstract:Single-molecule fluorescence experiments have shown that the conformation of the complex between Escherichia coli general NAD(P)H:flavin oxidoreductase (FRE) and flavin adenine dinucleotide (FAD) fluctuates over a range of Timescales between 10(-4) and 1 s. Here we use (15)N and (13)C relaxation dispersion NMR methods to study millisecond-Timescale Dynamics in the complex. In this time regime, the protein is extremely flexible, with residues that undergo conformational exchange located throughout the molecule. Three distinct regions of Dynamics are quantified, with two of them involving residues making contact to the donor (Tyr-35) and acceptor (FAD) sites that participate in the electron transfer reaction monitored in single-molecule experiments. Modulation of the donor-acceptor distance through these conformational exchange processes, occurring with rates of approximately 400 and 1,200 s(-1) (22 degrees C), affects the rate of electron transfer and partially accounts for the range of the observed Dynamics monitored in the fluorescence experiments.
Perttu Permi - One of the best experts on this subject based on the ideXlab platform.
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HACANCOi: a new H^α-detected experiment for backbone resonance assignment of intrinsically disordered proteins
Journal of Biomolecular NMR, 2020Co-Authors: Mikael Karjalainen, Helena Tossavainen, Maarit Hellman, Perttu PermiAbstract:Unidirectional coherence transfer is highly efficient in intrinsically disordered proteins (IDPs). Their elevated ps-ns Timescale Dynamics ensures long transverse (T_2) relaxation times allowing sophisticated coherence transfer pathway selection in comparison to folded proteins. ^1H^α-detection ensures non-susceptibility to chemical exchange with the solvent and enables chemical shift assignment of consecutive proline residues, typically abundant in IDPs. However, many IDPs undergo a disorder-to-order transition upon interaction with their target protein, which leads to the loss of the favorable relaxation properties. Long coherence transfer routes now result in prohibitively large decrease in sensitivity. We introduce a novel 4D ^1H^α-detected experiment HACANCOi, together with its 3D implementation, which warrant high sensitivity for the assignment of proline-rich regions in IDPs in complex with a globular protein. The experiment correlates ^1H^α_i, ^13C^α_i, ^15N_i and $$^{13} C^{\prime}_{i}$$ 13 C i ′ spins by transferring the magnetization concomitantly from ^13C^α_i to ^15N_i and $$^{13} C^{\prime}_{i}$$ 13 C i ′ . The B1 domain of protein G (GB1), and the enteropathogenic E. coli EspF in complex with human SNX9 SH3, serve as model systems to demonstrate the attainable sensitivity and successful sequential assignment.
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HACANCOi: a new Hα-detected experiment for backbone resonance assignment of intrinsically disordered proteins.
Journal of biomolecular NMR, 2020Co-Authors: Mikael Karjalainen, Helena Tossavainen, Maarit Hellman, Perttu PermiAbstract:Unidirectional coherence transfer is highly efficient in intrinsically disordered proteins (IDPs). Their elevated ps-ns Timescale Dynamics ensures long transverse (T2) relaxation times allowing sophisticated coherence transfer pathway selection in comparison to folded proteins. 1Hα-detection ensures non-susceptibility to chemical exchange with the solvent and enables chemical shift assignment of consecutive proline residues, typically abundant in IDPs. However, many IDPs undergo a disorder-to-order transition upon interaction with their target protein, which leads to the loss of the favorable relaxation properties. Long coherence transfer routes now result in prohibitively large decrease in sensitivity. We introduce a novel 4D 1Hα-detected experiment HACANCOi, together with its 3D implementation, which warrant high sensitivity for the assignment of proline-rich regions in IDPs in complex with a globular protein. The experiment correlates 1Hαi, 13Cαi, 15Ni and [Formula: see text] spins by transferring the magnetization concomitantly from 13Cαi to 15Ni and [Formula: see text]. The B1 domain of protein G (GB1), and the enteropathogenic E. coli EspF in complex with human SNX9 SH3, serve as model systems to demonstrate the attainable sensitivity and successful sequential assignment.
Andrew L Lee - One of the best experts on this subject based on the ideXlab platform.
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colocalization of fast and slow Timescale Dynamics in the allosteric signaling protein chey
Journal of Molecular Biology, 2013Co-Authors: Leanna R Mcdonald, Matthew J Whitley, Joshua A Boyer, Andrew L LeeAbstract:Abstract It is now widely recognized that Dynamics are important to consider for understanding allosteric protein function. However, Dynamics occur over a wide range of Timescales, and how these different motions relate to one another is not well understood. Here, we report an NMR relaxation study of Dynamics over multiple Timescales at both backbone and side-chain sites upon an allosteric response to phosphorylation. The response regulator, Escherichia coli CheY, allosterically responds to phosphorylation with a change in Dynamics on both the microsecond-to-millisecond (μs-ms) Timescale and the picosecond-to-nanosecond (ps-ns) Timescale. We observe an apparent decrease and redistribution of μs-ms Dynamics upon phosphorylation (and accompanying Mg2 + saturation) of CheY. Additionally, methyl groups with the largest changes in ps-ns Dynamics localize to the regions of conformational change measured by μs-ms Dynamics. The limited spread of changes in ps-ns Dynamics suggests a distinct relationship between motions on the μs-ms and ps-ns Timescales in CheY. The allosteric mechanism utilized by CheY highlights the diversity of roles Dynamics play in protein function.
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Multi-Timescale Dynamics study of FKBP12 along the rapamycin-mTOR binding coordinate.
Journal of molecular biology, 2010Co-Authors: Paul J. Sapienza, Randall V. Mauldin, Andrew L LeeAbstract:Drugs can affect function in proteins by modulating their flexibility. Despite this possibility, there are very few studies on how drug binding affects the Dynamics of target macromolecules. FKBP12 (FK506 binding protein 12) is a prolyl cis-trans isomerase and a drug target. The immunosuppressant drug rapamycin exerts its therapeutic effect by serving as an adaptor molecule between FKBP12 and the cell proliferation regulator mTOR (mammalian target of rapamycin). To understand the role of Dynamics in rapamycin-based immunosuppression and to gain insight into the role of Dynamics in the assembly of supramolecular complexes, we used (15)N, (13)C, and (2)H NMR spin relaxation to characterize FKBP12 along the binding coordinate that leads to cell cycle arrest. We show that sequential addition of rapamycin and mTOR leads to incremental rigidification of the FKBP12 backbone on the picosecond-nanosecond Timescale. Both binding events lead to perturbation of main-chain and side-chain Dynamics at sites distal to the binding interfaces, suggesting tight coupling interactions dispersed throughout the FKBP12-rapamycin interface. Binding of the first molecule, rapamycin, quenches microsecond-millisecond motions of the FKBP12 80's loop. This loop provides much of the surface buried at the protein-protein interface of the ternary complex, leading us to assert that preorganization upon rapamycin binding facilitates binding of the second molecule, mTOR. Widespread microsecond-millisecond motions of the backbone persist in the drug-bound enzyme, and we provide evidence that these slow motions represent coupled Dynamics of the enzyme and isomerization of the bound drug. Finally, the pattern of microsecond-millisecond Dynamics reported here in the rapamycin complex is dramatically different from the pattern in the complex with the structurally related drug FK506. This raises the important question of how two complexes that are highly isomorphic based on high-resolution static models have such different flexibilities in solution.
