Modeling helical proteins using residual dipolar couplings, sparse long-range distance constraints and a simple residue-based force field

Eggimann, Becky L.; Vostrikov, Vitaly V.; Veglia, Gianluigi; Siepmann, J. Ilja

doi:10.1007/s00214-013-1388-y

Cited by 3 publications

(3 citation statements)

References 73 publications

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“…Applications of solid-state NMR methods for biomembranes generally fall into two broad categories. First, one can estimate distances between nuclear spins from dipolar coupling tensors due to spin–spin interactions, − as in the case of unaligned (amorphous) samples. Some specific examples include dipolar recoupling measurements for rotating samples under magic-angle spinning (MAS).…”

Section: Solid-state Nmr Spectroscopy Of Biomembranesmentioning

confidence: 99%

Concepts and Methods of Solid-State NMR Spectroscopy Applied to Biomembranes

2017

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Concepts of solid-state NMR spectroscopy and applications to fluid membranes are reviewed in this paper. Membrane lipids with H-labeled acyl chains or polar head groups are studied usingH NMR to yield knowledge of their atomistic structures in relation to equilibrium properties. This review demonstrates the principles and applications of solid-state NMR by unifying dipolar and quadrupolar interactions and highlights the unique features offered by solid-state H NMR with experimental illustrations. For randomly oriented multilamellar lipids or aligned membranes, solid-stateH NMR enables direct measurement of residual quadrupolar couplings (RQCs) due to individual C-H-labeled segments. The distribution of RQC values gives nearly complete profiles of the segmental order parameters S as a function of acyl segment position (i). Alternatively, one can measure residual dipolar couplings (RDCs) for natural abundance lipid samples to obtain segmental S order parameters. A theoretical mean-torque model provides acyl-packing profiles representing the cumulative chain extension along the normal to the aqueous interface. Equilibrium structural properties of fluid bilayers and various thermodynamic quantities can then be calculated, which describe the interactions with cholesterol, detergents, peptides, and integral membrane proteins and formation of lipid rafts. One can also obtain direct information for membrane-bound peptides or proteins by measuring RDCs using magic-angle spinning (MAS) in combination with dipolar recoupling methods. Solid-state NMR methods have been extensively applied to characterize model membranes and membrane-bound peptides and proteins, giving unique information on their conformations, orientations, and interactions in the natural liquid-crystalline state.

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Section: Solid-state Nmr Spectroscopy Of Biomembranesmentioning

confidence: 99%

Concepts and Methods of Solid-State NMR Spectroscopy Applied to Biomembranes

2017

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“…Each of these proteins provide challenging cases. For example, 1A1Z is a difficult protein to characterize due to its helical nature [ 46 ] and structural anomalies that force it to sample atypical Ramachandran Space [ 47 ]. The protein 1D3Z also provide other unique challenges due to its helical nature and hypothesized internal dynamics.…”

Section: Methodsmentioning

confidence: 99%

Increased usability, algorithmic improvements and incorporation of data mining for structure calculation of proteins with REDCRAFT software package

et al. 2020

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Background Traditional approaches to elucidation of protein structures by Nuclear Magnetic Resonance spectroscopy (NMR) rely on distance restraints also known as Nuclear Overhauser effects (NOEs). The use of NOEs as the primary source of structure determination by NMR spectroscopy is time consuming and expensive. Residual Dipolar Couplings (RDCs) have become an alternate approach for structure calculation by NMR spectroscopy. In previous works, the software package REDCRAFT has been presented as a means of harnessing the information containing in RDCs for structure calculation of proteins. However, to meet its full potential, several improvements to REDCRAFT must be made. Results In this work, we present improvements to REDCRAFT that include increased usability, better interoperability, and a more robust core algorithm. We have demonstrated the impact of the improved core algorithm in the successful folding of the protein 1A1Z with as high as ±4 Hz of added error. The REDCRAFT computed structure from the highly corrupted data exhibited less than 1.0 Å with respect to the X-ray structure. We have also demonstrated the interoperability of REDCRAFT in a few instances including with PDBMine to reduce the amount of required data in successful folding of proteins to unprecedented levels. Here we have demonstrated the successful folding of the protein 1D3Z (to within 2.4 Å of the X-ray structure) using only N-H RDCs from one alignment medium. Conclusions The additional GUI features of REDCRAFT combined with the NEF compliance have significantly increased the flexibility and usability of this software package. The improvements of the core algorithm have substantially improved the robustness of REDCRAFT in utilizing less experimental data both in quality and quantity.

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“…Padgett left the consortium, Gao ( Central State ) rejoined, and Kelly Anderson ( Roanoke College , physical), Aimée Tomlinson ( North Georgia College , physical), and Sudeep Bhattacharyay and Jim Phillips ( University of Wisconsin‐Eau Claire , biophysical and physical) joined, bringing the total to 17 MERCURY investigators. We published 79 peer‐reviewed papers, [ 159–237 ] or 1.5 papers/faculty/year, which is three times the rate for physical science faculty at undergraduate institutions. [ 46 ] The Shields group's collaboration with Brooks Pate resulted in a Science paper on the structures and energetics of the gas‐phase water hexamer, [ 160 ] which has been cited over 250 times.…”

Section: Research Accomplishments (Intellectual Merit) and Transformamentioning

confidence: 99%

Twenty years of exceptional success: The molecular education and research consortium in undergraduate computational chemistry (MERCURY)

Shields

2020

Int J of Quantum Chemistry

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The molecular education and research consortium in undergraduate computational chemistry (MERCURY) consortium, established in 2000, has contributed greatly to the scientific development of faculty and undergraduates. The MERCURY faculty peer-reviewed publication rate from 2001 to 2019 of 1.7 papers/faculty/year is 3.4 times the rate of the physical science faculty at primarily undergraduate institutions. We have worked with over 1000 students on research projects since 2001, and 75% of our undergraduate research students have been under-represented in chemistry, either female or students of color. Approximately half of our alumni attend graduate school for the purpose of obtaining advanced degrees in STEM fields, and two-thirds are female and/or students of color. We have had more than 1600 attendees at 18 MERCURY conferences, including 111 invited speakers, 61 of whom have been female and/or faculty of color. In this paper, the research accomplishments, transformational outcomes, and scientific productivity of the MERCURY faculty are highlighted.

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Modeling helical proteins using residual dipolar couplings, sparse long-range distance constraints and a simple residue-based force field

Cited by 3 publications

References 73 publications

Concepts and Methods of Solid-State NMR Spectroscopy Applied to Biomembranes

Concepts and Methods of Solid-State NMR Spectroscopy Applied to Biomembranes

Increased usability, algorithmic improvements and incorporation of data mining for structure calculation of proteins with REDCRAFT software package

Twenty years of exceptional success: The molecular education and research consortium in undergraduate computational chemistry (MERCURY)

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