Smooth statistical torsion angle potential derived from a large conformational database via adaptive kernel density estimation improves the quality of NMR protein structures

Bermejo, Guillermo A.; Clore, G. Marius; Schwieters, Charles D.

doi:10.1002/pro.2163

Cited by 58 publications

(90 citation statements)

References 57 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…First, the conjoined rigid-body/torsion angle refinement approach narrows the conformational search space and permits efficient convergence to the structure that best accounts for all experimental data. Second, with the cross-linkers and cross-linked residues explicitly modeled and with flexible linker residues opting for certain rotamers (37), the conformational space possibly adopted by the protein-excited state is further narrowed. Third, the cross-links identified with high confidence are partially redundant.…”

Section: Discussionmentioning

confidence: 99%

Modeling Protein Excited-state Structures from “Over-length” Chemical Cross-links

Ding

Gong

et al. 2017

Journal of Biological Chemistry

View full text Add to dashboard Cite

Edited by Norma AllewellChemical cross-linking coupled with mass spectroscopy (CXMS) provides proximity information for the cross-linked residues and is used increasingly for modeling protein structures. However, experimentally identified cross-links are sometimes incompatible with the known structure of a protein, as the distance calculated between the cross-linked residues far exceeds the maximum length of the cross-linker. The discrepancies may persist even after eliminating potentially false cross-links and excluding intermolecular ones. Thus the "overlength" cross-links may arise from alternative excited-state conformation of the protein. Here we present a method and associated software DynaXL for visualizing the ensemble structures of multidomain proteins based on intramolecular cross-links identified by mass spectrometry with high confidence. Representing the cross-linkers and cross-linking reactions explicitly, we show that the protein excited-state structure can be modeled with as few as two over-length cross-links. We demonstrate the generality of our method with three systems: calmodulin, enzyme I, and glutamine-binding protein, and we show that these proteins alternate between different conformations for interacting with other proteins and ligands. Taken together, the over-length chemical cross-links contain valuable information about protein dynamics, and our findings here illustrate the relationship between dynamic domain movement and protein function.Present-day structural biology largely focuses on the predominant ground-state structures of proteins, which are most populated and readily detectable. Nevertheless, it is becoming clear that a protein can transiently adopt alternative, often lowly populated excited-state conformations. Dynamic interconversion between protein ground and excited states, together constituting the ensemble structures of a protein, enables the protein to perform its function (1, 2). For a multidomain protein, the dynamics usually involve the rearrangement between the domains, which can be essential for ligand recognition, catalytic activity, and allosteric modulation of the protein (3, 4). Despite technical advances in X-ray crystallography (5), nuclear magnetic resonance (NMR) spectroscopy (6), and cryo-electron microscopy (7), the excited states of proteins remain difficult to characterize. Among the existing techniques, NMR spectroscopy is known for identifying the excited states and for elucidating protein dynamics (6). Yet NMR requires a large quantity of purified, isotopically enriched recombinant proteins and is mainly applicable to proteins Ͻ50,000 Da.Chemical cross-linking of proteins coupled with mass spectrometry (CXMS) 4 is an emerging technique in structural biology and has been increasingly used for modeling protein structures (8, 9). The cross-linked residues that are identified by high resolution mass spectroscopy should be close to each other, within the reach of the cross-linker used. However, it has been shown that the straight-line distance between t...

show abstract

Section: Discussionmentioning

confidence: 99%

Modeling Protein Excited-state Structures from “Over-length” Chemical Cross-links

Ding

Gong

et al. 2017

Journal of Biological Chemistry

View full text Add to dashboard Cite

show abstract

“…The program TALOS + 47 was used to derive backbone dihedral angles from the assigned chemical shifts. The Xplor-NIH statistical torsion angle potential, torsionDB, 48 was used to further restrain other dihedral angles. Long-range amide HN-HN distances were derived from 1 H– 1 H NOE measurements.…”

Section: Methodsmentioning

confidence: 99%

Structural Insights into the Yersinia pestis Outer Membrane Protein Ail in Lipid Bilayers

2017

View full text Add to dashboard Cite

Yersinia pestis the causative agent of plague, is highly pathogenic and poses very high risk to public health. The outer membrane protein Ail (Adhesion invasion locus) is one of the most highly expressed proteins on the cell surface of Y. pestis, and a major target for the development of medical countermeasures. Ail is essential for microbial virulence and is critical for promoting the survival of Y. pestis in serum. Structures of Ail have been determined by X-ray diffraction and solution NMR spectroscopy, but the protein’s activity is influenced by the detergents in these samples, underscoring the importance of the surrounding environment for structure–activity studies. Here we describe the backbone structure of Ail, determined in lipid bilayer nanodiscs, using solution NMR spectroscopy. We also present solid-state NMR data obtained for Ail in membranes containing lipopolysaccharide (LPS), a major component of the bacterial outer membranes. The protein in lipid bilayers, adopts the same eight-stranded β-barrel fold observed in the crystalline and micellar states. The membrane composition, however, appears to have a marked effect on protein dynamics, with LPS enhancing conformational order and slowing down the 15N transverse relaxation rate. The results provide information about the way in which an outer membrane protein inserts and functions in the bacterial membrane.

show abstract

“…With regard to side chain conformation, WHAT IF and MolProbity indicate that both eefxPot and REPEL produce acceptable c1/c2 rotamer normality scores, with WHAT IF favoring eefxPot and MolProbity favoring REPEL. This is not surprising, since both sets of calculations were performed with torsionDB (29), which tends to have the greatest influence on side chain conformations that were not otherwise restrained.…”

Section: Nmr-restrained Structure Calculationsmentioning

confidence: 97%

“…The conformational energy component of E SYS includes terms for covalent bonds (E BON ), covalent bond angles (E ANG ), improper dihedral angles (E IMP ), and proper dihedral angles represented by empirical values (E DIHE ) or by statistical torsion-angle potentials such as torsionDB or Rama (28,29). The nonbonded energy component of E SYS can be represented either by a simple repulsive potential, implemented with the REPEL form of the XPLOR van der Waals function (E REPEL ) (27), or by the potential eefxPot (E EEF ) (20), which comprises terms for Lennard-Jones van der Waals energy (E VDW ), including both repulsive and attractive forces, electrostatic energy (E ELEC ), and solvation free energy (E SLV ).…”

Section: Description Of Eefxpotmentioning

confidence: 99%

“…In the simulated-annealing stage, k CDIH was set to 200 kcal mol -1 rad -2 , k DIST was increased geometrically from 2 to 30 kcal mol -1 Å À2 , and k CSA was increased geometrically from 0.01 to 0.1 kcal mol -1 ppm À2 . The torsionDB statistical torsion-angle potential (29) was included with a force constant set to k tDB ¼ 0.02 kcal mol -1 in the high-temperature stage and ramped geometrically from 0.02 to 2 kcal mol -1 during simulated annealing.…”

Section: Structure Calculationsmentioning

confidence: 99%

See 1 more Smart Citation

A Practical Implicit Membrane Potential for NMR Structure Calculations of Membrane Proteins

Tian

Schwieters

Opella

et al. 2015

Biophysical Journal

View full text Add to dashboard Cite

The highly anisotropic environment of the lipid bilayer membrane imposes significant constraints on the structures and functions of membrane proteins. However, NMR structure calculations typically use a simple repulsive potential that neglects the effects of solvation and electrostatics, because explicit atomic representation of the solvent and lipid molecules is computationally expensive and impractical for routine NMR-restrained calculations that start from completely extended polypeptide templates. Here, we describe the extension of a previously described implicit solvation potential, eefxPot, to include a membrane model for NMR-restrained calculations of membrane protein structures in XPLOR-NIH. The key components of eefxPot are an energy term for solvation free energy that works together with other nonbonded energy functions, a dedicated force field for conformational and nonbonded protein interaction parameters, and a membrane function that modulates the solvation free energy and dielectric screening as a function of the atomic distance from the membrane center, relative to the membrane thickness. Initial results obtained for membrane proteins with structures determined experimentally in lipid bilayer membranes show that eefxPot affords significant improvements in structural quality, accuracy, and precision. Calculations with eefxPot are straightforward to implement and can be used to both fold and refine structures, as well as to run unrestrained molecular-dynamics simulations. The potential is entirely compatible with the full range of experimental restraints measured by various techniques. Overall, it provides a useful and practical way to calculate membrane protein structures in a physically realistic environment.

show abstract

Smooth statistical torsion angle potential derived from a large conformational database via adaptive kernel density estimation improves the quality of NMR protein structures

Cited by 58 publications

References 57 publications

Modeling Protein Excited-state Structures from “Over-length” Chemical Cross-links

Modeling Protein Excited-state Structures from “Over-length” Chemical Cross-links

Structural Insights into the Yersinia pestis Outer Membrane Protein Ail in Lipid Bilayers

A Practical Implicit Membrane Potential for NMR Structure Calculations of Membrane Proteins

Contact Info

Product

Resources

About