16 research outputs found
Protein resonance assignment by BSHâCPâbased 3D solidâstate NMR experiments: A practical guide
Solid-state NMR (ssNMR) spectroscopy has evolved into a powerful method to obtain structural information and to study the dynamics of proteins at atomic resolution and under physiological conditions. The method is especially well suited to investigate insoluble and noncrystalline proteins that cannot be investigated easily by X-ray crystallography or solution NMR. To allow for detailed analysis of ssNMR data, the assignment of resonances to the protein atoms is essential. For this purpose, a set of three-dimensional (3D) spectra needs to be acquired. Band-selective homo-nuclear cross-polarization (BSH-CP) is an effective method for magnetization transfer between carbonyl carbon (CO) and alpha carbon (CA) atoms, which is an important transfer step in multidimensional ssNMR experiments. This tutorial describes the detailed procedure for the chemical shift assignment of the backbone atoms of 13Câ15N-labeled proteins by BSH-CP-based 13C-detected ssNMR experiments. A set of six 3D experiments is used for unambiguous assignment of the protein backbone as well as certain side-chain resonances. The tutorial especially addresses scientists with little experience in the field of ssNMR and provides all the necessary information for protein assignment in an efficient, time-saving approach.European Research Council
http://dx.doi.org/10.13039/501100000781Max Planck Society
http://dx.doi.org/10.13039/501100004189LeibnizâForschungsinstitut fĂźr Molekulare PharmakologiePeer Reviewe
Measurement of backbone hydrogen-deuterium exchange in the type III secretion system needle protein PrgI by solid-state NMR
In this report we present site-specific measurements of amide hydrogen-deuterium exchange rates in a protein in the solid state phase by MAS NMR. Employing perdeuteration, proton detection and a high external magnetic field we could adopt the highly efficient Relax-EXSY protocol previously developed for liquid state NMR. According to this method, we measured the contribution of hydrogen exchange on apparent 15N longitudinal relaxation rates in samples with differing D2O buffer content. Differences in the apparent T1 times allowed us to derive exchange rates for multiple residues in the type III secretion system needle protein
Accurate Determination of Motional Amplitudes in Biomolecules by Solid-State NMR
Protein dynamics are an intrinsically important factor
when considering
a proteinâs biological function. Understanding these motions
is often limited through the use of static structure determination
methods, namely, X-ray crystallography and cryo-EM. Molecular simulations
have allowed for the prediction of global and local motions of proteins
from these static structures. Nevertheless, determining local dynamics
at residue-specific resolution through direct measurement remains
crucial. Solid-state nuclear magnetic resonance (NMR) is a powerful
tool for studying dynamics in rigid or membrane-bound biomolecules
without prior structural knowledge with the help of relaxation parameters
such as T1 and T1Ď. However, these provide only a combined result of
amplitude and correlation times in the nanosecondâmillisecond
frequency range. Thus, direct and independent determination of the
amplitude of motions might considerably improve the accuracy of dynamics
studies. In an ideal situation, the use of cross-polarization would
be the optimal method for measuring the dipolar couplings between
chemically bound heterologous nuclei. This would unambiguously provide
the amplitude of motion per residue. In practice, however, the inhomogeneity
of the applied radio-frequency fields across the sample leads to significant
errors. Here, we present a novel method to eliminate this issue through
including the radio-frequency distribution map in the analysis. This
allows for direct and accurate measurement of residue-specific amplitudes
of motion. Our approach has been applied to the cytoskeletal protein
BacA in filamentous form, as well as to the intramembrane protease
GlpG in lipid bilayers
High resolution observed in 800Â MHz DNP spectra of extremely rigid type III secretion needles
The cryogenic temperatures at which dynamic nuclear polarization (DNP) solid-state NMR experiments need to be carried out cause line-broadening, an effect that is especially detrimental for crowded protein spectra. By increasing the magnetic field strength from 600 to 800Â MHz, the resolution of DNP spectra of type III secretion needles (T3SS) could be improved by 22Â %, indicating that inhomogeneous broadening is not the dominant effect that limits the resolution of T3SS needles under DNP conditions. The outstanding spectral resolution of this system under DNP conditions can be attributed to its low overall flexibility
Measurement of backbone hydrogen-deuterium exchange in the type III secretion system needle protein PrgI by solid-state NMR
Atomic-resolution structure of cytoskeletal bactofilin by solid-state NMR
Bactofilins are a recently discovered class of cytoskeletal proteins of which no atomic-resolution structure has been reported thus far. The bacterial cytoskeleton plays an essential role in a wide range of processes, including morphogenesis, cell division, and motility. Among the cytoskeletal proteins, the bactofilins are bacteria-specific and do not have a eukaryotic counterpart. The bactofilin BacA of the species Caulobacter crescentus is not amenable to study by x-ray crystallography or solution nuclear magnetic resonance (NMR) because of its inherent noncrystallinity and insolubility. We present the atomic structure of BacA calculated from solid-state NMRâderived distance restraints. We show that the core domain of BacA forms a right-handed β helix with six windings and a triangular hydrophobic core. The BacA structure was determined to 1.0 Ă
precision (heavy-atom root mean square deviation) on the basis of unambiguous restraints derived from four-dimensional (4D) HN-HN and 2D C-C NMR spectra
Sensitivity enhancement using paramagnetic relaxation in MAS solid-state NMR of perdeuterated proteins
Protein resonance assignment by BSHâCPâbased 3D solidâstate NMR experiments: A practical guide
Solid-state NMR (ssNMR) spectroscopy has evolved into a powerful method to obtain structural information and to study the dynamics of proteins at atomic resolution and under physiological conditions. The method is especially well suited to investigate insoluble and noncrystalline proteins that cannot be investigated easily by X-ray crystallography or solution NMR. To allow for detailed analysis of ssNMR data, the assignment of resonances to the protein atoms is essential. For this purpose, a set of three-dimensional (3D) spectra needs to be acquired. Band-selective homo-nuclear cross-polarization (BSH-CP) is an effective method for magnetization transfer between carbonyl carbon (CO) and alpha carbon (CA) atoms, which is an important transfer step in multidimensional ssNMR experiments. This tutorial describes the detailed procedure for the chemical shift assignment of the backbone atoms of 13Câ15N-labeled proteins by BSH-CP-based 13C-detected ssNMR experiments. A set of six 3D experiments is used for unambiguous assignment of the protein backbone as well as certain side-chain resonances. The tutorial especially addresses scientists with little experience in the field of ssNMR and provides all the necessary information for protein assignment in an efficient, time-saving approach.European Research Council
http://dx.doi.org/10.13039/501100000781Max Planck Society
http://dx.doi.org/10.13039/501100004189LeibnizâForschungsinstitut fĂźr Molekulare PharmakologiePeer Reviewe
Synthetic Access to a Hydrocarbon-Soluble Trifluorinated Ge(II) Compound and its Sn(II) Congener
Trifluorinated germanium anions attracted
attention of theoretical
chemists already in the late 1990s to predict their physical and chemical
properties. However these species were not synthesized in the laboratory,
although substantial evidence for their existence was obtained from
the mass spectrometry of GeF<sub>4</sub>. The present study shows
that controlled fluorination of LMNMe<sub>2</sub> (L = PhCÂ(N<sup><i>t</i></sup>Bu)<sub>2</sub>, M = Ge, Sn) using HF¡pyridine
in toluene leads to the formation of [LH<sub>2</sub>]<sup>+</sup>[MF<sub>3</sub>]<sup>â</sup> under elimination of HNMe<sub>2</sub>. The products contain the trifluorinated GeÂ(II) and SnÂ(II) anionic
species which are stabilized by interionic H¡¡¡F bonds.
The new compounds were characterized by single crystal X-ray structural
analysis, NMR spectroscopy, and elemental analysis
Atomic Structure and Handedness of the Building Block of a Biological Assembly
Noncovalent
supramolecular assemblies possess in general several
unique subunitâsubunit interfaces.The basic building block
of such an assembly consists of several subunits and contains all
unique interfaces. Atomic-resolution structures of monomeric subunits
are typically accessed by crystallography or solution NMR and fitted
into electron microscopy density maps. However, the structure of the
intact building block in the assembled state remains unknown with
this hybrid approach. Here, we present the solid-state NMR atomic
structure of the building block of the type III secretion system needle.
The building block structure consists of a homotetrameric subunit
complex with three unique supramolecular interfaces. Side-chain positions
at the interfaces were solved at atomic detail. The high-resolution
structure reveals unambiguously the helical handedness of the assembly,
determined to be right-handed for the type III secretion system needle.Additionally,
the axial rise per subunit could be extracted from the tetramer structure
and independently validated by mass-per-length measurements