Interpretation of biomolecular NMR spin relaxation parametersThis paper is one of a selection of papers published in this special issue entitled “Canadian Society of Biochemistry, Molecular & Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases” and has undergone the Journal's usual peer review process.

2010 ◽  
Vol 88 (2) ◽  
pp. 131-142 ◽  
Author(s):  
Tyler Reddy ◽  
Jan K. Rainey
Keyword(s):  
Spin Relaxation ◽  
Intrinsically Disordered Proteins ◽  
Nmr Relaxation ◽  
Disordered Proteins ◽  
Detailed Model ◽  
Intrinsically Disordered ◽  
Density Mapping ◽  
Model Free ◽  
Relaxation Experiments ◽  
Nmr Spin Relaxation

Biomolecular nuclear magnetic resonance (NMR) spin relaxation experiments provide exquisite information on the picosecond to nanosecond timescale motions of bond vectors. Spin–lattice (T1) and spin–spin (T2) relaxation times and the steady-state nuclear Overhauser effect (NOE) are the first set of parameters extracted from typical 15N or 13C NMR relaxation experiments. Therefore, verifying that T1, T2, and NOE are consistent with theoretical predictions is an important step before carrying out the more detailed model-free and reduced spectral density mapping analyses commonly employed. In this mini-review, we discuss the essential motional parameters used to describe biomolecular dynamics in the context of a variety of examples of folded and intrinsically disordered proteins and peptides in aqueous and membrane mimetic environments. Estimates of these parameters can be used as input for an online interface, introduced herein, allowing plotting of trends of T1, T2, and NOE with magnetic field strength. The plots may serve as a first-check to the spectroscopist preparing to embark on a detailed NMR relaxation analysis.

Triple resonance 15N NMR relaxation experiments for studies of intrinsically disordered proteins

2017 ◽  
Vol 69 (3) ◽  
pp. 133-146 ◽  
Author(s):  
Pavel Srb ◽  
Jiří Nováček ◽  
Pavel Kadeřávek ◽  
Alžbeta Rabatinová ◽  
Libor Krásný ◽  
...  
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Nmr Relaxation ◽  
Disordered Proteins ◽  
15N Nmr ◽  
Triple Resonance ◽  
Intrinsically Disordered ◽  
15N Nmr Relaxation ◽  
Relaxation Experiments

scholarly journals Probing Local Backbone Geometries in Intrinsically Disordered Proteins by Cross-Correlated NMR Relaxation

2013 ◽  
Vol 52 (17) ◽  
pp. 4604-4606 ◽  
Author(s):  
Jan Stanek ◽  
Saurabh Saxena ◽  
Leonhard Geist ◽  
Robert Konrat ◽  
Wiktor Koźmiński
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Nmr Relaxation ◽  
Disordered Proteins ◽  
Intrinsically Disordered

scholarly journals Detecting segmental anisotropic diffusion in disordered proteins by cross-correlated spin-relaxation

2021 ◽  
Author(s):  
Clemens Kauffmann ◽  
Irene Ceccolini ◽  
Georg Kontaxis ◽  
Robert Konrat
Keyword(s):  
Spin Relaxation ◽  
Anisotropic Diffusion ◽  
Intrinsically Disordered Proteins ◽  
Complex Dynamics ◽  
Disordered Proteins ◽  
Multiple Quantum ◽  
Ensemble Averaging ◽  
Intrinsically Disordered ◽  
Folded Proteins ◽  
Spin Pairs

Abstract. Among the numerous contributions of Geoffrey Bodenhausen to NMR spectroscopy his developments in the field of spin-relaxation methodology and theory will definitely have a long lasting impact. Starting with his seminal contributions to the excitation of multiple-quantum coherences he and his group thoroughly investigated the intricate relaxation properties of these “forbidden fruits” and developed experimental techniques to reveal the relevance of previously largely ignored cross-correlated relaxation (CCR) effects, as “the essential is invisible to the eyes”. Here we want to discuss CCR within the challenging context of intrinsically disordered proteins (IDPs) and emphasize its potential and relevance for the studies of structural dynamics of IDPs in the future years to come. Conventionally, dynamics of globularly folded proteins are modeled and understood as deviations from otherwise rigid structures tumbling in solution. However, with increasing protein flexibility, as observed for IDPs, this apparent dichotomy between structure and dynamics becomes blurred. Although complex dynamics and ensemble averaging might impair the extraction of mechanistic details even further, spin-relaxation uniquely encodes a protein’s structural memory, i.e. the temporal persistence of concerted motions and structural arrangements. Due to significant methodological developments, such as high-dimensional non-uniform sampling techniques, spin-relaxation in IDPs can now be monitored in unprecedented resolution. Not embedded within a rigid globular fold, conventional 15N spin probes might not suffice to capture the inherently local nature of IDP dynamics. To better describe and understand possible segmental motions of IDPs, we propose an experimental approach to detect the signature of diffusion anisotropy by quantifying cross-correlated spin relaxation of individual 15N1HN and 13C'13Cα spin pairs. By adapting Geoffrey Bodenhausen’s symmetrical reconversion principle to obtain zero frequency spectral density values we can define and demonstrate more sensitive means to characterize segmental anisotropic diffusion in IDPs.

The sequence–ensemble relationship in fuzzy protein complexes

2021 ◽  
Vol 118 (37) ◽  
pp. e2020562118
Author(s):  
San Hadži ◽  
Remy Loris ◽  
Jurij Lah
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Protein Complexes ◽  
Structural Characteristics ◽  
Nmr Relaxation ◽  
Structural Heterogeneity ◽  
Conformational Space ◽  
Disordered Proteins ◽  
Statistical Thermodynamic ◽  
Intrinsically Disordered ◽  
Two Parameters

Intrinsically disordered proteins (IDPs) interact with globular proteins through a variety of mechanisms, resulting in the structurally heterogeneous ensembles known as fuzzy complexes. While there exists a reasonable comprehension on how IDP sequence determines the unbound IDP ensemble, little is known about what shapes the structural characteristics of IDPs bound to their targets. Using a statistical thermodynamic model, we show that the target-bound ensembles are determined by a simple code that combines the IDP sequence and the distribution of IDP–target interaction hotspots. These two parameters define the conformational space of target-bound IDPs and rationalize the observed structural heterogeneity of fuzzy complexes. The presented model successfully reproduces the dynamical signatures of target-bound IDPs from the NMR relaxation experiments as well as the changes of interaction affinity and the IDP helicity induced by mutations. The model explains how the target-bound IDP ensemble adapts to mutations in order to achieve an optimal balance between conformational freedom and interaction energy. Taken together, the presented sequence–ensemble relationship of fuzzy complexes explains the different manifestations of IDP disorder in folding-upon-binding processes.

scholarly journals Structural and Aggregation Features of a Human κ-Casein Fragment with Antitumor and Cell-Penetrating Properties

Molecules ◽  
2019 ◽  
Vol 24 (16) ◽  
pp. 2919 ◽  
Author(s):  
Olga A. Chinak ◽  
Andrey V. Shernyukov ◽  
Sergey S. Ovcherenko ◽  
Evgeniy A. Sviridov ◽  
Victor M. Golyshev ◽  
...  
Keyword(s):  
Cytotoxic Activity ◽  
Intrinsically Disordered Proteins ◽  
Nmr Relaxation ◽  
Disordered Proteins ◽  
Breast Adenocarcinoma ◽  
Amino Acid Residues ◽  
Paramagnetic Resonance ◽  
Proteolytic Fragment ◽  
Intrinsically Disordered ◽  
A Site

Intrinsically disordered proteins play a central role in dynamic regulatory and assembly processes in the cell. Recently, a human κ-casein proteolytic fragment called lactaptin (8.6 kDa) was found to induce apoptosis of human breast adenocarcinoma MCF-7 and MDA-MB-231 cells with no cytotoxic activity toward normal cells. Earlier, we had designed some recombinant analogs of lactaptin and compared their biological activity. Among these analogs, RL2 has the highest antitumor activity, but the amino acid residues and secondary structures that are responsible for RL2′s activity remain unclear. To elucidate the structure–activity relations of RL2, we studied the structural and aggregation features of this fairly large intrinsically disordered fragment of human milk κ-casein by a combination of physicochemical methods: NMR, paramagnetic relaxation enhancement (PRE), Electron Paramagnetic Resonance (EPR), circular dichroism, dynamic light scattering, atomic force microscopy, and a cytotoxic activity assay. It was found that in solution, RL2 exists as stand-alone monomeric particles and large aggregates. Whereas the disulfide-bonded homodimer turned out to be more prone to assembly into large aggregates, the monomer predominantly forms single particles. NMR relaxation analysis of spin-labeled RL2 showed that the RL2 N-terminal region, which is essential not only for multimerization of the peptide but also for its proapoptotic action on cancer cells, is more ordered than its C-terminal counterpart and contains a site with a propensity for α-helical secondary structure.

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