[Show abstract][Hide abstract] ABSTRACT: Residual dipolar couplings (RDCs) are NMR parameters that provide both structural and dynamic information concerning inter-nuclear vectors, such as N-H(N) and Cα-Hα bonds within the protein backbone. Two approaches for extracting this information from RDCs are the model free analysis (MFA) (Meiler et al. in J Am Chem Soc 123:6098-6107, 2001; Peti et al. in J Am Chem Soc 124:5822-5833, 2002) and the direct interpretation of dipolar couplings (DIDCs) (Tolman in J Am Chem Soc 124:12020-12030, 2002). Both methods have been incorporated into iterative schemes, namely the self-consistent RDC based MFA (SCRM) (Lakomek et al. in J Biomol NMR 41:139-155, 2008) and iterative DIDC (Yao et al. in J Phys Chem B 112:6045-6056, 2008), with the goal of removing the influence of structural noise in the MFA and DIDC formulations. Here, we report a new iterative procedure entitled Optimized RDC-based Iterative and Unified Model-free analysis (ORIUM). ORIUM unifies theoretical concepts developed in the MFA, SCRM, and DIDC methods to construct a computationally less demanding approach to determine these structural and dynamic parameters. In all schemes, dynamic averaging reduces the actual magnitude of the alignment tensors complicating the determination of the absolute values for the generalized order parameters. To readdress this scaling issue that has been previously investigated (Lakomek et al. in J Biomol NMR 41:139-155, 2008; Salmon et al. in Angew Chem Int Edit 48:4154-4157, 2009), a new method is presented using only RDC data to establish a lower bound on protein motion, bypassing the requirement of Lipari-Szabo order parameters. ORIUM and the new scaling procedure are applied to the proteins ubiquitin and the third immunoglobulin domain of protein G (GB3). Our results indicate good agreement with the SCRM and iterative DIDC approaches and signify the general applicability of ORIUM and the proposed scaling for the extraction of inter-nuclear vector structural and dynamic content.
Journal of Biomolecular NMR 09/2013; · 2.85 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Micro-to-millisecond motions of proteins transmit pivotal signals for protein function. A powerful technique for the measurement of these motions is nuclear magnetic resonance spectroscopy. One of the most widely used methodologies for this purpose is the constant-time Carr-Purcell-Meiboom-Gill (CT-CPMG) relaxation dispersion experiment where kinetic and structural information can be obtained at atomic resolution. Extraction of accurate kinetics determined from CT-CPMG data requires refocusing frequencies that are much larger than the nuclei's exchange rate between states. We investigated the effect when fast processes are probed by CT-CPMG experiments via simulation and show that if the intrinsic relaxation rate [Formula: see text] is not known a priori the extraction of accurate kinetics is hindered. Errors on the order of 50 % in the exchange rate are attained when processes become fast, but are minimized to 5 % with a priori [Formula: see text] information. To alleviate this shortcoming, we developed an experimental scheme probing [Formula: see text] with large amplitude spin-lock fields, which specifically contains the intrinsic proton longitudinal Eigenrelaxation rate. Our approach was validated with ubiquitin and the Oscillatoria agardhii agglutinin (OAA). For OAA, an underestimation of 66 % in the kinetic rates was observed if [Formula: see text]is not included during the analysis of CT-CPMG data and result in incorrect kinetics and imprecise amplitude information. This was overcome by combining CT-CPMG with [Formula: see text] measured with a high power R1ρ experiment. In addition, the measurement of [Formula: see text] removes the ambiguities in choosing between different models that describe CT-CPMG data.
Journal of Biomolecular NMR 08/2013; · 2.85 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Dynamics governing the function of biomolecule is usually described as exchange processes and can be monitored at atomic resolution with nuclear magnetic resonance (NMR) relaxation dispersion data. Here, we present a new tool for the analysis of CPMG relaxation dispersion profiles (ShereKhan). The web-interface to ShereKhan provides a user-friendly environment for the analysis. AVAILABILITY: A stable version of ShereKhan, the web-application, and documentation are available at http://sherekhan.bionmr.org. CONTACT: email@example.com, firstname.lastname@example.org.
[Show abstract][Hide abstract] ABSTRACT: Protein-mediated polarization transfer: Ligands L(1) and L(2) that competitively bind to a protein are subject to indirect spin-polarization transfer through the binding site of the protein. If protons H(L1) of one ligand are hyperpolarized by dynamic nuclear polarization (DNP, see picture), signal intensities in the NMR spectrum of the second ligand become enhanced. The relative build-up of signal of the second ligand yields information on its binding epitope.
Angewandte Chemie International Edition 04/2012; 51(21):5179-82. · 11.34 Impact Factor