Characterization of the internal motions of a chimeric protein by 13C NMR highlights the important dynamic consequences of the engineering on a millisecond time scale

Conformational dynamics in peptide toxins: Implications for receptor interactions and molecular design

Peptide toxins are potent and often exquisitely selective probes of the structure and function of ion channels and receptors, and are therefore of significant interest to the pharmaceutical and biotech industries as both pharmacological tools and therapeutic leads. The three-dimensional structures of peptide toxins are essential as a basis for understanding their structure-activity relationships and their binding to target receptors, as well as in guiding the design of analogues with modified potency and/or selectivity for key targets. NMR spectroscopy has played a key role in elucidating the structures of peptide toxins and probing their structure-function relationships. In this article, we highlight the additional important contribution of NMR to characterising the dynamics of peptide toxins. We also compare the information available from NMR measurements with that afforded by molecular dynamics simulations. We describe several examples of the importance of dynamics measurements over a range of timescales for understanding the structure-function relationships of peptide toxins and their receptor engagement. Peptide toxins that inhibit the voltage-gated potassium channel K_V1.3 with pM affinities display different degrees of conformational flexibility, even though they contain multiple disulfide bonds, and this flexibility can affect the relative orientation of residues that have been shown to be critical for channel binding. Information on the dynamic properties of peptide toxins is important in the design of analogues or mimetics where receptor-bound structures are not available.

Low-Frequency Cooperative Dynamics in l-, d-, and dl-Alanine Crystals: A 13C and 15N Cross-Polarization Magic-Angle-Spinning NMR Study

Knowledge of the dynamical changes in molecular configurations in various amino acid structures over a wide range of time scales is important since such changes may influence the structural transformations and the diverse biological functionalities of proteins. Using the temperature dependence of the rotating-frame NMR spin-lattice relaxation times T(1rho) of protons as a probe, we have investigated the low-frequency (approximately 60-100 kHz) dynamics in the crystal structures of L-, D-, and DL- alanine (C(12)H(28)O(8)N(4)) polymorphs. The proton relaxation times T(1rho) were obtained from (13)C <-- (1)H and (15)N <-- (1)H cross-polarization magic-angle-spinning NMR experiments over a temperature range of 192-342 K. The data reveal that the time scales of these low-frequency dynamical processes are distinctly different from the localized, high-frequency rotational motion of methyl and amine groups. The strongly asymmetric T(1rho) versus temperature curves and the subtle dynamical differences between the DL-alanine and the L- and d-enantiomorphs indicate that these low-frequency processes are cooperative in nature and are sensitive to molecular packing.

Motions and structural variability within toxins: implication for their use as scaffolds for protein engineering

Animal toxins are small proteins built on the basis of a few disulfide bonded frameworks. Because of their high variability in sequence and biologic function, these proteins are now used as templates for protein engineering. Here we report the extensive characterization of the structure and dynamics of two toxin folds, the "three-finger" fold and the short alpha/beta scorpion fold found in snake and scorpion venoms, respectively. These two folds have a very different architecture; the short alpha/beta scorpion fold is highly compact, whereas the "three-finger" fold is a beta structure presenting large flexible loops. First, the crystal structure of the snake toxin alpha was solved at 1.8-A resolution. Then, long molecular dynamics simulations (10 ns) in water boxes of the snake toxin alpha and the scorpion charybdotoxin were performed, starting either from the crystal or the solution structure. For both proteins, the crystal structure is stabilized by more hydrogen bonds than the solution structure, and the trajectory starting from the X-ray structure is more stable than the trajectory started from the NMR structure. The trajectories started from the X-ray structure are in agreement with the experimental NMR and X-ray data about the protein dynamics. Both proteins exhibit fast motions with an amplitude correlated to their secondary structure. In contrast, slower motions are essentially only observed in toxin alpha. The regions submitted to rare motions during the simulations are those that exhibit millisecond time-scale motions. Lastly, the structural variations within each fold family are described. The localization and the amplitude of these variations suggest that the regions presenting large-scale motions should be those tolerant to large insertions or deletions.