Probing the Domain Motions of an Oligomeric Protein from Deep-Sea Hyperthermophile by Neutron Spin Echo

Abstract

challenge to structural biology. The folded domain structures for the scaffold protein PSD-95 were long known but such fragmentary knowledge lacks methods to assemble these pieces. We used single-molecule FRET studies with multi-parameter fluorescence detection [1] and filtered fluorescence correlation spectroscopy [2, 3] to describe the native state ensemble of this canonical scaffold protein. Our approach represents a solution to describing the flexibility in any multi-domain protein from nanoseconds to seconds. The five domains in PSD-95 partitioned into two independent supramodules. Intramolecular interactions were limited to neighboring domains, which did not interact without being tethered. Although MAGUK proteins are flexible, there are conformational preferences encoded in the primary sequence. [1.] McCann, J. J., Zheng, L. Rohrbeck, D., Felekyan, S., Kühnemuth, R., Sutton, R. B., Seidel, C. A. M., Bowen, M. E.; The supertertiary structure of the synaptic MAGuK scaffold proteins is conserved. Proc. Natl. Acad. Sci. USA. 109, 15775-15780 (2012). [2.] Felekyan, S., Kalinin, S., Sanabria, H., Valeri, A., Seidel, C. A. M.; Filtered FCS: Species auto and cross correlation functions highlight binding and dynamics in biomolecules.

Quasi-elastic Neutron Scattering Reveals Ligand-Induced Protein Dynamics of a G-Protein-Coupled Receptor

“…From theoretical predictions, the protein dynamics at different time scales can be approximately divided into three groups: , (i) a short-lived Gaussian-like ballistic region due to vibrations; (ii) fast dynamics in the β-relaxation region (ps–ns) governed by a logarithmic decay; followed by (iii) slow dynamics , in the α-relaxation region (μs–ms) given by a stretched-exponential decay. The correlation between dynamics and biological activity has been demonstrated on the μs–ms time scale, but fluctuations at the atomic level are much faster than this. ,, Our experimental results correspond to the β-relaxation region within the time window of picoseconds–nanoseconds.…”

Behavior of aqueous Tetrabutylammonium bromide - a combined approach of microscopic simulation and neutron scattering

“…As stated earlier our experimental data comes from neutron scattering where it is a common practice to measure the spectra as function of Q. The neutron scattering technique is a valuable tool to explore molecular structures and dynamics of biomacromolecules [10] [5] [11] [9] [40] in different length and time scale. Here Q presents the reciprocal wave vector (inverse of distance) which is the difference in momentum transfer [3] [56] (this is the reason for invoking the concept of Q in the analysis of our simulation).…”

Collective Excitations in Protein as a Measure of Balance Between its Softness and Rigidity

“…It is well accepted that the protein dynamics play a significant role in enzyme catalysis together with its native structure. , However, understanding of the relationship among a protein’s structure, dynamics, and function is still a major challenge in biophysical research. − Protein internal motions on the time scale from femtoseconds to milliseconds − are similar to those motions in supercooled liquids, glasses, and polymers. , Enzymatic reactions occur on the time scale of few microseconds to milliseconds due to slow binding and conformational changes in proteins . Nevertheless, recent studies have revealed that the catalytic reactions are also coupled to the fast motions (femtoseconds to picoseconds) in protein due to the formation and disruption of covalent bonds, hydrogen bonds, and transfer of electrons, protons, or hydride ions among different functional groups. − The long-range structural order in protein is minimal compared to the solid crystals.…”