Single point mutants of human γS-crystallin cause dominant congenital cataracts, a recent one of which involves the substitution of highly conserved glycine at 57th position with a bulkier tryptophan. Our high-resolution 3D structure of this G57W mutant (abbreviated hereafter as γS-G57W), reported recently revealed site-specific structural perturbations with higher aggregation and lower stability compared to its wild-type; a structural feature associated with important functional and therapeutic consequences. In this communication, we report for the first time, residue resolved conformational dynamics in both γS-WT and γS-G57W using solution NMR spectroscopy, and suggest how these differences could crucially affect the biochemistry of the mutant. Guided by our critical structural investigations, extensive conformational dynamics and biophysical studies presented here show that loss of structural stability arises from enhanced dynamics in Greek key motif 2 inducing flexibility in the N-terminal domain as opposed to its structurally unperturbed C-terminal counterpart. NMR spectral density correlations and internal dynamics comparisons with the wild-type suggest that the overall thermodynamic instability propagates from the mutated N-terminal β4-β5 loop providing a residue level understanding of the structural changes associated with this early onset of lens opacification. Our results highlight the vital role of conserved Greek key motifs in conferring structural stability to crystallins and provide crucial molecular insights into crystallin aggregation in the eye lens, which triggers cataract formation in children. Overall, this critical study provides a residue level understanding of how conformational changes affect the structure and function of crystallins in particular and proteins in general, during health and disease.
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http://dx.doi.org/10.1016/j.bbrc.2019.02.124 | DOI Listing |
J Chem Theory Comput
January 2025
Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland.
Time-averaged restraints from nuclear magnetic resonance (NMR) measurements have been implemented in the UNRES coarse-grained model of polypeptide chains in order to develop a tool for data-assisted modeling of the conformational ensembles of multistate proteins, intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered regions (IDRs), many of which are essential in cell biology. A numerically stable variant of molecular dynamics with time-averaged restraints has been introduced, in which the total energy is conserved in sections of a trajectory in microcanonical runs, the bath temperature is maintained in canonical runs, and the time-average-restraint-force components are scaled up with the length of the memory window so that the restraints affect the simulated structures. The new approach restores the conformational ensembles used to generate ensemble-averaged distances, as demonstrated with synthetic restraints.
View Article and Find Full Text PDFRSC Adv
January 2025
College of Agriculture and Biological Science, Dali University Dali 671000 China
The conformational dynamics and activation mechanisms of KRAS proteins are of great importance for targeted cancer therapy. However, the detailed molecular mechanics of KRAS activation induced by GTP binding remains unclear. In this study, we systematically investigated how GTP/GDP exchange affects the thermodynamic and kinetic properties of KRAS and explored the activation mechanism using molecular dynamics (MD) simulations, Markov state models (MSMs), and neural relational inference (NRI) models.
View Article and Find Full Text PDFAppl Spectrosc
January 2025
Department of Materials Science and Engineering, University of Delaware, Newark, DE, USA.
Time-resolved, rapid-scan Fourier transform infrared (FT-IR) difference spectra have been recorded upon illumination on photosynthetic reaction centers (RCs) from under fixed hydration conditions (relative humidity = 76%). Two different illumination schemes were adopted. Whereas the use of a laser flash (duration: 7 ns) made it possible to follow the kinetics of recombination of the light-induced state PQ to the neutral state PQ, the use of a 20.
View Article and Find Full Text PDFPhys Chem Chem Phys
January 2025
Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
Reaction and interaction dynamics of azobenzene-tethered DNA (photoresponsive DNA) with T7 RNA polymerase (T7RNAP) were studied after photoisomerization of azobenzene from the - to -forms using the transient grating (TG) and time-resolved fluorescence polarization techniques. Two types of photoresponsive DNA were examined: AzoPBD, tethered at the protein binding site, and AzoTATA, tethered at the unwinding site. A diffusion change was observed after photoexcitation of -AzoPBD within 1 ms, and this change is explained in terms of a structural change from a bent to an extended conformation upon the -to- photoisomerization.
View Article and Find Full Text PDFFood Res Int
February 2025
Department of Food Science and Technology, Punjab Agricultural University, Ludhiana, Punjab 141 004, India. Electronic address:
In the present study, the impact of ultrasonication treatment (US) at varying time duration (10 and 20 min) on pearl millet protein (PMP) was evaluated. The native and ultrasonicated PMP were evaluated for techno-functional properties, zeta potential, particle size, SEM, FTIR, thermal properties and dynamic rheology. The significant (p < 0.
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