اشترك بالحزمة الذهبية واحصل على وصول غير محدود شمرا أكاديميا
تسجيل مستخدم جديدSequence-specific size, structure, and stability of tight protein knots
132
0
0.0
(
0
)
تأليف
Joachim Dzubiella
اسأل ChatGPT حول البحث
ﻻ يوجد ملخص باللغة العربية
Approximately 1% of the known protein structures display knotted configurations in their native fold but their function is not understood. It has been speculated that the entanglement may inhibit mechanical protein unfolding or transport, e.g., as in cellular threading or translocation processes through narrow biological pores. Here we investigate tigh peptide knot (TPK) characteristics in detail by pulling selected 3_1 and 4_1-knotted peptides using all-atom molecular dynamics computer simulations. We find that the 3_1 and 4_1-TPK lengths are typically Delta l~4.7 nm and 6.9 nm, respectively, for a wide range of tensions (F < 1.5 nN), pointing to a pore diameter of ~2 nm below which a translocated knotted protein might get stuck. The 4_1-knot length is in agreement with recent AFM pulling experiments. Detailed TPK characteristics however, may be sequence-specific: we find a different size and structural behavior in polyglycines, and, strikingly, a strong hydrogen bonding and water molecule trapping capability of hydrophobic TPKs due to side chain shielding of the polar TPK core. Water capturing and release is found to be controlla ble by the tightening force in a few cases. These mechanisms result into a sequence-specific locking and metastability of TPKs what might lead to a blocking of knotted peptide transport at designated sequence-positions. Intriguingly, macroscopic tight 4_1-knot structures are reproduced microscopically (figure-of-eight vs. the pretzel) and can be tuned by sequence in contrast to mathematical predictions. Our findings may explain a function of knots in native proteins, challenge previous studies on macromolecular knots, and may find use in bio- and nanotechnology.
قيم البحث
اقرأ أيضاً
We review the background, theory and general equations for the analysis of equilibrium protein unfolding experiments, focusing on denaturant and heat-induced unfolding. The primary focus is on the thermodynamics of reversible folding/unfolding transi
tions and the experimental methods that are available for extracting thermodynamic parameters. We highlight the importance of modelling both how the folding equilibrium depends on a perturbing variable such as temperature or denaturant concentration, and the importance of modelling the baselines in the experimental observables.
The structure of a single alanine-based Ace-AEAAAKEAAAKA-Nme peptide in explicit aqueous electrolyte solutions (NaCl, KCl, NaI, and KF) at large salt concentrations (3-4 M) is investigated using 1 microsecond molecular dynamics (MD) computer simulati
ons. The peptide displays 71 alpha-helical structure without salt and destabilizes with the addition of NaCl in agreement with experiments of a somewhat longer version. It is mainly stabilized by direct and indirect (i+4)EK salt bridges between the Lys and Glu side chains and a concomitant backbone shielding mechanism. NaI is found to be a stronger denaturant than NaCl, while the potassium salts hardly show influence. Investigation of the molecular structures reveals that consistent with recent experiments Na+ has a much stronger affinity to side chain carboxylates and backbone carbonyls than K+, thereby weakening salt bridges and secondary structure hydrogen bonds. At the same time the large I- has a considerable affinity to the nonpolar alanine in line with recent observations of a large propensity of I- to adsorb to simple hydrophobes, and thereby assists Na+ in its destabilizing action. In the denatured states of the peptide novel long-lived (10-20 ns) loop-configurations are observed in which single Na+ ions and water molecules are hydrogen-bonded to multiple backbone carbonyls. In an attempt to analyze the denaturation behavior within the preferential interaction formalism, we find indeed that for the strongest denaturant, NaI, the protein is least hydrated. Additionally, a possible indication for protein denaturation might be a preferential solvation of the first solvation shell of the peptide backbone by the destabilizing cosolute (sodium).
We propose a novel method for refining force-field parameters of protein systems. In this method, the agreement of the secondary-structure stability and instability between the protein conformations obtained by experiments and those obtained by molec
ular dynamics simulations is used as a criterion for the optimization of force-field parameters. As an example of the applications of the present method, we refined the force-field parameter set of the AMBER ff99SB force field by searching the torsion-energy parameter spaces of $psi$ (N-C$^{alpha}$-C-N) and $zeta$ (C$^{beta}$-C$^{alpha}$-C-N) of the backbone dihedral angles. We then performed folding simulations of $alpha$-helical and $beta$-hairpin peptides, using the optimized force field. The results showed that the new force-field parameters gave structures more consistent with the experimental implications than the original AMBER ff99SB force field.
Sucralose is a commonly employed artificial sweetener that appears to destabilize protein native structures. This is in direct contrast to the bio-preservative nature of its natural counterpart, sucrose, which enhances the stability of biomolecules a
gainst environmental stress. We have further explored the molecular interactions of sucralose as compared to sucrose to illuminate the origin of the differences in their bio-preservative efficacy. We show that the mode of interactions of sucralose and sucrose in bulk solution differ subtly using hydration dynamics measurement and computational simulation. Sucralose does not appear to disturb the native state of proteins for moderate concentrations (<0.2 M) at room temperature. However, as the concentration increases, or in the thermally stressed state, sucralose appears to differ in its interactions with protein leading to the reduction of native state stability. This difference in interaction appears weak. We explored the difference in the preferential exclusion model using time-resolved spectroscopic techniques and observed that both molecules appear to be effective reducers of bulk hydration dynamics. However, the chlorination of sucralose appears to slightly enhance the hydrophobicity of the molecule, which reduces the preferential exclusion of sucralose from the protein-water interface. The weak interaction of sucralose with hydrophobic pockets on the protein surface differs from the behavior of sucrose. We experimentally followed up upon the extent of this weak interaction using isothermal titration calorimetry (ITC) measurements. We propose this as a possible origin for the difference in their bio-preservative properties.
The protein folding problem must ultimately be solved on all length scales from the atomic up through a hierarchy of complicated structures. By analyzing the stability of the folding process using physics and mathematics, this paper shows that featur
es without length scales, i.e. topological features, are potentially of central importance. Topology is a natural mathematical tool for the study of shape and we avail ourselves of that tool to examine the relationship between the amino acid sequence and the shapes of protein molecules. We apply what we learn to conjectures about their biological evolution.
سجل دخول لتتمكن من نشر تعليقات
التعليقات
جاري جلب التعليقات
سجل دخول لتتمكن من متابعة معايير البحث التي قمت باختيارها
