Structural Rigidity and Protein Thermostability in Variants of Lipase A from Bacillus subtilis

Abstract

Understanding the origin of thermostability is of fundamental importance in protein biochemistry. Opposing views on increased or decreased structural rigidity of the folded state have been put forward in this context. They have been related to differences in the temporal resolution of experiments and computations that probe atomic mobility. Here, we find a significant (p = 0.004) and fair (R 2 = 0.46) correlation between the structural rigidity of a well-characterized set of 16 mutants of lipase A from Bacillus subtilis (BsLipA) and their thermodynamic thermostability. We apply the rigidity theory-based Constraint Network Analysis (CNA) approach, analyzing directly and in a time-independent manner the statics of the BsLipA mutants. We carefully validate the CNA results on macroscopic and microscopic experimental observables and probe for their sensitivity with respect to input structures. Furthermore, we introduce a robust, local stability measure for predicting thermodynamic thermostability. Our results complement work that showed for pairs of homologous proteins that raising the structural stability is the most common way to obtain a higher thermostability. Furthermore, they demonstrate that related series of mutants with only a small number of mutations can be successfully analyzed by CNA, which suggests that CNA can be applied prospectively in rational protein design aimed at higher thermodynamic thermostability.

Basal Histamine H4 Receptor Activation: Agonist Mimicry by the Diphenylalanine Motif

“…then represents the chemical potential energy (E CNA ) due to non‐covalent bonding, obtained from the coarse‐grained, residue‐wise network representation of the underlying biomolecular structure . A per‐residue decomposition of Equation (4), which is the chemical potential energy of residue i obtained by summation over all n short‐range rigid contacts the residue is involved in (Figure S7 in the Supporting Information), is computed according to Equation : …”

“…DE CNA has been shown to be ar obustl ocal stability measure for predicting the thermals tability of proteins. [36] From the DE i,CNA values, we identified regionsi nt he receptors that correlate with the rank-ordering of the systems with respect to basal activity (Figure 8b): The structurals tability of the systems increases with increasing levels of basal activity for the regions enclosing residues F54 2.43 -P70 2.59 in helix TM II as well as W90 3.28 -T92 3.30 and S109 3.47 -D111 3.49 in helix TM III. In contrast, the structurals tabilityo ft he systemsd ecreases with increasing levels of basal activity for residues V184 5.48 -V190 5.54 in TM Vas well as A306 6.38 -G310 6.42 and V314 6.46 -A317 6.49 in TM VI.…”

Biallelic mutation of human SLC6A6 encoding the taurine transporter TAUT is linked to early retinal degeneration

“…Altered biomolecular stability along a constraint dilution trajectory was quantified based on neighbor stability maps (rc ij, neighbor with i, j being residue numbers; Eq. 1) (65).…”

“…yields the chemical potential energy (E CNA ) due to noncovalent bonding, obtained from the coarse-grained, residue-wise network representation of the underlying biomolecular structure (35,65). A per-residue decomposition of Eq.…”

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