Mechanical Network in Titin Immunoglobulin from Force Distribution Analysis

Abstract

The role of mechanical force in cellular processes is increasingly revealed by single molecule experiments and simulations of force-induced transitions in proteins. How the applied force propagates within proteins determines their mechanical behavior yet remains largely unknown. We present a new method based on molecular dynamics simulations to disclose the distribution of strain in protein structures, here for the newly determined high-resolution crystal structure of I27, a titin immunoglobulin (IG) domain. We obtain a sparse, spatially connected, and highly anisotropic mechanical network. This allows us to detect load-bearing motifs composed of interstrand hydrogen bonds and hydrophobic core interactions, including parts distal to the site to which force was applied. The role of the force distribution pattern for mechanical stability is tested by in silico unfolding of I27 mutants. We then compare the observed force pattern to the sparse network of coevolved residues found in this family. We find a remarkable overlap, suggesting the force distribution to reflect constraints for the evolutionary design of mechanical resistance in the IG family. The force distribution analysis provides a molecular interpretation of coevolution and opens the road to the study of the mechanism of signal propagation in proteins in general.

The Work of Titin Protein Folding as a Major Driver in Muscle Contraction

“…Once unfolded, the polypeptide becomes a random coil whose mean end-to-end distance is determined by the pulling force and scales with well-known polymer physics laws (63). For example, at 6.0 pN the folded I91 domain has an end-to-end length of approximately 4 nm (inferred from atomic coordinates, see PDB 1WAA (64)) while the extended polymer has a length of ~17 nm. Thus, the steps observed during the folding and unfolding transitions will have a size of 13 nm under a constant force of 6.0 pN.…”

Titin-based tension in the cardiac sarcomere: Molecular origin and physiological adaptations

“…1B). Unlike the N2B-Us and PEVK, Ig domains have well-defined structures that have been solved using NMR, x-ray crystallography, and small angle x-ray scattering techniques (Improta et al 1996; Mayans et al 2001; Von Castelmur et al 2008; Stacklies et al 2009). This has allowed for molecular dynamics experiments to study Ig domain dynamics at the atomic level (Lu et al 1998; Lee et al 2010), and, consequently, much more is known about the Ig domains than the PEVK and N2B-Us.…”

Effect of directional pulling on mechanical protein degradation by ATP-dependent proteolytic machines

“…1A). We selected titin I27 as a model domain for these studies because single-molecule and ensemble experiments have determined its mechanical, thermodynamic, and kinetic stability; less-stable variants have been well characterized; its forced unfolding has been studied by molecular dynamics simulations; and ClpXP and ClpAP unfolding, translocation, and degradation in the C-to-N direction have been analyzed in biochemical and optical-trapping experiments (8)(9)(10)(11)(12)(13)(14)(15). We find that the ClpXP and ClpAP AAA+ machines unfold wild-type and destabilized titin I27 domains much more rapidly when pulling from the N terminus than from the C terminus.…”