Accelerating Reaction Rates of Biomolecules by Using Shear Stress in Artificial Capillary Systems

Abstract

Biomimetics is a design principle within chemistry, biology, and engineering, but chemistry biomimetic approaches have been generally limited to emulating nature’s chemical toolkit while emulation of nature’s physical toolkit has remained largely unexplored. To begin to explore this, we designed biophysically mimetic microfluidic reactors with characteristic length scales and shear stresses observed within capillaries. We modeled the effect of shear with molecular dynamics studies and showed that this induces specific normally buried residues to become solvent accessible. We then showed using kinetics experiments that rates of reaction of these specific residues in fact increase in a shear-dependent fashion. We applied our results in the creation of a new microfluidic approach for the multidimensional study of cysteine biomarkers. Finally, we used our approach to establish dissociation of the therapeutic antibody trastuzumab in a reducing environment. Our results have implications for the efficacy of existing therapeutic antibodies in blood plasma as well as suggesting in general that biophysically mimetic chemistry is exploited in biology and should be explored as a research area.

Recent Advances and Emerging Challenges in the Molecular Modeling of Mechanobiological Processes

“…First, imposing a fluid flow requires one to rescale velocities of solvent molecules 60 or to mimic experimental setups by using moving interfaces. 61 Second, the sampling problem and the limited time scale of these simulations are similar to that observed when running SMDs at experimental pulling forces. For these reasons, coarsegrained biomolecular representations in implicit solvent offer a more direct implementation of hydrodynamic effects and they grant access to longer simulation time scales.…”

“…Modeling shear flow using all-atom approaches in explicit solvent faces some limitations. First, imposing a fluid flow requires one to rescale velocities of solvent molecules or to mimic experimental setups by using moving interfaces . Second, the sampling problem and the limited time scale of these simulations are similar to that observed when running SMDs at experimental pulling forces.…”

“…Second, the sampling problem and the limited time scale of these simulations are similar to that observed when running SMDs at experimental pulling forces. For these reasons, coarse-grained biomolecular representations in implicit solvent offer a more direct implementation of hydrodynamic effects and they grant access to longer simulation time scales. ,, Significant progress has been made in the recent years, such as the use of a lattice–Boltzmann scheme for solvent–solute hydrodynamic interactions, and improved coarse-grained models. ,, However, important challenges remain, because even long simulation time scales do not allow to observe significant conformational changes at experimental shear flows. , Employing enhanced sampling techniques, that are usually deployed in a rigorous thermodynamic framework, is not trivial when using these nonequilibrium techniques, but some interesting attempts can be noticed …”

“…33,64,65 However, important challenges remain, because even long simulation time scales do not allow to observe significant conformational changes at experimental shear flows. 33,61 Figure 3. Effect of force on the unfolding pathway as seen from the perspective of a multidimensional PMF.…”

Chemical and Enzymatic Methods for Post-Translational Protein–Protein Conjugation

“…It is also notable that disulfide bonds formed in bioconjugation can be unstable under physiological conditions, making these conjugates less useful as therapeutic agents. 81,82 Alternative approaches for selectively targeting lysine residues that overcome some of the challenges faced when using SPDP avoided the requirement for disulfide bond formation altogether. The cyclic compound thioimidate 2iminothiolane, commonly known as Traut's reagent, has been used to introduce a free thiol at lysine, which can subsequently react with a maleimide functional group installed at lysine on a second protein using bifunctional succinimidyl 4-(N-maleimidomethyl)cyclohexane-1-carboxylate (SMCC) reagents (Figure 7).…”