The Influence of Hydrophobic Mismatch on Structure and Dynamics of Transmembrane Helices and Lipid Bilayers

Membrane proteins with one or a few transmembrane (TM) helices are abundant and often involved in important TM-included signaling and regulation through formation of hetero- and homo-oligomers. Especially, solid-state NMR (SSNMR) is a powerful technique to describe the orientations of membrane proteins and peptides in their native membrane bilayer environments. However, it is still challenging to obtain the structural information of membrane protein. Since protein-lipid interaction and bilayer regulation of membrane protein functions are largely controlled by the hydrophobic match between the TM domain of membrane proteins and the surrounding lipid bilayer, the interplay between the structure and the energetics of lipid and protein components of biomembranes is one of long-standing interests in biophysics. Structural and dynamic changes of the TM helices in response to a hydrophobic mismatch as well as molecular forces governing such changes remain to be fully understood at the atomic level. In this dissertation, to systematically characterize responses of a TM helix and lipid adaptations to a hydrophobic mismatch, I have performed a total of 5.8-μs umbrella sampling simulations and calculated the potentials of mean force (PMFs) as a function of TM helix tilt angle under various mismatch conditions. Single-pass TM peptides called WALP were used in two lipid bilayers with different hydrophobic thicknesses to consider hydrophobic mismatch caused by either the TM length or the bilayer thickness. The deuterium (2H) quadrupolar splitting (DQS), one of the SSNMR observables, has been used to characterize the orientations of various single-pass TM helices using a semi-static rigid-body model such as the geometric analysis of labeled alanine (GALA) method. However, dynamic information of these TM helices, which could be related to important biological function, can be missing or misinterpreted with the semi-static model. The result in Chapter 3 demonstrates that SSNMR ensemble dynamics provides a means to extract orientational and dynamic information of TM helices from their SSNMR observables and to explain the discrepancy between molecular dynamics simulation and GALA-based interpretation of DQS data. Finally, this dissertation describes the influence of hydrophobic mismatch on structure and dynamics of TM helices and lipid bilayers through molecular dynamics simulation of Gramicidin A (gA) channel in various lipid bilayers. The structure and dynamics of the gA channel as well as important lipid properties were investigated to address the influence by various hydrophobic mismatch conditions

Regularization and Kernelization of the Maximin Correlation Approach

Robust classification becomes challenging when each class consists of multiple subclasses. Examples include multi-font optical character recognition and automated protein function prediction. In correlation-based nearest-neighbor classification, the maximin correlation approach (MCA) provides the worst-case optimal solution by minimizing the maximum misclassification risk through an iterative procedure. Despite the optimality, the original MCA has drawbacks that have limited its wide applicability in practice. That is, the MCA tends to be sensitive to outliers, cannot effectively handle nonlinearities in datasets, and suffers from having high computational complexity. To address these limitations, we propose an improved solution, named regularized maximin correlation approach (R-MCA). We first reformulate MCA as a quadratically constrained linear programming (QCLP) problem, incorporate regularization by introducing slack variables in the primal problem of the QCLP, and derive the corresponding Lagrangian dual. The dual formulation enables us to apply the kernel trick to R-MCA so that it can better handle nonlinearities. Our experimental results demonstrate that the regularization and kernelization make the proposed R-MCA more robust and accurate for various classification tasks than the original MCA. Furthermore, when the data size or dimensionality grows, R-MCA runs substantially faster by solving either the primal or dual (whichever has a smaller variable dimension) of the QCLP.Comment: Submitted to IEEE Acces

Revisiting Hydrophobic Mismatch with Free Energy Simulation Studies of Transmembrane Helix Tilt and Rotation

This is the publisher's version. Copyright 2010 by Elsevier.Protein-lipid interaction and bilayer regulation of membrane protein functions are largely controlled by the hydrophobic match between the transmembrane (TM) domain of membrane proteins and the surrounding lipid bilayer. To systematically characterize responses of a TM helix and lipid adaptations to a hydrophobic mismatch, we have performed a total of 5.8-μs umbrella sampling simulations and calculated the potentials of mean force (PMFs) as a function of TM helix tilt angle under various mismatch conditions. Single-pass TM peptides called WALPn (n = 16, 19, 23, and 27) were used in two lipid bilayers with different hydrophobic thicknesses to consider hydrophobic mismatch caused by either the TM length or the bilayer thickness. In addition, different flanking residues, such as alanine, lysine, and arginine, instead of tryptophan in WALP23 were used to examine their influence. The PMFs, their decomposition, and trajectory analysis demonstrate that 1), tilting of a single-pass TM helix is the major response to a hydrophobic mismatch; 2), TM helix tilting up to ∼10° is inherent due to the intrinsic entropic contribution arising from helix precession around the membrane normal even under a negative mismatch; 3), the favorable helix-lipid interaction provides additional driving forces for TM helix tilting under a positive mismatch; 4), the minimum-PMF tilt angle is generally located where there is the hydrophobic match and little lipid perturbation; 5), TM helix rotation is dependent on the specific helix-lipid interaction; and 6), anchoring residues at the hydrophilic/hydrophobic interface can be an important determinant of TM helix orientation

Cross-Class Feature Augmentation for Class Incremental Learning

We propose a novel class incremental learning approach by incorporating a feature augmentation technique motivated by adversarial attacks. We employ a classifier learned in the past to complement training examples rather than simply play a role as a teacher for knowledge distillation towards subsequent models. The proposed approach has a unique perspective to utilize the previous knowledge in class incremental learning since it augments features of arbitrary target classes using examples in other classes via adversarial attacks on a previously learned classifier. By allowing the cross-class feature augmentations, each class in the old tasks conveniently populates samples in the feature space, which alleviates the collapse of the decision boundaries caused by sample deficiency for the previous tasks, especially when the number of stored exemplars is small. This idea can be easily incorporated into existing class incremental learning algorithms without any architecture modification. Extensive experiments on the standard benchmarks show that our method consistently outperforms existing class incremental learning methods by significant margins in various scenarios, especially under an environment with an extremely limited memory budget

Experimental investigation on turbulent flow overlying permeable walls

A turbulent flow overlying a permeable wall can be subdivided into two distinct flow regions separated by a permeable interface. The first is the surface (or free) flow region, which overlies the interface. The second is the subsurface (or pore) flow region, which occurs within the permeable wall. While the near-wall surface flow can be turbulent, deep within the bed the subsurface flow is often laminar and can be described by Darcy's law (a balance of viscous and pressure forces). Thus, a region must exist between these two extremes where the flow undergoes a transition from inertia-dominated turbulence to viscous-dominated, laminar flow across the permeable interface. This region, typically termed the 'transitional layer,' develops across the permeable interface where non-linear flow interactions between the free flow and the pore flow take place. Accessing this region either experimentally or computationally is extremely challenging, with the latter limited by direct physical of optical access near and within the bed. The goal of this study was to explore the role of wall permeability and surface topography in flow interactions across a permeable interface and the corresponding turbulent boundary layer modifications in the surface flow region. The turbulent flow overlying impermeable and permeable walls with identical surface topography was explored experimentally using the particle-image velocimetry technique coupled with a unique refractive-index matching flow environment, whereby the latter provided full optical access to the flow in the vicinity of and within the permeable interface and the former allowed the acquisition of instantaneous velocity fields in this region with this optical access. Utilizing velocity statistics and conditional averaging, quantitative assessments were made for turbulent boundary layer modifications imposed by permeability and topography as well as the role of these effects in the mutual interplay between the surface and subsurface flows. Surface topography is found to intensify these interactions across the transitional layer, meaning that it enhances mass, momentum and energy transport between these two flow regimes. In addition, it was found that the larger scales of the surface-layer flow modulate the smaller scales near the permeable interface and within the bed itself. This effect was previously identified in canonical turbulent boundary layers (both smooth and rough), but the results presented herein highlight the enhancement of modulation effects owing to permeability. This physical linkage between the surface and subsurface flows across the transitional layer could provide a new framework for modeling such effects based on this unique dynamic connection between the two flow regimes

Transmembrane Helix Assembly by Window Exchange Umbrella Sampling

A method of window exchange umbrella sampling molecular dynamics simulation is employed for transmembrane helix assembly. An analytical expression for the average acceptance probability between neighboring windows is derived and combined with the first passage time optimization method to predetermine a parameter set in an optimal range. With the parameter set, the method provides a substantially more efficient sampling of helix-helix interfaces together with the potential of mean force along the helix-helix distance of a transmembrane helix-dimer model, compared to the umbrella sampling method