Microscopic Characterization of Membrane Transporter Function by In Silico Modeling and Simulation

Abstract

Membrane transporters mediate one of the most fundamental processes in biology. They are the main gatekeepers controlling active traffic of materials in a highly selective and regulated manner between different cellular compartments demarcated by biological membranes. At the heart of the mechanism of membrane transporters lie protein conformational changes of diverse forms and magnitudes, which closely mediate critical aspects of the transport process, most importantly the coordinated motions of remotely located gating elements and their tight coupling to chemical processes such as binding, unbinding and translocation of transported substrate and cotransported ions, ATP binding and hydrolysis, and other molecular events fueling uphill transport of the cargo. An increasing number of functional studies have established the active participation of lipids and other components of biological membranes in the function of transporters and other membrane proteins, often acting as major signaling and regulating elements. Understanding the mechanistic details of these molecular processes require methods that offer high spatial and temporal resolutions. Computational modeling and simulations technologies empowered by advanced sampling and free energy calculations have reached a sufficiently mature state to become an indispensable component of mechanistic studies of membrane transporters in their natural environment of the membrane. In this article, we provide an overview of a number of major computational protocols and techniques commonly used in membrane transporter modeling and simulation studies. The article also includes practical hints on effective use of these methods, critical perspectives on their strengths and weak points, and examples of their successful applications to membrane transporters, selected from the research performed in our own laboratory.

Characterization of Lipid–Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation

“…For explicit lipid membranes, complications such as membrane curvature and undulation, lipid entanglement, and protein structural changes may simply be artifacts caused by poor placement of the protein, rendering the necessity to properly prepare the initial system. A variety of techniques have been developed to construct membrane-embedded protein complexes; some of them use MD as a method to refine the placement along the process. − …”

Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance

“…The intrinsically dynamic conformational landscape of the membrane carriers, which is absent in most membrane channels, makes MD a valuable tool to investigate their transport cycle. Indeed, MD-based methods, such as Molecular Dynamics flexible fitting, , have been instrumental in generating atomistic models for membrane transporters − and channels , based on low resolution cryoelectron microscopy or X-ray scattering densities, exploiting homology models or available structures in alternative conformational states. The long time scales of the transport cycle of carriers bring about challenges for simulation studies.…”

Advances and Challenges in Rational Drug Design for SLCs

“…SLC38A9 is associated with mTOR activation in cancer [31] and shares a sequence identity of 61.9% with the zebrafish homolog, making it useful to generate homology models suitable for rational design. The new structural information on SLCs, combined with superior computational power and the maturation of computational chemistry tools, such as ligand docking [13], next generation membrane protein Molecular Dynamics (MD) simulation approaches [32], free energy perturbation estimation [33], as well as advanced machine learning (ML) architectures (e.g., autoencoder) [34] is expected to expedite the characterization of human SLCs. Here, we outline recent studies characterizing the substrate specificities of biomedically important SLC nutrient transporters, and the discovery of small molecule modulators of these proteins using computer-aided drug design (CADD).…”

“…Specifically, some transporters such as LeuT, have a timescale of transport ranging from milliseconds to seconds, making all-atom MD simulations extremely computationally demanding and often unfeasible [66]. Although methods such as steered MD [67] and umbrella sampling [68] can simulate at longer timescales, these approaches are often limited by the availability of suitable resolution protein structures and forcefields [32]. It should also be noted that large conformational changes are difficult to approximate with MD simulations, at a resolution sufficient for drug design.…”