Ali Ghavami

Size-dependent leak of soluble and membrane proteins through the yeast nuclear pore complex

The permeability of the bakers yeast nuclear pore complex for multidomain proteins of different sizes, both soluble and transmembrane, was measured. The permeability for soluble proteins correlated with models of the disordered phase of wild-type and mutant NPCs generated using a one bead per amino acid molecular dynamics model.

Probing the Disordered Domain of the Nuclear Pore Complex through Coarse-Grained Molecular Dynamics Simulations

The distribution of disordered proteins (FG-nups) that line the transport channel of the nuclear pore complex (NPC) is investigated by means of coarse-grained molecular dynamics simulations. A one-bead-per-amino-acid model is presented that accounts for the hydrophobic/hydrophilic and electrostatic interactions between different amino acids, polarity of the solvent, and screening of free ions. The results indicate that the interaction of the FG-nups forms a high-density, doughnut-like distribution inside the NPC, which is rich in FG-repeats. We show that the obtained distribution is encoded in the amino-acid sequence of the FG-nups and is driven by both electrostatic and hydrophobic interactions. To explore the relation between structure and function, we have systematically removed different combinations of FG-nups from the pore to simulate inviable and viable NPCs that were previously studied experimentally. The obtained density distributions show that the maximum density of the FG-nups inside the pore does not exceed 185 mg/mL in the inviable NPCs, whereas for the wild-type and viable NPCs, this value increases to 300 mg/mL. Interestingly, this maximum density is not correlated to the total mass of the FG-nups, but depends sensitively on the specific combination of essential Nups located in the central plane of the NPC.

Energetics of Transport through the Nuclear Pore Complex

Molecular transport across the nuclear envelope in eukaryotic cells is solely controlled by the nuclear pore complex (NPC). The NPC provides two types of nucleocytoplasmic transport: passive diffusion of small molecules and active chaperon-mediated translocation of large molecules. It has been shown that the interaction between intrinsically disordered proteins that line the central channel of the NPC and the transporting cargoes is the determining factor, but the exact mechanism of transport is yet unknown. Here, we use coarse-grained molecular dynamics simulations to quantify the energy barrier that has to be overcome for molecules to pass through the NPC. We focus on two aspects of transport. First, the passive transport of model cargo molecules with different sizes is studied and the size selectivity feature of the NPC is investigated. Our results show that the transport probability of cargoes is significantly reduced when they are larger than ∼5 nm in diameter. Secondly, we show that incorporating hydrophobic binding spots on the surface of the cargo effectively decreases the energy barrier of the pore. Finally, a simple transport model is proposed which characterizes the energy barrier of the NPC as a function of diameter and hydrophobicity of the transporting particles.

Coarse-Grained Potentials for Local Interactions in Unfolded Proteins

Recent studies have revealed the key role of natively unfolded proteins in many important biological processes. In order to study the conformational changes of these proteins, a one-bead-per-amino-acid coarse grained (CG) model is developed, and a method is proposed to extract the potential functions for the local interactions between CG beads. Experimentally obtained Ramachandran data for the coil regions of proteins are converted into distributions of pseudo-bond and pseudo-dihedral angles between neighboring alpha-carbons in the polypeptide chain. These are then used to derive bending and torsion potentials, which are residue and sequence specific. The validity of the developed model is testified by studying the radius of gyration as well as the hydrodynamic properties of chemically denatured proteins.

Nucleoporin's Like Charge Regions Are Major Regulators of FG Coverage and Dynamics Inside the Nuclear Pore Complex

Nucleocytoplasmic transport has been the subject of a large body of research in the past few decades. Recently, the focus of investigations in this field has shifted from studies of the overall function of the nuclear pore complex (NPC) to the examination of the role of different domains of phenylalanine-glycine nucleoporin (FG Nup) sequences on the NPC function. In our recent bioinformatics study, we showed that FG Nups have some evolutionarily conserved sequence-based features that might govern their physical behavior inside the NPC. We proposed the ‘like charge regions’ (LCRs), sequences of charged residues with only one type of charge, as one of the features that play a significant role in the formation of FG network inside the central channel. In this study, we further explore the role of LCRs in the distribution of FG Nups, using a recently developed coarse-grained molecular dynamics model. Our results demonstrate how LCRs affect the formation of two transport pathways. While some FG Nups locate their FG network at the center of the NPC forming a homogeneous meshwork of FG repeats, other FG Nups cover the space adjacent to the NPC wall. LCRs in the former group, i.e. FG Nups that form an FG domain at the center, tend to regulate the size of the highly dense, doughnut-shaped FG meshwork and leave a small low FG density area at the center of the pore for passive diffusion. On the other hand, LCRs in the latter group of FG Nups enable them to maximize their interactions and cover a larger space inside the NPC to increase its capability to transport numerous cargos at the same time. Finally, a new viewpoint is proposed that reconciles different models for the nuclear pore selective barrier function.

Coarse-Grained Molecular Dynamics of the Natively-Unfolded Domain of the NPC

Transport through the nuclear pore complex (NPC) is mediated through natively unfolded FG-Nups. In this study, we address several questions regarding the role of FG-Nups by means of a one-bead-per-amino acid (1 BPA) molecular dynamics model. We show that inside the NPC the FG-Nups collectively form a high-density, doughnut-like distribution, which is rich in FG repeats. This specific doughnut shape is encoded in the amino acid sequence of the FG-Nups. We compare our simulations with permeability experiments and find a strong correlation between passive transport through the NPC and the average density of the FG-Nups at the central core region of the pore. Furthermore, we use umbrella sampling to obtain the potential of mean force (PMF) distribution for model kap–cargo complexes along the central axis of the pore. We find that the energy barrier for passive transport is size dependent, with inert cargo molecules larger than 5 nm in diameter effectively being excluded from transport. PMF curves of the Kap–cargo complexes show that the presence of several hydrophobic binding spots on the surface of large cargo complexes can lower the energy barrier below kBT for an optimal spacing of 1.4 nm, which is close to reported experimental values. Finally, we capture our simulations in a simple transport model which describes the energy barrier of the NPC as a function of diameter and hydrophobicity of the Kap–cargo complex, highlighting the sensitive balance between cargo being trapped, expelled, and transported.

Towards a Coarse-Grained Model for Unfolded Proteins

It is widely accepted that many biological systems benefit from the specific and unique properties of unfolded proteins. In order to study the conformational dynamics of these proteins, we propose an implicit solvent one-bead per amino-acid coarse-grained (CG) model. For the local backbone interactions, experimentally-obtained Ramachandran plots for the coil regions of proteins are converted into distributions of pseudo-bond and pseudo-dihedral angles between neighboring alpha-carbons in the CG chain. The obtained density plots are then used to derive bending and torsion potentials, which are residue- and sequence-specific. Our results show that the local interactions can be captured by specifically accounting for the presence of Proline and Glycine in the amino-acid sequence. An upper and lower bound is suggested for the radius of gyration of denatured proteins based on their specific sequence composition.