Biology subjects

Straub, J. E.

Publications and source records attributed to Straub, J. E..

10 recordsLinked to original sources

bioRxiv2025

Accurate determination of the preferred aggregation number of a micelle-encapsulated membrane protein dimer

The preferred aggregation number of dodeclyphoshocholine (DPC) micelles [Formula] encapsulating dimeric and higher order protein assemblies is difficult to determine via experimental techniques due to uncertainty in dimer geometry and heterogeneity in the conformational ensemble. Dimerization of the Amyloid Precursor Protein transmembrane domain (C99) is a particular step of importance in the production of amyloid-{beta} protein and the amyloid cascade. Molecular dynamics simulations of the C99 dimer and other transmembrane proteins have been performed to compliment micelle-phase protein structure studies. It has often been assumed that the value of [Formula] is the same as that of the pure, empty micelle. Here, we provide a convenient method for testing that assumption, while also accounting for the finite-size effects inherent in computer simulations of micelle self-assembly. Employing large, unbiased, coarsegrained molecular dynamics simulations of DPC and C99 dimer self-assembly, we determined the radius of gyration to be 21.6 {+/-} 2.0 [A] for the micelle-encapsulated dimer, and 16.0 {+/-} 1.0 [A] for the pure DPC micelle. Using these radii of gyration, we performed all-atom simulations of DPC-encapsulated C99 dimers with preferred aggregation numbers of 100 and 54 DPC to test the effect of using an expected versus a naive estimate of aggregation number on the structure of the transmembrane protein dimer. Through atomistic simulations, we determined that the transmembrane dimeric structure displays different characteristics depending on the aggregation number of the micelle, in addition to increased water penetration and micelle defects when the aggregation number is too small.

biophysics↗

bioRxiv2025

Exploring the kinetics and mechanism of phase separation in ternary lipid mixtures containing APP C99 using atomistic vs coarse-grained MD simulations

The phase separation of lipid bilayers, composed of mixtures of saturated and unsaturated lipids and cholesterol, is a topic of fundamental importance in membrane biophysics and cell biology. The formation of lipid domains, including liquid-disordered domains enriched in unsaturated lipids and liquid-ordered domains enriched in saturated lipids and cholesterol is believed to be essential to the function of many membrane proteins. Experiment, theory, and simulation have been used to develop a general understanding of the thermodynamic driving forces underlying phase separation in ternary and quaternary lipid mixtures. However, the kinetics of early events in lipid phase separation in the presence of transmembrane proteins remain relatively understudied. Using large-scale all-atom and coarse-grained simulations, we explore the kinetics and phase separation of ternary lipid mixtures of saturated lipid, unsaturated lipid, and cholesterol. Order parameters employed in the Cahn-Hilliard theory provide insight into the kinetics and mechanism of lipid phase separation. We observe three distinct time regimes in the phase separation process: a shorter time exponential phase followed by a power law phase followed by a longer time plateau phase. Comparison of lipid, protein and lipid-protein dynamics between all-atom and coarse-grained models identifies both quantitative and qualitative differences and similarities in the phase separation kinetics. Moreover, timescaling of dynamics of AA and CG simulation yields a similar kinetic mechanism of phase separation. The findings of this study elucidate fundamental aspects of membrane biophysics and the ongoing efforts to define the role of lipid rafts in the structure and function of cellular membrane.

biophysics↗

bioRxiv2023

Synergistic computational and experimental studies of a phosphoglycosyltransferase membrane/ligand ensemble

Complex glycans serve important functions in all living systems. Many of these intricate and byzantine biomolecules are assembled employing biosynthetic pathways wherein the constituent enzymes are membrane associated. A signature feature of the stepwise assembly processes is the essentiality of unusual linear long-chain polyprenol phosphate-linked substrates, such as un-decaprenol phosphate in bacteria. In this study we focus on a small enzyme, PglC from Campylobacter, structurally characterized for the first time in 2018, as a detergent solubilized construct. PglC is a monotopic phosphoglycosyl transferase (PGT), that embodies the functional core structure of the entire enzyme superfamily and catalyzes the first membrane-committed step in a glycoprotein assembly pathway. The size of the enzyme is significant as it enables high level computation and relatively facile, for a membrane protein, experimental analysis. Our ensemble computational and experimental results reveal a specific interaction of undecaprenol phosphate with PGT cationic residues and suggest a role for critical conformational transitions and electrostatic steering in substrate recognition, overcoming significant energetic barriers to binding. The study highlights that computation, guided by fundamental chemical principles, can advance the study of biochemical processes at membrane bilayers and provide chemical insight at a molecular level that cannot be derived by experiment alone. Insert Table of Contents artwork here O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=169 SRC="FIGDIR/small/539694v1_ufig1.gif" ALT="Figure 1"> View larger version (100K): org.highwire.dtl.DTLVardef@19a38d9org.highwire.dtl.DTLVardef@a41d8org.highwire.dtl.DTLVardef@168e48borg.highwire.dtl.DTLVardef@1749bd8_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2023

Sizes, Conformational fluctuations, and SAXS profiles for Intrinsically Disordered Proteins

The preponderance of Intrinsically Disordered Proteins (IDPs) in the eukaryotic proteome, and their ability to interact with each other, folded proteins, RNA, and DNA for functional purposes, have made it important to quantitatively characterize their biophysical properties. Toward this end, we developed the transferable Self-Organized Polymer (SOP-IDP) model to calculate the properties of several IDPs. The values of the radius of gyration (Rg) obtained from SOP-IDP simulations are in excellent agreement (correlation coefficient of 0.96) with those estimated from SAXS experiments. For AP180 and Epsin, the predicted values of the hydrodynamic radii (Rhs) are in quantitative agreement with those from Fluorescence Correlation Spectroscopy (FCS) experiments. Strikingly, the calculated SAXS spectra for thirty-six IDPs are also nearly superimposable on the experimental profiles. The dependence of Rg and the mean end-to-end distance (Ree) on chain length, N, follows Florys scaling law, R {approx} aN 0.588 ( = g, and e), suggesting that globally IDPs behave as synthetic polymers in a good solvent. The values of ag, and ae are 0.20 nm and 0.48 nm respectively. Surprisingly, finite size corrections to scaling, expected on theoretical grounds, are negligible for Rg and Ree. In contrast, only by accounting for the finite sizes of the IDPs, the dependence of experimentally measurable Rh on N can be quantitatively explained using{nu} = 0.588. Although Flory scaling law captures the estimates for Rg, Ree, and Rh accurately, the spread of the simulated data around the theoretical curve is suggestive of of sequence-specific features that emerge through a fine-grained analysis of the conformational ensembles using hierarchical clustering. Typically, the ensemble of conformations partitiones into three distinct clusters, having different equilibrium populations and structural properties. Without any further readjustments to the parameters of the SOP-IDP model, we also obtained excellent agreement with paramagnetic relaxation enhancement (PRE) measurements for -synuclein. The transferable SOP-IDP model sets the stage for several applications, including the study of phase separation in IDPs and interactions with nucleic acids.

biophysics↗

bioRxiv2022

Energy landscapes of Aβ monomers are sculpted in accordance with Ostwald's rule of stages

The transition from a disordered to an assembly-competent and sparsely populated monomeric state (N*) in amyloidogenic sequences is a crucial event in the aggregation cascade. Using a well-calibrated model for Intrinsically Disordered Proteins (IDPs), we show that the N* states, which bear considerable resemblance to distinct polymorphic fibril structures found in experiments, not only appear as excitations on the monomer free energy landscapes of A{beta}40 and A{beta}42 but also initiate the aggregation cascade. Interestingly, for A{beta}42, the transitions to the different N* states are in accord with Ostwalds rule of stages, with the least stable structures forming ahead of thermodynamically favored structures, which appear only on longer time-scales. Despite having similar topographies, the A{beta}40 and A{beta}42 monomer landscapes exhibit different extent of ruggedness, particularly in the vicinity of N* states, which we show have profound implications in dictating the intramolecular diffusion rates, and subsequent self-assembly into higher order structures. The network of connected kinetic states, which for A{beta}42 is considerably more complex than for A{beta}40, shows that the most favored dimerization routes proceed via the N* states. Direct transition between the disordered ground states within the monomer and dimer basins is less likely. The Ostwalds rule of stages holds widely, qualitatively explaining the unusual features in other fibril forming IDPs, such as Fused in Sarcoma (FUS). Similarly, the N* theory accounts for dimer formation in small disordered polyglutamine peptides, implicated in the Huntington disease. Graphical TOC Entry O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

biophysics↗

bioRxiv2021

Sequence determines the switch in the fibril forming regions in the low complexity FUS protein and its variants

Residues spanning distinct regions of the low-complexity domain of the RNA-binding protein, Fused in Sarcoma (FUS-LC), form fibril structures with different core morphologies. NMR experiments show that the 214 residue FUS-LC forms a fibril with an S-bend (core-1, residues 39-95), while the rest of the protein is disordered. In contrast, the fibrils of the C-terminal variant (FUS-LC-C; residues 111-214) has a U-bend topology (core-2, residues 112-150). Absence of the U-bend in FUS-LC implies that the two fibril cores do not coexist. Computer simulations show that these perplexing findings could be understood in terms of the population of sparsely-populated fibril-like excited states in the monomer. The propensity to form core-1 is higher compared to core-2. We predict that core-2 forms only in truncated variants that do not contain the core-1 sequence. At the monomer level, sequence-dependent enthalpic effects determine the relative stabilities of the core-1 and core-2 topologies. TOC graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=164 SRC="FIGDIR/small/451535v2_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@f81959org.highwire.dtl.DTLVardef@4859f3org.highwire.dtl.DTLVardef@96aecorg.highwire.dtl.DTLVardef@4ab94e_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2020

Differences in the free energies between the excited states of Aβ40 and Aβ42 monomers encode their distinct aggregation propensities

The early events in the aggregation of the intrinsically disordered peptide, A{beta}, involve transitions from the disordered lowest free energy ground state to assembly-competent states. Are the finger-prints of order found in the amyloid fibrils encoded in the conformations that the monomers access at equilibrium? If so, could the enhanced aggregation rate of A{beta}42 compared to A{beta}40 be rationalized from the sparsely populated high free energy states of the monomers? Here, we answer these questions in the affirmative using coarse-grained simulations of the SOP-IDP model of A{beta}40 and A{beta}42. Although both the peptides have practically identical ensemble-averaged properties, characteristic of random coils (RCs), the conformational ensembles of the two monomers exhibit sequence-specific heterogeneity. Hierarchical clustering of conformations reveals that both the peptides populate high free energy aggregation-prone (N*) states, which resemble the monomers in the fibril structure. The free energy gap between the ground (RC) and the N* states of A{beta}42 peptide is smaller than for A{beta}40. By relating the populations of excited states of the two peptides to the fibril formation time scales using an empirical formula, we explain nearly quantitatively the faster aggregation rate of A{beta}42 relative to A{beta}40. The N* concept accounts for fibril polymorphs, leading to the prediction that the less stable N* state of A{beta}42, encoding for the U-bend fibril, should form earlier than the structure with the S-bend topology, which is in accord with the Ostwalds rule rationalizing crystal polymorph formation. Significance StatementAlzheimers disease (AD), a rampant neurodegenerative disorder, is caused by the accumulation of pathological aggregates, primarily composed of the two isoforms A{beta}40 and A{beta}42. Experiments have shown that A{beta}42 is more aggregation-prone compared to A{beta}40. However, the molecular origin of this apparent anomaly remains elusive. Here, we provide a microscopic basis for the different aggregation rates in terms of the distinct populations of high free energy excited fibril-like states (N*) that are encoded in the monomer spectra. The N* theory explains the emergence of fibril polymorphs, and predicts the relative kinetic stabilities of A{beta}42 fibrils using Ostwalds rule of stages. Our work shows that sequence-specific conformational heterogeneity of the monomer ensembles provides important cues for understanding protein aggregation.

biophysics↗

bioRxiv2018

Regimes of Complex Lipid Bilayer Phases Induced by Cholesterol Concentration in MD Simulation.

Cholesterol is essential to the formation of phase separated lipid domains in membranes. Lipid domains can exist in different thermodynamic phases depending on the molecular composition, and play significant roles in determining structure and function of membrane proteins. We investigate the role of cholesterol in the structure and dynamics of ternary lipid mixtures displaying phase separation using Molecular Dynamics simulations, employing a physiologically-relevant span of cholesterol concentration. We find that cholesterol can induce formation of three regimes of phase behavior, I) miscible liquid disordered bulk, II) phase separated, domain registered coexistence of liquid disordered and liquid ordered and domains, and III) phase separated, domain-anti-registered coexistence of liquid-disordered and newly-identified nanoscopic gel domains composed of cholesterol threads we name \"cholesterolic gel\" domains. These findings are validated and discussed in the context of current experimental knowledge, models of cholesterol spatial distributions, and models of ternary lipid mixture phase separation.

biophysics↗

bioRxiv2018

Sequence effects on size, shape, and structural heterogeneity in Intrinsically Disordered Proteins

Intrinsically disordered proteins (IDPs) lack well-defined three-dimensional structures, thus challenging the archetypal notion of structure-function relationships. Determining the ensemble of conformations that IDPs explore under physiological conditions is the first step towards understanding their diverse cellular functions. Here, we quantitatively characterize the structural features of IDPs as a function of sequence and length using coarse-grained simulations. For diverse IDP sequences, with the number of residues (NT) ranging from 24 to 441, our simulations not only reproduce the radii of gyration (Rg) obtained from experiments, but also predict the full scattering intensity profiles in very good agreement with Small Angle X-ray Scattering experiments. The Rg values are well-described by the standard Flory scaling law, [Formula], with v {approx} 0.588, making it tempting to assert that IDPs behave as polymers in a good solvent. However, clustering analysis reveals that the menagerie of structures explored by IDPs is diverse, with the extent of heterogeneity being highly sequence-dependent, even though ensemble-averaged properties, such as the dependence of Rg on chain length, may suggest synthetic polymer-like behavior in a good solvent. For example, we show that for the highly charged Prothymosin-, a substantial fraction of conformations is highly compact. Even if the sequence compositions are similar, as is the case for -Synuclein and a truncated construct from the Tau protein, there are substantial differences in the conformational heterogeneity. Taken together, these observations imply that metrics based on net charge or related quantities alone, cannot be used to anticipate the phases of IDPs, either in isolation or in complex with partner IDPs or RNA. Our work sets the stage for probing the interactions of IDPs with each other, with folded protein domains, or with partner RNAs, which are critical for describing the structures of stress granules and biomolecular condensates with important cellular functions. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=82 SRC="FIGDIR/small/427476v2_ufig1.gif" ALT="Figure 1"> View larger version (12K): org.highwire.dtl.DTLVardef@1b50bd9org.highwire.dtl.DTLVardef@11cf542org.highwire.dtl.DTLVardef@29ebb5org.highwire.dtl.DTLVardef@31e965_HPS_FORMAT_FIGEXP M_FIG Graphical TOC Entry C_FIG

biophysics↗

bioRxiv2018

Molecular basis for a novel systemic form of human hereditary apoA-I amyloidosis with vision loss

Hereditary apolipoprotein A-I (apoA-I) amyloidosis (AApoAI) is a life-threatening incurable genetic disorder whose molecular underpinnings and the full spectrum of afflicted organs are unclear. We report a new form of AApoAI with amyloid deposition in multiple organs, including an unprecedented retinal amyloidosis. Genetic and proteomic analyses identified Glu34Lys apoA-I as the fibrillar protein causing the clinical manifestations. A life-saving combined hepatorenal transplantation was performed for one Glu34Lys carrier. To elucidate structural underpinnings for amyloidogenic properties of Glu34Lys, we generated its recombinant globular domain and compared the conformation and dynamics of its lipid-free form with those of two other naturally occurring apoA-I variants, Phe71Tyr (amyloidogenic) and Leu159Arg (non-amyloidogenic). All variants showed reduced stability and altered aromatic residue packing. Molecular dynamics simulations revealed local helical unfolding and suggested that transient opening of Trp72 induced mutation-dependent structural perturbations in a sensitive region, including the major amyloid hotspot residues 14-22. We posit that a shift from the \"closed\" to an \"open\" orientation of Trp72 modulates structural protection of amyloid hotspots, suggesting a previously unknown early step in protein misfolding.

molecular biology↗