Biology subjects

Li, M. S.

Publications and source records attributed to Li, M. S..

7 recordsLinked to original sources

bioRxiv2024

Serotonin Promotes Vesicular Association and Fusion by Modifying Lipid Bilayers

The primary event in chemical neurotransmission involves the fusion of a membrane-limited vesicle at the plasma membrane and the subsequent release of its chemical neurotransmitter cargo. The cargo itself is not known to have any effect on the fusion event. However, amphiphilic monoamine neurotransmitters (e.g. serotonin and dopamine) are known to strongly interact with lipid bilayers and to affect their mechanical properties, which can in principle impact membrane-mediated processes. Here we probe whether serotonin can enhance the association and fusion of artificial lipid vesicles in vitro. We employ Fluorescence Correlation Spectroscopy and Total Internal Reflection Fluorescence microscopy to measure the attachment and fusion of vesicles whose lipid compositions mimic the major lipid components of synaptic vesicles. We find that association between vesicles and supported lipid bilayers are strongly enhanced in a serotonin dose-dependent manner, and this drives an increase in the rate of spontaneous fusion. Molecular dynamics simulations and fluorescence spectroscopy data show that serotonin insertion increases the water content of the hydrophobic part of the bilayer. This suggests that the enhanced membrane association is likely driven by an energetically favourable drying transition. Other monoamines such as dopamine and norepinephrine, but not other related species such as tryptophan, show similar effects on membrane association. Our results reveal a lipid bilayer-mediated mechanism by which monoamines can themselves modulate vesicle fusion, potentially adding to the control toolbox for the tightly regulated process of neurotransmission in vivo. TOC graphics O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=68 SRC="FIGDIR/small/576155v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@2717c5org.highwire.dtl.DTLVardef@899c21org.highwire.dtl.DTLVardef@697232org.highwire.dtl.DTLVardef@c850a0_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2023

Protocols for Multi-Scale Molecular Dynamics Simulations in Amber and Gromacs: a Case Study of Intrinsically Disordered Amyloid Beta

Intrinsically disordered proteins (IDPs) present challenges to conventional experimental techniques due to their large-scale conformational fluctuations and the transient occurrence of structural elements. This work illustrates computational methods for studying IDPs at various levels of resolution. The included simulation protocol offers a step-by-step guide on how to conduct molecular dynamics (MD) simulations and analyze the results using the Amber and Gromacs packages, employing both all-atom and coarse-grained approaches. This protocol can be easily adapted to study other biomacromolecules, including folded and disordered proteins and peptides. Furthermore, it is discussed in this work how to perform standard molecular modeling operations, such as amino-acid substitutions (mutagenesis) and insertions of residues missing in a protein structure, as well as how to incorporate post-translational modifications into the simulations, such as disulfide bonds, which are often crucial for proteins to attain their physiologically functional structure. In conventional MD studies, disulfide bonds are typically fixed at the preparation step and remain unchanged throughout the simulations, unable to break or reform. Here, in contrast, a dynamic approach is presented. It involves adequate distance restraints applied to the sulfur atoms of selected cysteine residues, allowing disulfide bonds to break and reform during the simulation. The effectiveness of these methodologies is demonstrated by examining a model IDP, the monomeric form of 1-42 amyloid-{beta} (A{beta}42), both with and without disulfide bonds, at different levels of resolution. This study not only contributes to our understanding of the role of disulfide bonds but also provides detailed simulation protocols that can serve as a foundation for future investigations. SUMMARYGiven the challenges of experimental studies on intrinsically disordered proteins, this manuscript demonstrates step-by-step protocols for conducting all-atom and coarse-grained molecular dynamics simulations using two widespread packages, Amber and Gromacs. The monomeric form of 1-42 amyloid-{beta} (A{beta}42) is used as an example, from which insights into the structure, dynamics and physicochemical properties of this protein can be obtained.

molecular biology↗

bioRxiv2022

A New Class of Protein Misfolding is Observed in All-atom Folding Simulations

Several mechanisms intrinsic to a proteins primary structure are known to cause monomeric protein misfolding. Coarse-grained simulations, in which multiple atoms are represented by a single interaction site, have predicted a novel mechanism of misfolding exists involving off-pathway, non-covalent lasso entanglements, which are distinct from protein knots and slip knots. These misfolded states can be long-lived kinetic traps, and in some cases are structurally similar to the native state according to those simulations. Here, we examine whether such misfolded states occur in long-time-scale, physics-based all-atom simulations of protein folding. We find they do indeed form, estimate they can persist for weeks, and some have characteristics similar to the native state. Digestion patterns from Limited Proteolysis Mass Spectrometry are consistent with the presence of changes in entanglement in these proteins. These results indicate monomeric proteins can exhibit subpopulations of misfolded, self-entangled states that can explain long-timescale changes in protein structure and function in vivo. One-Sentence SummaryEntangled misfolded states form in physics-based all-atom simulations of protein folding and have characteristics similar to the native state.

biophysics↗

bioRxiv2021

Synonymous mutations can alter protein dimerization through localized interface misfolding involving self-entanglements

Synonymous mutations in messenger RNAs (mRNAs) can reduce protein-protein binding affinities by more than half despite leaving the proteins amino acid sequence unaltered. Here, we use coarse-grain simulations of protein synthesis, ejection from the ribosome, post-translational dynamics, and dimerization to understand how synonymous mutations can influence the dimerization of the two E. coli homodimers oligoribonuclease and ribonuclease T. We synthesize each protein from its wildtype, fastest- and slowest-translating synonymous mRNAs and calculate the ensemble-average interaction energy between the resulting dimers. We find, similar to experiments with other dimers, that oligoribonucleases dimerization is altered by synonymous mutations. Relative to wildtype, the dimer interaction energy becomes 4% and 10% stronger, respectively, when translated from its fastest- and slowest-translating mRNAs. Ribonuclease T dimerization, however, is insensitive to synonymous mutations. The structural and kinetic origin of these changes are misfolded states containing non-covalent lasso-entanglements, many of which structurally perturb the dimer interface, whose probability of occurrence depends on translation speed. Translation of the fast- and slow-translating mRNAs of oligoribonuclease decreases the population of these misfolded states relative to wildtype. For ribonuclease T, however, these misfolded populations are insensitive to synonymous mutations. Entanglements cause altered dimerization energies for oligoribonuclease as there is a significant association (odds ratio: 50) between non-native self-entanglements and weak-binding dimer conformations. These conclusions are independent of model resolution, as entangled structures persist in long-time-scale all-atom simulations. Thus, non-native changes in entanglement is a mechanism through which oligomer structure and function can be altered. SIGNIFICANCE STATEMENTSynonymous mutations affect a range of post-translational protein functions, including dimerization, without altering the amino acid sequence of the encoded protein. This suggests that proteins somehow retain a "memory" of their translation-elongation kinetics long after synthesis is complete. Here, we demonstrate that synonymous mutations can change the likelihood that nascent proteins misfold into self-entangled conformations. These self-entangled structures are similar to the native state but with key conformational perturbations that disrupt the dimer interface, reducing their ability to dimerize. Rearrangement of such self-entangled states to the native state is a slow process, offering a structural explanation for how translation-elongation kinetics can influence long-time-scale protein-protein binding affinities.

biophysics↗

bioRxiv2021

Ribosome elongation kinetics of consecutively charged residues are coupled to electrostatic force

The speed of protein synthesis can dramatically change when consecutively charged residues are incorporated into an elongating nascent protein by the ribosome. The molecular origins of this class of allosteric coupling remain unknown. We demonstrate, using multi-scale simulations, that positively charged residues generate large forces that pull the P-site amino acid away from the A-site amino acid. Negatively charged residues generate forces of similar magnitude but opposite direction. And that these conformational changes, respectively, raise and lower the transition state barrier height to peptide bond formation, explaining how charged residues mechanochemically alter translation speed. This mechanochemical mechanism is consistent with in vivo ribosome profiling data exhibiting a proportionality between translation speed and the number of charged residues, experimental data characterizing nascent chain conformations, and a previously published cryo-EM structure of a ribosome-nascent chain complex containing consecutive lysines. These results expand the role of mechanochemistry in translation, and provide a framework for interpreting experimental results on translation speed. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=64 SRC="FIGDIR/small/455055v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@14714eeorg.highwire.dtl.DTLVardef@1af3ad7org.highwire.dtl.DTLVardef@1402740org.highwire.dtl.DTLVardef@d11c04_HPS_FORMAT_FIGEXP M_FIG C_FIG For table of contents use only.

biophysics↗

bioRxiv2020

A computational model to unravel the function of amyloid-β peptide in contact with a phospholipid membrane

The normal synapse activity involves the release of copper and other divalent cations in the synaptic region. These ions have a strong impact on the membrane properties, especially when the membrane has charged groups, like it is the case of synapse. In this work we use an atomistic computational model of dimyristoyl-phosphatidylcholine (DMPC) membrane bilayer. We perturb this model with a simple model of divalent cation (Mg2+), and with a single amyloid-{beta} (A{beta}) peptide of 42 residues, both with and without a single Cu2+ ion bound to the N-terminus. In agreement with experimental results reported in the literature, the model confirms that divalent cations locally destabilize the DMPC membrane bilayer, and, for the first time, that the monomeric form of A{beta} helps in avoiding the interactions between divalent cations and DMPC, preventing significant effects on the DMPC bilayer properties. These results are discussed in the frame of a protective role of diluted A{beta} peptide floating in the synaptic region. Author summaryWe modelled the behavior of a Mg2+ divalent cation, with the size of Zn2+ and Cu2+, in contact with a phosphatidyl lipid bilayer. We also modelled the monomeric amyloid-{beta} peptide 1-42, both free and Cu-loaded, the latter mimicking the final step of the binding between the peptide and the divalent cation. On the basis of the simulation results, we propose that the peptide hinders the strong interactions between the divalent cation and the membrane.

biophysics↗

bioRxiv2019

Mechanical and thermodynamic properties of Aβ42, Aβ40 and α-synuclein fibrils: A coarse-grained method to complement experimental studies

We perform molecular dynamics simulation on several relevant biological fibrils associated with neurodegenerative diseases such as A{beta}40, A{beta}42, and the {beta}-synuclein systems to obtain a molecular understanding and interpretation of nanomechanical characterization experiments. The computational method is versatile and addresses a new subarea within the mechanical characterization of heterogeneous soft materials. We investigate both the elastic and thermodynamic properties of the biological fibrils in order to substantiate experimental nanomechanical characterization techniques that are quickly developing and reaching dynamic imaging with video rate capabilities. The computational method qualitatively reproduces results of experiments with biological fibrils, validating its use in extrapolation to macroscopic material properties. Our computational techniques can be used for the co-design of new experiments aiming to unveil nanomechanical properties of biological fibrils from a molecular understanding point of view. Our approach allows a comparison of diverse elastic properties of the latter fibrils, which enables the detailed analysis of the mechanical response at the molecular level. For these systems, the simulation approach indicates qualitative agreement with the experimental estimations of the elastic moduli for three different types of deformation, i.e. tensile (YL), shear (S), and indentation (YT ). From our analysis, we find a significant elastic anisotropy between axial and transverse directions (i.e. YT>YL) for all systems. Interestingly, our results indicate a higher mechanostability in the case of A{beta}42 fibrils than in the case of {beta}40, suggesting a significant correlation between mechanical stability and aggregation propensity (rate) in amyloid systems, that is, the higher the mechanical stability the faster the fibril formation. Finally, we find that -synuclein fibrils are thermally less stable than {beta}-amyloid fibrils. We anticipate that our molecular-level analysis of the mechanical response under different deformation conditions for the range of fibrils considered here will provide significant insights for the experimental observations.

biophysics↗