Liquid-liquid phase separation of α-synuclein is highly sensitive to sequence complexity.

The Parkinson's-associated protein α-synuclein (α-syn) can undergo liquid-liquid phase separation (LLPS), which typically leads to the formation of amyloid fibrils. The coincidence of LLPS and amyloid formation has complicated the identification of the molecular determinants unique to LLPS of α-syn. Moreover, the lack of strategies to selectively perturb LLPS makes it difficult to dissect the biological roles specific to α-syn LLPS, independent of fibrillation.

Liquid-liquid phase separation of α-synuclein is highly sensitive to sequence complexity.

The Parkinson's-associated protein α-synuclein (α-syn) can undergo liquid-liquid phase separation (LLPS), which typically leads to the formation of amyloid fibrils. The coincidence of LLPS and amyloid formation has complicated the identification of the molecular determinants unique to LLPS of α-syn. Moreover, the lack of strategies to selectively perturb LLPS makes it difficult to dissect the biological roles specific to α-syn LLPS, independent of fibrillation.

Fibril treatment changes protein interactions of tau and α-synuclein in human neurons.

In several neurodegenerative disorders, the neuronal proteins tau and α-synuclein adopt aggregation-prone conformations capable of replicating within and between cells. To better understand how these conformational changes drive neuropathology, we compared the interactomes of tau and α-synuclein in the presence or the absence of recombinant fibril seeds. Human embryonic stem cells with an inducible neurogenin-2 transgene were differentiated into glutamatergic neurons expressing (1) WT 0N4R tau, (2) mutant (P301L) 0N4R tau, (3) WT α-synuclein, or (4) mutant (A53T) α-synuclein, each genetically fused to a promiscuous biotin ligase (BioID2).

Spiers Memorial Lecture: Analysis and design of membrane-interactive peptides.

Membrane-peptide interactions play critical roles in many cellular and organismic functions, including protection from infection, remodeling of membranes, signaling, and ion transport. Peptides interact with membranes in a variety of ways: some associate with membrane surfaces in either intrinsically disordered conformations or well-defined secondary structures. Peptides with sufficient hydrophobicity can also insert vertically as transmembrane monomers, and many associate further into membrane-spanning helical bundles.

A novel optical biosensor for the early diagnosis of sepsis and severe Covid-19: the PROUD study.

Background: The accuracy of a new optical biosensor (OB) point-of-care device for the detection of severe infections is studied.

Methods: The OB emits different wavelengths and outputs information associated with heart rate, pulse oximetry, levels of nitric oxide and kidney function. At the first phase, recordings were done every two hours for three consecutive days after hospital admission in 142 patients at high-risk for sepsis by placing the OB on the forefinger.

Robust Sequence Determinants of α-Synuclein Toxicity in Yeast Implicate Membrane Binding.

Protein conformations are shaped by cellular environments, but how environmental changes alter the conformational landscapes of specific proteins remains largely uncharacterized, in part due to the challenge of probing protein structures in living cells. Here, we use deep mutational scanning to investigate how a toxic conformation of α-synuclein, a dynamic protein linked to Parkinson's disease, responds to perturbations of cellular proteostasis. In the context of a course for graduate students in the UCSF Integrative Program in Quantitative Biology, we screened a comprehensive library of α-synuclein missense mutants in yeast cells treated with a variety of small molecules that perturb cellular processes linked to α-synuclein biology and pathobiology.

A Wristwatch-Based Wireless Sensor Platform for IoT Health Monitoring Applications.

A wristwatch-based wireless sensor platform for IoT wearable health monitoring applications is presented. The paper describes the platform in detail, with a particular focus given to the design of a novel and compact wireless sub-system for 868 MHz wristwatch applications. An example application using the developed platform is discussed for arterial oxygen saturation (SpO) and heart rate measurement using optical photoplethysmography (PPG).

Deep mutational scanning reveals the structural basis for α-synuclein activity.

Defining the biologically active structures of proteins in their cellular environments remains challenging for proteins with multiple conformations and functions, where only a minor conformer might be associated with a given function. Here, we use deep mutational scanning to probe the structure and dynamics of α-synuclein, a protein known to adopt disordered, helical and amyloid conformations. We examined the effects of 2,600 single-residue substitutions on the ability of intracellularly expressed α-synuclein to slow the growth of yeast.

Secondary Forces in Protein Folding.

A complete inventory of the forces governing protein folding is critical for productive protein modeling, including structure prediction and design, as well as understanding protein misfolding diseases of clinical significance. The dominant contributors to protein folding include the hydrophobic effect and conventional hydrogen bonding, along with Coulombic and van der Waals interactions. Over the past few decades, important additional contributors have been identified, including C-H···O hydrogen bonding, →π* interactions, C5 hydrogen bonding, chalcogen bonding, and interactions involving aromatic rings (cation-π, X-H···π, π-π, anion-π, and sulfur-arene).

Detailed Histologic Evaluation of Eosinophilic Esophagitis in Pediatric Patients Presenting with Dysphagia or Abdominal Pain and Comparison of the Histology between the Two Groups.

EoE in children presents with four main symptoms. Most common symptoms exhibited by our clinic population are dysphagia (D) and abdominal pain (AP). Despite similar treatments, we found in an earlier study that the outcomes between these two groups were different.

Potential of Sub-GHz Wireless for Future IoT Wearables and Design of Compact 915 MHz Antenna.

Internet of Things (IoT) technology is rapidly emerging in medical applications as it offers the possibility of lower-cost personalized healthcare monitoring. At the present time, the 2.45 GHz band is in widespread use for these applications but in this paper, the authors investigate the potential of the 915 MHz ISM band in implementing future, wearable IoT devices.

The n→π* Interaction.

The carbonyl group holds a prominent position in chemistry and biology not only because it allows diverse transformations but also because it supports key intermolecular interactions, including hydrogen bonding. More recently, carbonyl groups have been found to interact with a variety of nucleophiles, including other carbonyl groups, in what we have termed an n→π* interaction. In an n→π* interaction, a nucleophile donates lone-pair (n) electron density into the empty π* orbital of a nearby carbonyl group.

4-Fluoroprolines: Conformational Analysis and Effects on the Stability and Folding of Peptides and Proteins.

Proline is unique among proteinogenic amino acids because a pyrrolidine ring links its amino group to its side chain. This heterocycle constrains the conformations of the main chain and thus templates particular secondary structures. Proline residues undergo post-translational modification at the 4-position to yield 4-hydroxyproline, which is especially prevalent in collagen.

A prevalent intraresidue hydrogen bond stabilizes proteins.

Current limitations in de novo protein structure prediction and design suggest an incomplete understanding of the interactions that govern protein folding. Here we demonstrate that previously unappreciated hydrogen bonds occur within proteins between the amide proton and carbonyl oxygen of the same residue. Quantum calculations, infrared spectroscopy, and nuclear magnetic resonance spectroscopy show that these interactions share hallmark features of canonical hydrogen bonds.

n→π* Interactions Are Competitive with Hydrogen Bonds.

Because carbonyl groups can participate in both hydrogen bonds and n→π* interactions, these two interactions likely affect one another. Herein, enhancement of an amidic n→π* interaction is shown to reduce the ability of β-keto amides to tautomerize to the enol, indicating decreased hydrogen-bonding capacity of the amide carbonyl group. Thus, an n→π* interaction can have a significant effect on the strength of a hydrogen bond to the same carbonyl group.

Thioamides in the collagen triple helix.

To probe noncovalent interactions within the collagen triple helix, backbone amides were replaced with a thioamide isostere. This subtle substitution is the first in the collagen backbone that does not compromise thermostability. A triple helix with a thioamide as a hydrogen bond donor was found to be more stable than triple helices assembled from isomeric thiopeptides.

n→π* interactions engender chirality in carbonyl groups.

An n→π* interaction stems from the delocalization of the electron pair (n) of a donor group into the antibonding orbital (π*) of a carbonyl group. Crystallographic analyses of five pairs of diastereoisomers demonstrate that an n→π* interaction can induce chirality in an otherwise planar, prochiral carbonyl group. Thus, a subtle delocalization of electrons can have stereochemical consequences.

A key n→π* Interaction in N-acyl homoserine lactones.

Many Gram-negative bacteria employ N-acyl homoserine lactones (AHLs) as signal molecules for quorum sensing. The binding of AHLs to their target LuxR-type receptor proteins can effect changes in growth, virulence, and other phenotypes. LuxR-type receptors therefore present attractive pharmaceutical targets for control of bacterial pathogenesis.

Signatures of n→π* interactions in proteins.

The folding of proteins is directed by a variety of interactions, including hydrogen bonding, electrostatics, van der Waals' interactions, and the hydrophobic effect. We have argued previously that an n→π* interaction between carbonyl groups be added to this list. In an n→π* interaction, the lone pair (n) of one carbonyl oxygen overlaps with the π* antibonding orbital of another carbonyl group.

Interplay of hydrogen bonds and n→π* interactions in proteins.

Protein structures are stabilized by multiple weak interactions, including the hydrophobic effect, hydrogen bonds, electrostatic effects, and van der Waals interactions. Among these interactions, the hydrogen bond is distinct in having its origins in electron delocalization. Recently, another type of electron delocalization, the n→π* interaction between carbonyl groups, has been shown to play a role in stabilizing protein structure.

n→π* interactions in poly(lactic acid) suggest a role in protein folding.

Poly(lactic acid) (PLA) is a versatile synthetic polyester. We noted that this depsipeptide analog of polyalanine has a helical structure that resembles a polyproline II helix. Using natural bond orbital analysis, we find that n→π* interactions between sequential ester carbonyl groups contribute 0.

n→π* interactions of amides and thioamides: implications for protein stability.

Carbonyl-carbonyl interactions between adjacent backbone amides have been implicated in the conformational stability of proteins. By combining experimental and computational approaches, we show that relevant amidic carbonyl groups associate through an n→π* donor-acceptor interaction with an energy of at least 0.27 kcal/mol.

Role of electrostatics in differential binding of RalGDS to Rap mutations E30D and K31E investigated by vibrational spectroscopy of thiocyanate probes.

The human protein Rap1A (Rap) is a member of the Ras superfamily of GTPases that binds to the downstream effector Ral guanine nucleotide dissociation stimulator (RalGDS). Although Ras and Rap have nearly identical amino acid sequences and structures along the effector binding surface, the charge reversal mutation Rap K31E has previously been shown to increase the dissociation constant of Rap-RalGDS docking to values similar to that of Ras-RalGDS docking. This indicates that the difference in charge at position 31 could provide a mechanism for Ral to distinguish two structurally similar but functionally distinct GTPases, which would be of vital importance for appropriate biological function.