How Vibrational Notations Can Spoil Infrared Spectroscopy: A Case Study on Isolated Methanol.

Unraveling methanol's infrared spectrum has challenged spectroscopists for a century, with numerous loose ends still to be explored. We engage in this exploration based on experiments of isolating single methanol molecules in solid argon and neon matrices. We report infrared spectra of methanol in its natural isotopic composition and with partial and full deuteration.

The Dsc ubiquitin ligase complex identifies transmembrane degrons to degrade orphaned proteins at the Golgi.

The Golgi apparatus is essential for protein sorting, yet its quality control mechanisms are poorly understood. Here we show that the Dsc ubiquitin ligase complex uses its rhomboid pseudo-protease subunit, Dsc2, to assess the hydrophobic length of α-helical transmembrane domains (TMDs) at the Golgi. Thereby the Dsc complex likely interacts with orphaned ER and Golgi proteins that have shorter TMDs and ubiquitinates them for targeted degradation.

CDR L3 Loop Rearrangement Switches Multispecific SPE-7 IgE Antibody From Hapten to Protein Binding.

The monoclonal IgE antibody SPE-7 was originally raised against a 2,4-dinitrophenyl (DNP) target. Through its ability to adopt multiple conformations, the antibody is capable of binding to a diverse range of small haptens and large proteins. The present study examines a dataset of experimentally determined crystal structures of the SPE-7 antibody to gain insight into the mechanisms that contribute to its multispecificity.

Ca1.1 voltage-sensing domain III exclusively controls skeletal muscle excitation-contraction coupling.

Skeletal muscle contractions are initiated by action potentials, which are sensed by the voltage-gated calcium channel (Ca1.1) and are conformationally coupled to calcium release from intracellular stores. Notably, Ca1.

Zero-Point-Energy Driven Isotopic Exchange of the [HO] anion Probed by Mid-Infrared Action Spectroscopy.

We present the first observation of vibrational transitions in the [HO] anion, an intermediate in the anion-molecule reaction of water, HO, and hydride, H, using a laser-induced isotopic H/D exchange reaction action spectroscopy scheme applied to anions. The observed bands are assigned as the fundamental and first overtone of the HO-H vibrational stretching mode, based on anharmonic calculations within the vibrational perturbation theory and vibrational configuration interaction. Although the DO·D species has the lowest energy, our experiments confirm the DO·H isotope to be a sink of the H/D exchange reaction.

Solving the Puzzle of the Carbonic Acid Vibrational Spectrum - an Anharmonic Story.

Against the general belief that carbonic acid is too unstable for synthesis, it was possible to synthesize the solid as well as gas-phase carbonic acid. It was suggested that solid carbonic acid might exist in Earth's upper troposphere and in the harsh environments of other solar bodies, where it undergoes a cycle of synthesis, decomposition, and dimerization. To provide spectroscopic data for probing the existence of extraterrestrial carbonic acid, matrix-isolation infrared (MI-IR) spectroscopy has shown to be essential.

Pathogenicity of de novo CACNA1D Ca channel variants predicted from sequence co-variation.

Voltage-gated L-type Cav1.3 Ca channels support numerous physiological functions including neuronal excitability, sinoatrial node pacemaking, hearing, and hormone secretion. De novo missense mutations in the gene of their pore-forming α1-subunit (CACNA1D) induce severe gating defects which lead to autism spectrum disorder and a more severe neurological disorder with and without endocrine symptoms.

The Role of Force Fields and Water Models in Protein Folding and Unfolding Dynamics.

Protein folding is a fascinating, not fully understood phenomenon in biology. Molecular dynamics (MD) simulations are an invaluable tool to study conformational changes in atomistic detail, including folding and unfolding processes of proteins. However, the accuracy of the conformational ensembles derived from MD simulations inevitably relies on the quality of the underlying force field in combination with the respective water model.

Determining internal coordinate sets for optimal representation of molecular vibration.

Arising from the harmonic approximation in solving the vibrational Schrödinger equation, normal modes dissect molecular vibrations into distinct degrees of freedom. Normal modes are widely used as they give rise to descriptive vibrational notations and are convenient for expanding anharmonic potential energy surfaces as an alternative to higher-order Taylor series representations. Usually, normal modes are expressed in Cartesian coordinates, which bears drawbacks that can be overcome by switching to internal coordinates.

Asymmetric contribution of a selectivity filter gate in triggering inactivation of CaV1.3 channels.

Voltage-dependent and Ca2+-dependent inactivation (VDI and CDI, respectively) of CaV channels are two biologically consequential feedback mechanisms that fine-tune Ca2+ entry into neurons and cardiomyocytes. Although known to be initiated by distinct molecular events, how these processes obstruct conduction through the channel pore remains poorly defined. Here, focusing on ultrahighly conserved tryptophan residues in the interdomain interfaces near the selectivity filter of CaV1.

The immunoglobulin A isotype of the Arabian camel () preserves the dualistic structure of unconventional single-domain and canonical heavy chains.

Introduction: The evolution of adaptive immunity in resulted in the concurrent expression of classic heterotetrameric and unconventional homodimeric heavy chain-only IgG antibodies. Heavy chain-only IgG bears a single variable domain and lacks the constant heavy (C) γ1 domain required for pairing with the light chain. It has not been reported whether this distinctive feature of IgG is also observed in the IgA isotype.

Structural Basis of the Immunological Cross-Reactivity between Kiwi and Birch Pollen.

Allergies related to kiwi consumption have become a growing health concern, with their prevalence on the rise. Many of these allergic reactions are attributed to cross-reactivity, particularly with the major allergen found in birch pollen. This cross-reactivity is associated with proteins belonging to the pathogenesis-related class 10 (PR-10) protein family.

Addressing Challenges of Macrocyclic Conformational Sampling in Polar and Apolar Solvents: Lessons for Chameleonicity.

We evaluated a workflow to reliably sample the conformational space of a set of 47 peptidic macrocycles. Starting from SMILES strings, we use accelerated molecular dynamics simulations to overcome high energy barriers, in particular, the cis-trans isomerization of peptide bonds. We find that our approach performs very well in polar solvents like water and dimethyl sulfoxide.

PEP-Patch: Electrostatics in Protein-Protein Recognition, Specificity, and Antibody Developability.

The electrostatic properties of proteins arise from the number and distribution of polar and charged residues. Electrostatic interactions in proteins play a critical role in numerous processes such as molecular recognition, protein solubility, viscosity, and antibody developability. Thus, characterizing and quantifying electrostatic properties of a protein are prerequisites for understanding these processes.

Structure and Dynamics Guiding Design of Antibody Therapeutics and Vaccines.

Antibodies and other new antibody-like formats have emerged as one of the most rapidly growing classes of biotherapeutic proteins. Understanding the structural features that drive antibody function and, consequently, their molecular recognition is critical for engineering antibodies. Here, we present the structural architecture of conventional IgG antibodies alongside other formats.

Asymmetric Contribution of a Selectivity Filter Gate in Triggering Inactivation of Ca1.3 Channels.

Voltage-dependent and Ca-dependent inactivation (VDI and CDI, respectively) of Ca channels are two biologically consequential feedback mechanisms that fine-tune Ca entry into neurons and cardiomyocytes. Although known to be initiated by distinct molecular events, how these processes obstruct conduction through the channel pore remains poorly defined. Here, focusing on ultra-highly conserved tryptophan residues in the inter-domain interfaces near the selectivity filter of Ca1.

Establishing a cell-based screening workflow for determining the efficiency of CYP2C9 metabolism: moving towards the use of breath volatiles in personalised medicine.

The use of volatile biomarkers in exhaled breath as predictors to individual drug response would advance the field of personalised medicine by providing direct information on enzyme activity. This would result in enormous benefits, both for patients and for the healthcare sector. Non-invasive breath tests would also gain a high acceptance by patients.

Cross-linking disulfide bonds govern solution structures of diabodies.

In the last years, antibodies have emerged as a promising new class of therapeutics, due to their combination of high specificity with long serum half-life and low risk of side-effects. Diabodies are a popular novel antibody format, consisting of two F domains connected with short linkers. Like IgG antibodies, they simultaneously bind two target proteins.

Evolution of the Immunoglobulin Isotypes-Variations of Biophysical Properties among Animal Classes.

The adaptive immune system arose around 500 million years ago in jawed fish, and, since then, it has mediated the immune defense against pathogens in all vertebrates. Antibodies play a central role in the immune reaction, recognizing and attacking external invaders. During the evolutionary process, several immunoglobulin isotypes emerged, each having a characteristic structural organization and dedicated function.

Vibrational Predissociation Spectra of C N and C N : Bending and Stretching Vibrations.

We present infrared predissociation spectra of C N (H ) and C  N (H ) in the 300-1850 cm range. Measurements were performed using the FELion cryogenic ion trap end user station at the Free Electron Lasers for Infrared eXperiments (FELIX) laboratory. For C N (H ), we detected the CCN bending and CC-N stretching vibrations.

Structural basis of epitope selectivity and potent protection from malaria by PfCSP antibody L9.

A primary objective in malaria vaccine design is the generation of high-quality antibody responses against the circumsporozoite protein of the malaria parasite, Plasmodium falciparum (PfCSP). To enable rational antigen design, we solved a cryo-EM structure of the highly potent anti-PfCSP antibody L9 in complex with recombinant PfCSP. We found that L9 Fab binds multivalently to the minor (NPNV) repeat domain, which is stabilized by a unique set of affinity-matured homotypic, antibody-antibody contacts.

High Intrinsic Oncogenic Potential in the Myc-Box-Deficient Myc3 Protein.

The proto-oncogene has been intensively studied primarily in vertebrate cell culture systems. Myc transcription factors control fundamental cellular processes such as cell proliferation, cell cycle control and stem cell maintenance. Myc interacts with the Max protein and Myc/Max heterodimers regulate thousands of target genes.

Structural mechanism of Fab domain dissociation as a measure of interface stability.

Therapeutic antibodies should not only recognize antigens specifically, but also need to be free from developability issues, such as poor stability. Thus, the mechanistic understanding and characterization of stability are critical determinants for rational antibody design. In this study, we use molecular dynamics simulations to investigate the melting process of 16 antigen binding fragments (Fabs).

Structural Characterization of Nanobodies during Germline Maturation.

Camelid heavy-chain antibody variable domains (VH), nanobodies, are the smallest-known functional antibody fragments with high therapeutic potential. In this study, we investigate a VH binding to hen egg-white lysozyme (HEL). We structurally and dynamically characterized the conformational diversity of four VH variants to elucidate the antigen-binding process.