An integrated native mass spectrometry and top-down proteomics method that connects sequence to structure and function of macromolecular complexes.

Mass spectrometry (MS) has become a crucial technique for the analysis of protein complexes. Native MS has traditionally examined protein subunit arrangements, while proteomics MS has focused on sequence identification. These two techniques are usually performed separately without taking advantage of the synergies between them. Here we describe the development of an integrated native MS and top-down proteomics method using Fourier-transform ion cyclotron resonance (FTICR) to analyse macromolecular protein complexes in a single experiment. We address previous concerns of employing FTICR MS to measure large macromolecular complexes by demonstrating the detection of complexes up to 1.8 MDa, and we demonstrate the efficacy of this technique for direct acquirement of sequence to higher-order structural information with several large complexes. We then summarize the unique functionalities of different activation/dissociation techniques. The platform expands the ability of MS to integrate proteomics and structural biology to provide insights into protein structure, function and regulation

Evolution mechanism of organic macromolecular structure during lignite pyrolysis

Understanding the mechanisms governing coal pyrolysis reactions, particularly in relation to the coal macromolecular structure, is crucial for improving energy efficiency and facilitating the transition of coal into a clean energy source. This study employs cutting-edge techniques, such as High-Resolution Transmission Electron Microscopy (HRTEM) and Thermogravimetric Analysis coupled with Fourier Transform Infrared Spectroscopy and Mass Spectrometry (TG–FTIR–MS), to analyze lignite and its residual solid samples subjected to pyrolysis across a range of temperatures from 300 °C to 1100 °C. The variational characteristics of the macromolecular structure during coal pyrolysis are examined. Utilizing molecular dynamics simulations, we analyze the evolution mechanism of the macromolecular carbon structure of organic matter during the coal pyrolysis process. The results show that the pyrolysis can be divided into three distinct phases: activation (30–300 °C), pyrolysis (300–650 °C), and condensation (650–1200 °C). During these phases, the coal structure undergoes complex transformations, including folding, twisting, shedding of small molecular side chains, and breaking of macromolecular side chains, ultimately leading to the directional arrangement of structural fragments. The structural units initially undergo decomposition, followed by growth and alignment in a certain direction. The spatial distribution of aromatic structural units evolves from local ordering to complete disordering, culminating in larger-scale, three-dimensional ordering. The order of bond breaking within the macromolecular structure of lignite pyrolysis is: oxygen-containing functional groups (such as C–O and COOH) \u3e aliphatic structure (N–C and C–C) \u3e aromatic structure (C[dbnd]C). By uncovering the reaction intermediates and pathways involved in lignite pyrolysis, this research provides a comprehensive quantitative description of the coal pyrolysis process. These insights offer invaluable theoretical support for the industrial-scale pyrolysis of coal, paving the way for more efficient and sustainable utilization of this crucial energy resource

PDBe: improved accessibility of macromolecular structure data from PDB and EMDB

© 2015 The Authors. Published by OUP. This is an open access article available under a Creative Commons licence. The published version can be accessed at the following link on the publisher’s website: https://doi.org/10.1093/nar/gkv1047The Protein Data Bank in Europe (http://pdbe.org) accepts and annotates depositions of macromolecular structure data in the PDB and EMDB archives and enriches, integrates and disseminates structural information in a variety of ways. The PDBe website has been redesigned based on an analysis of user requirements, and now offers intuitive access to improved and value-added macromolecular structure information. Unique value-added information includes lists of reviews and research articles that cite or mention PDB entries as well as access to figures and legends from full-text open-access publications that describe PDB entries. A powerful new query system not only shows all the PDB entries that match a given query, but also shows the 'best structures' for a given macromolecule, ligand complex or sequence family using data-quality information from the wwPDB validation reports. A PDBe RESTful API has been developed to provide unified access to macromolecular structure data available in the PDB and EMDB archives as well as value-added annotations, e.g. regarding structure quality and up-to-date cross-reference information from the SIFTS resource. Taken together, these new developments facilitate unified access to macromolecular structure data in an intuitive way for non-expert users and support expert users in analysing macromolecular structure data.The Wellcome Trust [88944, 104948]; UK Biotechnology and Biological Sciences Research Council [BB/J007471/1, BB/K016970/1, BB/M013146/1, BB/M011674/1]; National Institutes of Health [GM079429]; UK Medical Research Council [MR/L007835/1]; European Union [284209]; CCP4; European Molecular Biology Laboratory (EMBL). Funding for open access charge: The Wellcome Trust.Published versio

Influence of ions and pH on formation of solid and liquid-like melanin

Melanin is a natural pigment with broadband absorption and effective ability to dissipate the energy absorbed. The macromolecular structure of melanin shows a delicate balance between short-range ordered and disordered structures without being a random aggregate. The presence of ions or the variation in pH or ionic strength can alter the self-assembly process which subsequently changes the structure of melanin. To understand these relationships, this study investigates the influence of ions and pH in melanin formation. The types of ions present and pH have a profound influence on the formation and structure of melanin particles, while only minor changes are observed in the absorption and excitation-emission analysis. In some conditions, the formation of discernible particles with significant refractive index contrast is avoided while retaining the spectroscopic characteristics of melanin, leading to liquid-like melanin. These findings identify potential pathways which can be used to manipulate the melanin macromolecular structure while providing the desired spectral properties to enable novel bio-engineering applications.

Structural Dynamics of Free Proteins in Diffraction

Among the macromolecular patterns of biological significance, right-handed α-helices are perhaps the most abundant structural motifs. Here, guided by experimental findings, we discuss both ultrafast initial steps and longer-time-scale structural dynamics of helix-coil transitions induced by a range of temperature jumps in large, isolated macromolecular ensembles of an α-helical protein segment thymosin β_9 (Tβ_9), and elucidate the comprehensive picture of (un)folding. In continuation of an earlier theoretical work from this laboratory that utilized a simplistic structure-scrambling algorithm combined with a variety of self-avoidance thresholds to approximately model helix-coil transitions in Tβ_9, in the present contribution we focus on the actual dynamics of unfolding as obtained from massively distributed ensemble-convergent MD simulations which provide an unprecedented scope of information on the nature of transient macromolecular structures, and with atomic-scale spatiotemporal resolution. In addition to the use of radial distribution functions of ultrafast electron diffraction (UED) simulations in gaining an insight into the elementary steps of conformational interconversions, we also investigate the structural dynamics of the protein via the native (α-helical) hydrogen bonding contact metric which is an intuitive coarse graining approach. Importantly, the decay of α-helical motifs and the (globular) conformational annealing in Tβ_9 occur consecutively or competitively, depending on the magnitude of temperature jump

Impact of macromolecular crowding on DNA replication

Enzymatic activities in vivo occur in a crowded environment composed of many macromolecules. This environment influences DNA replication by increasing the concentration of the constituents, desolvation, decreasing the degrees of freedom for diffusion and hopping of proteins onto DNA, and enhancing binding equilibria and catalysis. However, the effect of macromolecular crowding on protein structure is poorly understood. Here we examine macromolecular crowding using the replication system of bacteriophage T7 and we show that it affects several aspects of DNA replication; the activity of DNA helicase increases and the sensitivity of DNA polymerase to salt is reduced. We also demonstrate, using SAXS analysis, that the complex between DNA helicase and DNA polymerase/trx is far more compact in a crowded environment. The highest enzymatic activity corresponds to the most compact structure. Better knowledge of the effect of crowding on structure and activity will enhance mechanistic insight beyond information obtained from NMR and X-ray structures