Living creatures use ATP as the “universal energy currency”. ATP-ases are assemblies of molecules that break down ATP into smaller molecules using the energy released to power myriad biological reactions. Molecular motors are ATP-ases that convert this chemical energy into mechanical work on other molecules. The AAA+ ATPases are examples of such molecular machines that perform mechanical work to remodel nearly every type of macromolecule, in cells from all kingdoms of life. A long-standing, largely unanswered question about the functional mechanism of the AAA+ ATPases is how do the rings of chemically identical subunits that make up these assemblies interact with their target macromolecules? The authors address this question by studying Enhancer Binding Proteins (bEBPs) in bacteria, AAA+ ATPases that remodel the σ54-form of RNA polymerase (Eσ54) that is present in complexes with promoter DNA. This remodeling or shape transformation is essential to allow transcription and subsequent expression of genes that allow for nutrient acquisition, complex developmental programs, and virulence as pathogens.

In the current work the authors used isothermal calorimetry (ITC), crystallography and 3D reconstruction from EM single particles along with time-resolved and static small angle X-ray scattering (TR-SAXS and SAXS, respectively) at BioCAT to monitor …

SAXS analysis of IDE. Pair distribution functions and scattering curves of WT IDE and IDE R767A (C and D), and IDE S132C/E817C (E and F). Curve fitting is based on atomic models using the program CRYSOL (single model) or OLIGOMER (mixture). D2/D3, D2/D3 pivot; D1/D4, D1/D4 pivot; C, closed state; M, monomer; D, dimer; T, tetramer. The diagrams and ratios shown below the scattering profiles represent the distribution of mixture that could best fit the SAXS data.

Proteins in living organisms face acute and chronic challenges to their integrity, which require proteostatic processes to protect their functions. Proper protein function is ensured through protein turnover through a balance between synthesis and proteolysis. Amyloidogenic peptides, such as amyloid β (Aβ) and amylin, present a major challenge to proteostasis, because they can form toxic aggregates that impair diverse physiological functions and contribute to human diseases. Insulin-degrading enzyme (IDE), a Zn²⁺-metalloprotease, prefers to degrade amyloidogenic peptides to prevent the formation of amyloid fibrils. Thus, IDE retards the progression of Alzheimer’s disease.

IDE possesses an enclosed catalytic chamber that engulfs and degrades its peptide substrates; however, the molecular mechanism of IDE function, including substrate access to …

Type II collagen is the principal extracellular matrix (ECM) component of mammalian cartilage. It has been shown that lamprey (a cartilagenus fish) notochord collagen fibrils are indistinguishable from human cartilage fibrils, their differences being minor amino acid sequences and in the specific arrangement of the fibrils to build their respective ECM’s. Recently, the Orgel group demonstrated that a human anti-biglycan antibody had the capacity to ‘deconstruct’ lamprey notochord type II collagen fibril bundles to give a pure source of ‘thin-fibril’ collagen fibrils that are primarily composed of type II collagen. This procedure provides both a possible explanation for the initiation of Rheumatoid arthritis and a means of studying the structural arrangement of tissue.

This work comprised two principal methods: 1) Using highly focused microbeam at BioCAT to locate the most crystalline portions of a notochord sample, and collecting data from this region over extended periods of time (>15 minutes) using a cryojet. 2) Analysis of TEM data from fibril cross-sections to identity the arrangement of collagen microfibrils within the thin-fibrils. Using the first method, the Orgel group determined the quasi-hexagonal packing of the notchord tissue (previously thought to be tetragonal due to limitations in data available) and the 2D …

Rheumatoid arthritis (RA) is a systemic autoimmune inflammatory and destructive joint disorder that affects tens of millions of people worldwide. Normal healthy joints maintain a balance between the synthesis of extracellular matrix (ECM) molecules and the proteolytic degradation of damaged ones. In the case of RA, this balance is shifted toward matrix destruction due to increased production of cleavage enzymes and the presence of (autoimmune) immunoglobulins resulting from an inflammation induced immune response.

In this study, the authors demonstrate that a polyclonal antibody against the proteoglycan biglycan (BG) causes tissue destruction that may be analogous to that of RA affected tissues. The effect of the antibody is more potent than various harsh chemical and/or …

The Hawkmoth Manduca sexta is an emerging model system for a wide range of studies in integrative biology. The flight muscles are particularly interesting in that, unlike most insect flight muscle, but like vertebrate skeletal and cardiac muscles, they are a synchronous muscle where each stimulus generates one muscle twitch. The length tension curve also shows intriguing similarities to mammalian cardiac muscle even though the sarcomere structure is known to be quite different. Another property of the muscle is that the dorsal-most region of the flight muscle is ca. 5 degrees C cooler than the ventral muscle closer to the midline to the body. (Such spatial temperature gradients are also likely to occur in large muscles in mammals but this has not been well investigated). In Manduca flight muscle these spatial gradients lead to a spatial variation in power production spanning from positive to negative values across …

In many biological processes, various substances undergo phase transitions, where they are transformed from one state (solid, liquid, or gas) to another. Wiskott-Aldrich Syndrome Proteins (WASP) function as intracellular …

The nucleic acid RNA plays an important role in protein synthesis in cells. However, noncoding RNAs also exist that are not converted into proteins, but still play important roles in many biological processes. RNA molecules aggregate into complex tertiary structures, producing globular forms stabilized by various interactions. Proteins, ligands, and other RNA molecules recognize tertiary folded RNAs and result in the biochemical pathways that affect all aspects of cellular metabolism. Using small-angle X-ray scattering (SAXS) at the …

Flying insects are among the most successful species on our planet. Flight is very metabolically demanding and many insects have found a clever way to reduce energy costs in their flight muscles by employing a process called “stretch activation, which has been recognized since the 1960s as an interesting and physiologically important phenomenon, but a mechanistic explanation has been elusive. Now, research at the Biophysics Collaborative Access Team x-ray facility at the U.S. Department of Energy’s Advanced Photon Source provides another, important step toward a full explanation of stretch activation, which also plays an important role in mammalian cardiac expansion and contraction.

How stretch activation works in the heart is unknown. As contractions propagate through the heart, the contraction of one piece of muscle tissue stretches adjacent muscle, thereby activating it. The end result is a very strong contraction at the end of systole aiding cardiac ejection. Heart muscle is much less organized structurally than insect muscle and is thus …

It’s not stretching the truth to say that flexibility is an important and desirable human physiological trait. We owe our flexibility to a protein called elastin, and elastin derives its properties from a building-block molecule called …

How does one prove that the protein isolated from a 68-million-year-old dinosaur bone is not a contamination from the intervening millenia or from the lab? This is the task of a research team who say they have isolated peptides of the common structural protein, collagen, from bones of Tyrannosaurus rex and Brachylophosauraus canadensis. Although the team had previously presented multiple lines of evidence supporting the veracity of the find, the fact that the age of the peptides far exceeds any previous predictions of how long a protein could resist degradation has generated controversy. In their current work, the researchers used x-ray diffraction data collected utilizing the BioCAT 18-ID x-ray beamline at the U.S. Department of Energy Office of Science’s Advanced Photon Source at Argonne National Laboratory to generate a model of collagen structure on which to overlay the …