Pyruvate kinase muscle isoform 2 (PKM2) is a key glycolytic enzyme and transcriptional coactivator and is critical for tumor metabolism. In cancer cells, native tetrameric PKM2 is phosphorylated or acetylated, which initiates a switch to a dimeric/monomeric form that translocates into the nucleus, causing oncogene transcription. However, it is not known how these post-translational modifications (PTMs) disrupt the oligomeric state of PKM2. We explored this question via crystallographic and biophysical analyses of PKM2 mutants containing residues that mimic phosphorylation and acetylation. We find that the PTMs elicit major structural reorganization of the fructose 1,6-bisphosphate (FBP), an allosteric activator, binding site, impacting the interaction with FBP and causing a disruption in oligomerization. To gain insight into how these modifications might cause unique outcomes in cancer cells, we examined the impact of increasing the intracellular pH (pHi) from ∼7.1 (in normal cells) to ∼7.5 (in cancer cells). Biochemical studies of WT PKM2 (wtPKM2) and the two mimetic variants demonstrated that the activity decreases as the pH is increased from 7.0 to 8.0, and wtPKM2 is optimally active and amenable to FBP-mediated allosteric regulation at pHi 7.5. However, the PTM mimetics exist as a mixture of tetramer and dimer, indicating that physiologically dimeric fraction is important and might be necessary for the modified PKM2 to translocate into the nucleus. Thus, our findings provide insight into how PTMs and pH regulate PKM2 and offer a broader understanding of its intricate allosteric regulation mechanism by phosphorylation or acetylation.

Defining discontinuous antigenic epitopes remains a substantial challenge, as exemplified by the case of lipid transfer polyproteins, which are common pollen allergens. Hydrogen/deuterium exchange monitored by NMR can be used to map epitopes onto folded protein surfaces, but only if the complex rapidly dissociates. Modifying the standard NMR-exchange measurement to detect substoichiometric complexes overcomes this time scale limitation and provides new insights into recognition of lipid transfer polyprotein by antibodies. In the future, this new and exciting development should see broad application to a range of tight macromolecular interactions.

RNA-protein interfaces control key replication events during the HIV-1 life cycle. The viral trans-activator of transcription (Tat) protein uses an archetypal arginine-rich motif (ARM) to recruit the host positive transcription elongation factor b (pTEFb) complex onto the viral trans-activation response (TAR) RNA, leading to activation of HIV transcription. Efforts to block this interaction have stimulated production of biologics designed to disrupt this essential RNA-protein interface. Here, we present four co-crystal structures of lab-evolved TAR-binding proteins (TBPs) in complex with HIV-1 TAR. Our results reveal that high-affinity binding requires a distinct sequence and spacing of arginines within a specific β2-β3 hairpin loop that arose during selection. Although loops with as many as five arginines were analyzed, only three arginines could bind simultaneously with major-groove guanines. Amino acids that promote backbone interactions within the β2-β3 loop were also observed to be important for high-affinity interactions. Based on structural and affinity analyses, we designed two cyclic peptide mimics of the TAR-binding β2-β3 loop sequences present in two high-affinity TBPs (KD values of 4.2 ± 0.3 and 3.0 ± 0.3 nm). Our efforts yielded low-molecular weight compounds that bind TAR with low micromolar affinity (KD values ranging from 3.6 to 22 μm). Significantly, one cyclic compound within this series blocked binding of the Tat-ARM peptide to TAR in solution assays, whereas its linear counterpart did not. Overall, this work provides insight into protein-mediated TAR recognition and lays the ground for the development of cyclic peptide inhibitors of a vital HIV-1 RNA-protein interaction.

Cation diffusion facilitator (CDF) proteins are a conserved family of divalent transition metal cation transporters. CDF proteins are usually composed of two domains: the transmembrane domain, in which the metal cations are transported through, and a regulatory cytoplasmic C-terminal domain (CTD). Each CDF protein transports either one specific metal or multiple metals from the cytoplasm, and it is not known whether the CTD takes an active regulatory role in metal recognition and discrimination during cation transport. Here, the model CDF protein MamM, an iron transporter from magnetotactic bacteria, was used to probe the role of the CTD in metal recognition and selectivity. Using a combination of biophysical and structural approaches, the binding of different metals to MamM CTD was characterized. Results reveal that different metals bind distinctively to MamM CTD in terms of their binding sites, thermodynamics, and binding-dependent conformations, both in crystal form and in solution, which suggests a varying level of functional discrimination between CDF domains. Furthermore, these results provide the first direct evidence that CDF CTDs play a role in metal selectivity. We demonstrate that MamM's CTD can discriminate against Mn2+, supporting its postulated role in preventing magnetite formation poisoning in magnetotactic bacteria via Mn2+ incorporation.

Intrinsically disordered protein domains often have multiple binding partners. It is plausible that the strength of pairing with specific partners evolves from an initial low affinity to a higher affinity. However, little is known about the molecular changes in the binding mechanism that would facilitate such a transition. We previously showed that the interaction between two intrinsically disordered domains, NCBD and CID, likely emerged in an ancestral deuterostome organism as a low-affinity interaction that subsequently evolved into a higher-affinity interaction before the radiation of modern vertebrate groups. Here we map native contacts in the transition states of the low-affinity ancestral and high-affinity human NCBD/CID interactions. We show that the coupled binding and folding mechanism is overall similar but with a higher degree of native hydrophobic contact formation in the transition state of the ancestral complex and more heterogeneous transient interactions, including electrostatic pairings, and an increased disorder for the human complex. Adaptation to new binding partners may be facilitated by this ability to exploit multiple alternative transient interactions while retaining the overall binding and folding pathway.

Systemic antibody light chains (AL) amyloidosis is characterized by deposition of amyloid fibrils derived from a particular antibody light chain. Cardiac involvement is a major risk factor for mortality. Using MAS solid-state NMR, we studied the fibril structure of a recombinant light chain fragment corresponding to the fibril protein from patient FOR005, together with fibrils formed by protein sequence variants that are derived from the closest germline (GL) sequence. Both analyzed fibril structures were seeded with ex-vivo amyloid fibrils purified from the explanted heart of this patient. We find that residues 11-42 and 69-102 adopt β-sheet conformation in patient protein fibrils. We identify arginine-49 as a key residue that forms a salt bridge to aspartate-25 in the patient protein fibril structure. In the germline sequence, this residue is replaced by a glycine. Fibrils from the GL protein and from the patient protein harboring the single point mutation R49G can be both heterologously seeded using patient ex-vivo fibrils. Seeded R49G fibrils show an increased heterogeneity in the C-terminal residues 80-102, which is reflected by the disappearance of all resonances of these residues. By contrast, residues 11-42 and 69-77, which are visible in the MAS solid-state NMR spectra, show 13Cα chemical shifts that are highly like patient fibrils. The mutation R49G thus induces a conformational heterogeneity at the C terminus in the fibril state, whereas the overall fibril topology is retained. These findings imply that patient mutations in FOR005 can stabilize the fibril structure.

Replication protein A (RPA) is a eukaryotic ssDNA-binding protein and contains three subunits: RPA70, RPA32, and RPA14. Phosphorylation of the N-terminal region of the RPA32 subunit plays an essential role in DNA metabolism in processes such as replication and damage response. Phosphorylated RPA32 (pRPA32) binds to RPA70 and possibly regulates the transient RPA70-Bloom syndrome helicase (BLM) interaction to inhibit DNA resection. However, the structural details and determinants of the phosphorylated RPA32–RPA70 interaction are still unknown. In this study, we provide molecular details of the interaction between RPA70 and a mimic of phosphorylated RPA32 (pmRPA32) using fluorescence polarization and NMR analysis. We show that the N-terminal domain of RPA70 (RPA70N) specifically participates in pmRPA32 binding, whereas the unphosphorylated RPA32 does not bind to RPA70N. Our NMR data revealed that RPA70N binds pmRPA32 using a basic cleft region. We also show that at least 6 negatively charged residues of pmRPA32 are required for RPA70N binding. By introducing alanine mutations into hydrophobic positions of pmRPA32, we found potential points of contact between RPA70N and the N-terminal half of pmRPA32. We used this information to guide docking simulations that suggest the orientation of pmRPA32 in complex with RPA70N. Our study demonstrates detailed features of the domain-domain interaction between RPA70 and RPA32 upon phosphorylation. This result provides insight into how phosphorylation tunes transient bindings between RPA and its partners in DNA resection.

The recent structural elucidation of ex vivo Drosophila Orb2 fibrils revealed a novel amyloid formed by interdigitated Gln and His residue side chains belonging to the prion-like domain. However, atomic-level details on the conformational transitions associated with memory consolidation remain unknown. Here, we have characterized the nascent conformation and dynamics of the prion-like domain (PLD) of Orb2A using a nonconventional liquid-state NMR spectroscopy strategy based on 13C detection to afford an essentially complete set of 13Cα, 13Cβ, 1Hα, and backbone 13CO and 15N assignments. At pH 4, where His residues are protonated, the PLD is disordered and flexible, except for a partially populated α-helix spanning residues 55–60, and binds RNA oligos, but not divalent cations. At pH 7, in contrast, His residues are predominantly neutral, and the Q/H segments adopt minor populations of helical structure, show decreased mobility and start to self-associate. At pH 7, the His residues do not bind RNA or Ca2+, but do bind Zn2+, which promotes further association. These findings represent a remarkable case of structural plasticity, based on which an updated model for Orb2A functional amyloidogenesis is suggested.

Mouse embryonic stem cells (mESCs) display unique mechanical properties, including low cellular stiffness in contrast to differentiated cells, which are stiffer. We have previously shown that mESCs lacking the clathrin heavy chain (Cltc), an essential component for clathrin-mediated endocytosis (CME), display a loss of pluripotency and an enhanced expression of differentiation markers. However, it is not known whether physical properties such as cellular stiffness also change upon loss of Cltc, similar to what is seen in differentiated cells, and if so, how these altered properties specifically impact pluripotency. Using atomic force microscopy (AFM), we demonstrate that mESCs lacking Cltc display higher Young's modulus, indicative of greater cellular stiffness, compared with WT mESCs. The increase in stiffness was accompanied by the presence of actin stress fibers and accumulation of the inactive, phosphorylated, actin-binding protein cofilin. Treatment of Cltc knockdown mESCs with actin polymerization inhibitors resulted in a decrease in the Young's modulus to values similar to those obtained with WT mESCs. However, a rescue in the expression profile of pluripotency factors was not obtained. Additionally, whereas WT mouse embryonic fibroblasts could be reprogrammed to a state of pluripotency, this was inhibited in the absence of Cltc. This indicates that the presence of active CME is essential for the pluripotency of embryonic stem cells. Additionally, whereas physical properties may serve as a simple readout of the cellular state, they may not always faithfully recapitulate the underlying molecular fate.

Transient receptor potential vanilloid 1 (TRPV1) channel is a multimodal receptor that is responsible for nociceptive, thermal, and mechanical sensations. However, which biomolecular partners specifically interact with TRPV1 remains to be elucidated. Here, we used cDNA library screening of genes from mouse dorsal root ganglia combined with patch-clamp electrophysiology to identify the voltage-gated potassium channel auxiliary subunit Kvβ1 physically interacting with TRPV1 channel and regulating its function. The interaction was validated in situ using endogenous dorsal root ganglia neurons, as well as a recombinant expression model in HEK 293T cells. The presence of Kvβ1 enhanced the expression stability of TRPV1 channels on the plasma membrane and the nociceptive current density. Surprisingly, Kvβ1 interaction also shifted the temperature threshold for TRPV1 thermal activation. Using site-specific mapping, we further revealed that Kvβ1 interacted with the membrane-distal domain and membrane-proximal domain of TRPV1 to regulate its membrane expression and temperature-activation threshold, respectively. Our data therefore suggest that Kvβ1 is a key element in the TRPV1 signaling complex and exerts dual regulatory effects in a site-specific manner.

The kinesin-3 family contains the fastest and most processive motors of the three neuronal transport kinesin families, yet the sequence of states and rates of kinetic transitions that comprise the chemomechanical cycle and give rise to their unique properties are poorly understood. We used stopped-flow fluorescence spectroscopy and single-molecule motility assays to delineate the chemomechanical cycle of the kinesin-3, KIF1A. Our bacterially expressed KIF1A construct, dimerized via a kinesin-1 coiled-coil, exhibits fast velocity and superprocessivity behavior similar to WT KIF1A. We established that the KIF1A forward step is triggered by hydrolysis of ATP and not by ATP binding, meaning that KIF1A follows the same chemomechanical cycle as established for kinesin-1 and -2. The ATP-triggered half-site release rate of KIF1A was similar to the stepping rate, indicating that during stepping, rear-head detachment is an order of magnitude faster than in kinesin-1 and kinesin-2. Thus, KIF1A spends the majority of its hydrolysis cycle in a one-head-bound state. Both the ADP off-rate and the ATP on-rate at physiological ATP concentration were fast, eliminating these steps as possible rate-limiting transitions. Based on the measured run length and the relatively slow off-rate in ADP, we conclude that attachment of the tethered head is the rate-limiting transition in the KIF1A stepping cycle. Thus, KIF1A's activity can be explained by a fast rear-head detachment rate, a rate-limiting step of tethered-head attachment that follows ATP hydrolysis, and a relatively strong electrostatic interaction with the microtubule in the weakly bound post-hydrolysis state.

Physicists have developed a deep understanding of the fundamental laws of nature through careful observations, experiments, and precise measurements. However, what if artificial intelligence (AI) could uncover governing laws of […]

The post Archetype AI’s Newton Model Masters Physics From Raw Data appeared first on HPCwire.

PITTSBURGH, Feb. 22, 2024 — Ansys and Intel Foundry have collaborated to provide multiphysics signoff solutions for Intel’s innovative 2.5D chip assembly technology, which uses EMIB technology to connect the […]

The post Ansys, Intel Foundry Collaborate on Multiphysics Analysis Solution for EMIB 2.5D Assembly Tech appeared first on HPCwire.

PITTSBURGH, June 19, 2024 — Ansys today announced that it is adopting NVIDIA Omniverse application programming interfaces (APIs) to offer 3D-IC designers valuable insights from Ansys’ physics solver results through […]

The post Ansys Enables 3D Multiphysics Visualization of Next-Gen 3D-IC Designs with NVIDIA Omniverse appeared first on HPCwire.

Use #physnobel on Twitter to submit your questions. The 2014 Nobel Prize in Physics will be announced on Tuesday, October 7. Join guests Charles Day of Physics Today, Andrew Grant of Science News, Jennifer Ouellette of Cocktail Party Physics and Amanda Yoho of Starts With A Bang! as they discuss predictions for possible winners. Who are the best contenders, and who are the potential "dark horse" candidates? Which major physics finds of this year might stand a shot at a win in the future? Victoria Jaggard and Helen Thompson of Smithsonian.com will be your hosts for the event. Tune in on October 2, and submit your questions on Twitter. Charles Day is the Online Editor for Physics Today magazine. Follow him on Twitter @CSRDay Andrew Grant is the physics reporter for Science News magazine. Follow him on Twitter @sci_grant Jennifer Ouellette is a science writer and blogger at Cocktail Party Physics. Follow her on Twitter @JenLucPiquant Amanda Yoho is a graduate student in theoretical and computational cosmology at Case Western Reserve University and a blogger at Starts With A Bang! Follow her on Twitter @mandaYoho Victoria Jaggard is the science editor for Smithsonian.com. Follow her on Twitter @vmjaggard99 Helen Thompson is a science reporter for Smithsonian.com. Follow her on Twitter @wwrfd

The act of dive bombing during World War II was a death defying trial of skill and nerve. You aimed your plane down, four miles above the ocean and plummeted at speeds of up to 275 miles per hour

John Hopfield and Geoffrey Hinton shared the award for their work on artificial neural networks and machine learning

Many teachers are tapped to teach physics without prior training or experience. A new study explores a possible solution.

Introduction

Multiphysics is an integral part of the concepts around digital twins. In this post, I want to discuss the mechanical aspects of multiphysics in system simulations, which are critical for 3D-IC, multi-die, and chiplet design.

The physical world in which we live is growing ever more electrified. Think of the transformation that the cell phone has brought into our lives, as has the present-day migration to electronic vehicles (EVs). These products are not only feats of electronic engineering but of mechanical as well, as the electronics find themselves in new and novel forms such as foldable phones and flying cars (eVOTLs). Here, engineering domains must co-exist and collaborate to bring about the best end products possible.

Start with the electronics—chips, chiplets, IC packaging, PCB, and modules. But now put these into a new form factor that can be dropped or submerged in water or accelerated along a highway. What about drop testing, aerodynamics, and aeroacoustics? These largely computational fluid dynamics (CFD) and/or mechanical multiphysics phenomena must also be accounted for. And then how does the drop testing impact the electrical performance? The world of electronics and its vast array of end products is pushing us beyond pure electrical engineering to be more broadly minded and develop not only heterogeneous products but heterogeneous engineering teams as well.

Cadence's Unique Expertise

It's at this crossroad of complexity and electronic proliferation that Cadence shines. Let's take, for example, the latest push for higher-performing high-bandwidth memory (HBM) devices and AI data center expansion. These technologies are growing from several layers to 12, and I can't emphasize enough the importance of teamwork and integrated solutions in tackling the challenges of advanced packaging technologies and how collaboration is shaping the future of semiconductor innovation and paving the way for cutting-edge developments in the industry.

These layered electronics are powered, and power creates heat. Heat needs to be understood, and thus, the thermal integrity issues uncovered along the way must be addressed. However, electronic thermal issues are just the first domino in a chain of interdependencies. What about the thermal stress and warpage that can be caused by the powering of these stacked devices? How does that then lend to mechanical stress and even material fatigue as the temperature cycles from high to low and back through the use of the electronic device? This is just one example in a long list of many...

Cadence Multiphysics Analysis Offerings

The confluence of electrical, mechanical, and CFD is exactly why Cadence expanded into multiphysics at a significant rate starting in 2019 with the announcement of the Clarity 3D Solver and Celsius Thermal Solver products for electromagnetic (EM) and thermal multiphysics system simulations. Recent acquisitions of Numeca, Pointwise, and Cascade (now branded within Cadence as the Fidelity CFD Platform) as well as Future Facilities (now the Cadence Reality Digital Twin product line) are all adding CFD expertise. The recent addition of Beta CAE brings mechanical multiphysics to the suite of solutions available from Cadence. The full breadth of these multiphysics system analyses, spanning EM, thermal, signal integrity/power integrity (SI/PI), CFD, and now mechanical, creates a platform for digital twinning across a wide array of applications. You can learn more by viewing Cadence's Reality Digital Twin platform launch on the keynote stage at NVIDIA's GTC in March, as well as this Designed with Cadence video: NV5, NVIDIA, and Cadence Collaboration Optimizes Data Centers.

Conclusion

Ever more sophisticated electronic designs are in demand to fulfill the needs of tomorrow's technologies, driving a convergence of electrical and mechanical aspects of multiphysics in system simulations. To successfully produce the exciting new products of the future, both domains must be able to collaborate effectively and efficiently. Cadence is fully committed to developing and providing our customers with the software products they need to enable this electrical/mechanical evolution. From EM, to thermal, to SI/PI, CFD, and mechanical, Cadence is enabling digital twinning across a wide array of applications that are forging pathways to the future.

For more information on Cadence's multiphysics system analysis offerings, visit our webpage and download our brochure.

Strange solids called temporal metamaterials finally make it possible to investigate the controversial idea of quantum friction – and push special relativity to its limits

Simple words like "force" and "particle" can mislead us as to what reality is actually like. Physicist Matt Strassler unpacks how to see things more clearly

Daniele Oriti’s pursuit of a theory of quantum gravity has led him to the startling conclusion that the laws of nature don’t exist independently of us – a perspective shift that could yield fresh breakthroughs

Could the universe's missing matter be hiding in a "dark" extra dimension? We now have simple ways to test this outlandish idea - and the existence of extra dimensions more generally

Strange solids called temporal metamaterials finally make it possible to investigate the controversial idea of quantum friction – and push special relativity to its limits

While time is relative, it still flows in one direction for every observer. We don’t yet understand why, but some physicists are looking for answers that invoke the evolution of entropy, says Chanda Prescod-Weinstein

A jiggling robot has revealed the ideal vibrating speed to free jumbled fibres

In the quantum realm, a particle’s properties can be separate from the particle itself, including its angular momentum – which could require a rethinking of fundamental laws

In 2022, physicists were excited by hints that something was wrong with our understanding of the universe - but new results have put that in doubt

Simple words like "force" and "particle" can mislead us as to what reality is actually like. Physicist Matt Strassler unpacks how to see things more clearly

Daniele Oriti’s pursuit of a theory of quantum gravity has led him to the startling conclusion that the laws of nature don’t exist independently of us – a perspective shift that could yield fresh breakthroughs

Could the universe's missing matter be hiding in a "dark" extra dimension? We now have simple ways to test this outlandish idea - and the existence of extra dimensions more generally

The symbols and mathematical operations used in the laws of physics follow a pattern that could reveal something fundamental about the universe

Kelley makes a Morgen Wonk. Chris loves the smell of Gundam in the morning. Phil plays some Mathfinder while listening to his favorite new band, Creepy Lego Waifus. The cake has arrived.

The post RPG Cast – Episode 728: “Cats With Jiggle Physics” appeared first on RPGamer.

The 2024 Nobel prize in physics has gone to John Hopfield and Geoffrey Hinton for discoveries that enabled machine learning and are key to the development of artificial intelligence models like ChatGPT

Two pioneers of artificial intelligence have won the Nobel Prize in physics for discoveries and inventions that formed the building blocks of machine learning.

Ever wondered how tennis pros are able to hit the ball with so much force, at extreme angles with incredible accuracy while still keeping it in the court? It comes down to physics. WSJ’s Daniela Hernandez explains what you can learn from the physics that give tennis pros their edge. Photo composite: Adele Morgan

National award-winning science teacher K Sureshkumar’s pedagogical laboratory in Thiruvananthapuram enables students of high school to conduct experiments in Physics and learn the concepts themselves

In this new series of columns, James McKenzie explores the value and relevance of physicists to industry

London : Sternberg Press ; Madrid : Fundación TBA21, [2024]

Physics professor Rhett Allain breaks down amazing feats of physics from superheroes in movies and television and explains how accurate their depictions really are. How realistic are "superhero" landings? Is the kinetic energy suit from "Black Panther" possible? Even with superpowers, is it physically feasible for Superman to lift a large building? Rhett Allain is an Associate Professor of Physics at Southeastern Louisiana University.

Emily Kuhn, a former gymnast and current physics PhD student at Yale University, explains all the math behind the amazing flips and turns we see during the Olympic gymnastics competitions. Emily explains why "The Biles" tumbling routine is so difficult as well as the types of forces acting on these gymnasts every time they use the uneven bars.

Dr. Michio Kaku, a professor of theoretical physics, answers the internet's burning questions about physics. Can Michio explain "string theory" to the layperson? What is a quark? What is the "God Equation"? How do black holes distort time? Is the best physicist ever Albert Einstein or Richard Feynman? Or someone else? Michio answers all these questions and much more!

Physicist Jeffrey Hazboun visits WIRED to answer the internet's swirling questions about physics. How does one split an atom? Is light a wave or a particle...or both? How soon will the universe end? Is time travel is possible given physicists' current understanding? Director: Lisandro Perez-Rey Director of Photography: AJ Young Editor: Marcus Niehaus Talent: Jeffrey Hazboun Creative Producer: Justin Wolfson Line Producer: Joseph Buscemi Associate Producer: Paul Gulyas Production Manager: Peter Brunette Production and Equipment Manager: Kevin Balash Casting Producer: Vanessa Brown Camera Operator: Lucas Vilicich Sound Mixer: Kara Johnson Production Assistant: Fernando Barajas Post Production Supervisor: Alexa Deutsch Post Production Coordinator: Ian Bryant Supervising Editor: Doug Larsen Additional Editor: Paul Tael Assistant Editor: Billy Ward

Hinton, often referred to as the “Godfather of artificial intelligence,” alongside Hopfield, an American scientist working at Princeton, have utilised principles from physics to create algorithms and neural networks that underpin today’s AI technologies

IOP Publishing Limited

Bratislava : Geophysical Institute, Slovak Academy of Sciences, 1998-

IEEE / Institute of Electrical and Electronics Engineers Incorporated