Aminopeptidase N (APN, CD13) is a transmembrane ectopeptidase involved in many crucial cellular functions. Besides its role as a peptidase, APN also mediates signal transduction and is involved in the activation of matrix metalloproteinases (MMPs). MMPs function in tissue remodeling within the extracellular space and are therefore involved in many human diseases, such as fibrosis, rheumatoid arthritis, tumor angiogenesis, and metastasis, as well as viral infections. However, the exact mechanism that leads to APN-driven MMP activation is unclear. It was previously shown that extracellular 14-3-3 adapter proteins bind to APN and thereby induce the transcription of MMPs. As a first step, we sought to identify potential 14-3-3–binding sites in the APN sequence. We constructed a set of phosphorylated peptides derived from APN to probe for interactions. We identified and characterized a canonical 14-3-3–binding site (site 1) within the flexible, structurally unresolved N-terminal APN region using direct binding fluorescence polarization assays and thermodynamic analysis. In addition, we identified a secondary, noncanonical binding site (site 2), which enhances the binding affinity in combination with site 1 by many orders of magnitude. Finally, we solved crystal structures of 14-3-3σ bound to mono- and bis-phosphorylated APN-derived peptides, which revealed atomic details of the binding mode of mono- and bivalent 14-3-3 interactions. Therefore, our findings shed some light on the first steps of APN-mediated MMP activation and open the field for further investigation of this important signaling pathway.

Members of the B-cell lymphoma (BCL-2) protein family regulate mitochondrial outer membrane permeabilization (MOMP), a phenomenon in which mitochondria become porous and release death-propagating complexes during the early stages of apoptosis. Pro-apoptotic BCL-2 proteins oligomerize at the mitochondrial outer membrane during MOMP, inducing pore formation. Of current interest are endogenous factors that can inhibit pro-apoptotic BCL-2 mitochondrial outer membrane translocation and oligomerization. A mitochondrial-derived peptide, Humanin (HN), was reported being expressed from an alternate ORF in the mitochondrial genome and inhibiting apoptosis through interactions with the pro-apoptotic BCL-2 proteins. Specifically, it is known to complex with BAX and BID. We recently reported the fibrillation of HN and BAX into β-sheets. Here, we detail the fibrillation between HN and BID. These fibers were characterized using several spectroscopic techniques, protease fragmentation with mass analysis, and EM. Enhanced fibrillation rates were detected with rising temperatures or pH values and the presence of a detergent. BID fibers are similar to those produced using BAX; however, the structures differ in final conformations of the BCL-2 proteins. BID fibers display both types of secondary structure in the fiber, whereas BAX was converted entirely to β-sheets. The data show that two distinct segments of BID are incorporated into the fiber structure, whereas other portions of BID remain solvent-exposed and retain helical structure. Similar analyses show that anti-apoptotic BCL-xL does not form fibers with humanin. These results support a general mechanism of sequestration of pro-apoptotic BCL-2 proteins into fibers by HN to inhibit MOMP.

Programmed ribosomal frameshifting (PRF) is a mechanism used by arteriviruses like porcine reproductive and respiratory syndrome virus (PRRSV) to generate multiple proteins from overlapping reading frames within its RNA genome. PRRSV employs −1 PRF directed by RNA secondary and tertiary structures within its viral genome (canonical PRF), as well as a noncanonical −1 and −2 PRF that are stimulated by the interactions of PRRSV nonstructural protein 1β (nsp1β) and host protein poly(C)-binding protein (PCBP) 1 or 2 with the viral genome. Together, nsp1β and one of the PCBPs act as transactivators that bind a C-rich motif near the shift site to stimulate −1 and −2 PRF, thereby enabling the ribosome to generate two frameshift products that are implicated in viral immune evasion. How nsp1β and PCBP associate with the viral RNA genome remains unclear. Here, we describe the purification of the nsp1β:PCBP2:viral RNA complex on a scale sufficient for structural analysis using small-angle X-ray scattering and stochiometric analysis by analytical ultracentrifugation. The proteins associate with the RNA C-rich motif as a 1:1:1 complex. The monomeric form of nsp1β within the complex differs from previously reported homodimer identified by X-ray crystallography. Functional analysis of the complex via mutational analysis combined with RNA-binding assays and cell-based frameshifting reporter assays reveal a number of key residues within nsp1β and PCBP2 that are involved in complex formation and function. Our results suggest that nsp1β and PCBP2 both interact directly with viral RNA during formation of the complex to coordinate this unusual PRF mechanism.

Alice Santonastaso
Dec 1, 2020; 61:1687-1696
Research Articles

Oktawia Nilsson
Nov 17, 2020; 0:jlr.RA120000920v1-jlr.RA120000920
Research Articles

Gerhard Liebisch
Dec 1, 2020; 61:1539-1555
Special Report

Apolipoprotein A-I (ApoA-I) of high-density lipoprotein (HDL) is essential for the transportation of cholesterol between peripheral tissues and the liver. However, specific mutations in Apolipoprotein A-I (ApoA-I) of high-density lipoprotein (HDL) are responsible for a late-onset systemic amyloidosis, the pathological accumulation of protein fibrils in tissues and organs. Carriers of these mutations do not exhibit increased cardiovascular disease risk despite displaying reduced levels of ApoA-I/ HDL-cholesterol. To explain this paradox, we show that the HDL particle profile of patients carrying either L75P or L174S ApoA-I amyloidogenic variants a higher relative abundance of the 8.4 nm vs 9.6 nm particles, and that serum from patients, as well as reconstituted 8.4 and 9.6 nm HDL particles (rHDL), possess increased capacity to catalyze cholesterol efflux from macrophages. Synchrotron radiation circular dichroism and hydrogen-deuterium exchange revealed that the variants in 8.4 nm rHDL have altered secondary structure composition and display a more flexible binding to lipids compared to their native counterpart. The reduced HDL-cholesterol levels of patients carrying ApoA-I amyloidogenic variants are thus balanced by higher proportion of small, dense HDL particles and better cholesterol efflux due to altered, region-specific protein structure dynamics.

Lipoprotein (a) [Lp(a)] is characterized by an LDL-like composition in terms of lipids and apoB100, and by one copy of a unique glycoprotein, apo(a). The apo(a) structure is mainly based on the repetition of tandem kringle domains with high homology to plasminogen kringles 4 and 5. Among them, kringle IV type 2 (KIV-2) is present in a highly variable number of genetically encoded repeats, whose length is inversely related to Lp(a) plasma concentration and cardiovascular risk. Despite it being the major component of apo(a), the actual function of KIV-2 is still unclear. Here, we describe the first high-resolution crystallographic structure of this domain. It shows a general fold very similar to other KIV domains with high and intermediate affinity for the lysine analog, -aminocaproic acid. Interestingly, KIV-2 presents a lysine binding site (LBS) with a unique shape and charge distribution. KIV-2 affinity for predicted small molecule binders was found to be negligible in surface plasmon resonance experiments; and with the LBS being nonfunctional, we propose to rename it "pseudo-LBS". Further investigation of the protein by computational small-molecule docking allowed us to identify a possible heparin-binding site away from the LBS, which was confirmed by specific reverse charge mutations abolishing heparin binding. This study opens new possibilities to define the pathogenesis of Lp(a)-related diseases and to facilitate the design of specific therapeutic drugs.

A comprehensive and standardized system to report lipid structures analyzed by MS is essential for the communication and storage of lipidomics data. Herein, an update on both the LIPID MAPS classification system and shorthand notation of lipid structures is presented for lipid categories Fatty Acyls (FA), Glycerolipids (GL), Glycerophospholipids (GP), Sphingolipids (SP), and Sterols (ST). With its major changes, i.e., annotation of ring double bond equivalents and number of oxygens, the updated shorthand notation facilitates reporting of newly delineated oxygenated lipid species as well. For standardized reporting in lipidomics, the hierarchical architecture of shorthand notation reflects the diverse structural resolution powers provided by mass spectrometric assays. Moreover, shorthand notation is expanded beyond mammalian phyla to lipids from plant and yeast phyla. Finally, annotation of atoms is included for the use of stable isotope-labeled compounds in metabolic labeling experiments or as internal standards. This update on lipid classification, nomenclature, and shorthand annotation for lipid mass spectra is considered a standard for lipid data presentation.

The organic anion transporters (OATs) and organic anion–transporting polypeptides (OATPs) belong to the solute carrier (SLC) transporter superfamily and play important roles in handling various endogenous and exogenous compounds of anionic charge. The OATs and OATPs are often implicated in drug therapy by impacting the pharmacokinetics of clinically important drugs and, thereby, drug exposure in the target organs or cells. Various mechanisms (e.g. genetic, environmental, and disease-related factors, drug-drug interactions, and food-drug interactions) can lead to variations in the expression and activity of the anion drug-transporting proteins of OATs and OATPs, possibly impacting the therapeutic outcomes. Previous investigations mainly focused on the regulation at the transcriptional level and drug-drug interactions as competing substrates or inhibitors. Recently, evidence has accumulated that cellular trafficking, post-translational modification, and degradation mechanisms serve as another important layer for the mechanisms underlying the variations in the OATs and OATPs. This review will provide a brief overview of the major OATs and OATPs implicated in drug therapy and summarize recent progress in our understanding of the post-translational modifications, in particular ubiquitination and degradation pathways of the individual OATs and OATPs implicated in drug therapy.

Infrastructure Management Contracts: Improving Energy Asset Management in Displacement Settings Research paper sysadmin 17 April 2019

This paper highlights a number of options for managing electricity infrastructure in refugee camps and outlines the challenges, opportunities and operational implications associated with them. It takes the Kalobeyei settlement in Kenya as a case study.

• Building and maintaining electricity infrastructure to power offices, businesses, households and other operations in displacement settings is difficult. It is especially challenging for the Office of the United Nations High Commissioner for Refugees (UNHCR) and its partner agencies, because supplying electricity is not their core business.
• Private-sector companies exist that are willing and able to develop infrastructure management contracts to provide energy as a service in displacement settings. However, institutional barriers within humanitarian agencies persist, with short budgeting cycles in particular preventing humanitarian agencies from entering into the sorts of long-term service agreements required by the private sector.
• A number of options exist to leverage the expertise of the private sector through ‘public–private partnership’ (P3) structures. Such mechanisms can promote more efficient management of infrastructure by drawing on private-sector experience and expertise, incentivizing appropriate risk-sharing and providing options to leverage private capital in project development.
• Field work from the Kalobeyei settlement in Kenya suggests that a solar/diesel hybrid mini-grid solution was the most economical option to power camp services and infrastructure there. Compared to distributed diesel generation, the annual savings in operating costs were estimated at $49,880, with the additional investment paid back within 3.6 years.
• Humanitarian agencies need to be willing to change their policies to enable long-term service agreements. Alternatively (or, more likely, in conjunction with this option), financial mechanisms such as partial risk guarantees need to be developed to offset some of the risks. This change will need high-level support from donors and humanitarian agencies.
• Once the first infrastructure management contracts can be signed and tested in displacement locations (through the use of donor funding or otherwise) and associated data collected, it will ease the way for future investments in these types of projects.

There is nothing quite like the excitement of discovery in science—of finding something no one else knew and seeing a story unfold. One has to be part of an emerging picture to feel the elation. These moments in a lifetime are few and far between, but they fuel enthusiasm and keep one going. They are embedded in struggles and joys of everyday life, years of establishing what Louis Pasteur called “the prepared mind,” working with mentors, trainees, and colleagues, failures and successes. This article recalls 1) how I got to be a biochemist; 2) my contributions as an educator and researcher, especially regarding meprin metalloproteases; and 3) my participation in communities of science. Perhaps my reflections will help an aspiring scientist see how fulfilling a career in science can be.

March 14, 2024 — Keysight Technologies, Inc. and Q-CTRL are partnering to integrate key infrastructure quantum software to accelerate quantum processor development, characterization, and key proof of principle scientific demonstrations. An interesting […]

The post Keysight and Q-CTRL Team Up to Accelerate Infrastructure Quantum Software appeared first on HPCwire.

March 26, 2024 — Scientists at the Department of Energy’s Oak Ridge National Laboratory have determined how to avoid costly and potentially irreparable damage to large metallic parts fabricated through […]

The post ORNL Develops Solution to Residual Stress Challenges in 3D-Printed Metal Structures appeared first on HPCwire.

α-Neurexins are essential and highly expressed presynaptic cell-adhesion molecules that are frequently linked to neuropsychiatric and neurodevelopmental disorders. Despite their importance, how the elaborate extracellular sequences of α-neurexins contribute to synapse function is poorly understood. We recently characterized the presynaptic gain-of-function phenotype caused by a missense mutation in an evolutionarily conserved extracellular sequence of neurexin-3α (A687T) that we identified in a patient diagnosed with profound intellectual disability and epilepsy. The striking A687T gain-of-function mutation on neurexin-3α prompted us to systematically test using mutants whether the presynaptic gain-of-function phenotype is a consequence of the addition of side-chain bulk (i.e., A687V) or polar/hydrophilic properties (i.e., A687S). We used multidisciplinary approaches in mixed-sex primary hippocampal cultures to assess the impact of the neurexin-3α^A687 residue on synapse morphology, function and ligand binding. Unexpectedly, neither A687V nor A687S recapitulated the neurexin-3α A687T phenotype. Instead, distinct from A687T, molecular replacement with A687S significantly enhanced postsynaptic properties exclusively at excitatory synapses and selectively increased binding to neuroligin-1 and neuroligin-3 without changing binding to neuroligin-2 or LRRTM2. Importantly, we provide the first experimental evidence supporting the notion that the position A687 of neurexin-3α and the N-terminal sequences of neuroligins may contribute to the stability of α-neurexin–neuroligin-1 trans-synaptic interactions and that these interactions may specifically regulate the postsynaptic strength of excitatory synapses.

Rodent jaws evolved structurally to support dual functionality, for either biting or chewing food. Rodent hands also function dually during food handling, for actively manipulating or statically holding food. How are these oral and manual functions coordinated? We combined electrophysiological recording of muscle activity and kilohertz kinematic tracking to analyze masseter and hand actions as mice of both sexes handled food. Masseter activity was organized into two modes synchronized to hand movement modes. In holding/chewing mode, mastication occurred as rhythmic (~5 Hz) masseter activity while the hands held food below the mouth. In oromanual/ingestion mode, bites occurred as lower-amplitude aperiodic masseter events that were precisely timed to follow regrips (by ~200 ms). Thus, jaw and hand movements are flexibly coordinated during food handling: uncoupled in holding/chewing mode and tightly coordinated in oromanual/ingestion mode as regrip–bite sequences. Key features of this coordination were captured in a simple model of hierarchically orchestrated mode-switching and intramode action sequencing. We serendipitously detected an additional masseter-related action, tooth sharpening, identified as bouts of higher-frequency (~13 Hz) rhythmic masseter activity, which was accompanied by eye displacement, including rhythmic proptosis, attributable to masseter contractions. Collectively, the findings demonstrate how a natural, complex, and goal-oriented activity is organized as an assemblage of distinct modes and complex actions, adapted for the divisions of function arising from anatomical structure. These results reveal intricate, high-speed coordination of disparate effectors and show how natural forms of dexterity can serve as a model for understanding the behavioral neurobiology of multi-body-part coordination.

Archaeologists uncover an exciting find: a tomb that predates most of the others in the area by around 2,000 years. Inside, is a series of perfectly preserved inscriptions on a panel known as a "false door’."

David Baker, Demis Hassabis and John M. Jumper revealed how amino acids shape protein structure, a finding that could aid in drug discovery

The recent excavation beneath the Treasury has revealed 12 complete human skeletons and a trove of grave goods dating back 2,000 years

Infrastructure, materials, and mining group Raubex has reported a sharp climb in interim profit, helped by a pickup in SA road construction activity.

Patrick Walsh, an economist at the U.S. Environmental Protection Agency, will give the talk, “Distributional Impacts of Flood Adaptation and Infrastructure Funding in New Zealand,” at noon on Wednesday, Dec. 4, in 157 Hosler Building on Penn State's University Park campus. 

Plan will create new public-private entity and new economic development division at the Department of State WILMINGTON, Del. – Governor John Carney announced a plan on Wednesday to create a public-private partnership and strategically realign Delaware’s economic development efforts, with a new focus on promoting innovation, supporting Delaware’s entrepreneurs, and leveraging private sector resources to […]

Through a cooperative agreement with the U.S. Department of Agriculture’s (USDA) Agricultural Marketing Service (AMS), more than $1.7 million in competitive grant funding is available for projects designed to build resilience across the middle of Delaware’s food supply chain. The Delaware Department of Agriculture (DDA) announced they are accepting applications for the Resilient Food Systems Infrastructure Program (RFSI) through April 30, 2024.

The Delaware Department of Natural Resources and Environmental Control, in conjunction with the Division of Public Health, will begin soliciting for new water quality improvement projects March 24 as DNREC and DPH start to develop 2022 Clean Water State Revolving Fund (CWSRF) and Drinking Water State Revolving (DWSRF) project priority lists.

WILMINGTON, Del. – Delaware Governor John Carney, U.S. Senators Tom Carper and Chris Coons, and Congresswoman Lisa Blunt Rochester (all D-Del.) today announced that Delaware will receive $11,021,366 from the Centers for Disease Control and Prevention (CDC) to strengthen the First State’s public health workforce and infrastructure. Nationwide, the CDC is awarding $3.2 billion to […]

The Delaware Department of Natural Resources and Environmental Control (DNREC), in conjunction with the Delaware Division of Public Health (DPH), will begin soliciting for new water quality improvement projects Thursday, Jan. 12 as DNREC and DPH start to develop 2023 Clean Water State Revolving Fund (CWSRF) and Drinking Water State Revolving (DWSRF) project priority lists.

The State of Delaware took a significant step towards a cleaner transportation future today, celebrating its receipt of 14.3 million thanks to the U.S. Environmental Protection Agency’s (EPA) “Climate Pollution Reduction Grant” (CPRG) program. This grant, the result of the Federal Inflation Reduction Act and the Biden-Harris Administration’s Investing in America agenda, will be used to […]

DOVER, Del. – Governor Carney joined Lieutenant Governor Bethany Hall-Long, Department of Transportation Secretary Nicole Majeski, Department of Natural Resources and Environmental Control Secretary Shawn Garvin, elected officials and advocates on Friday afternoon to outline investments in the state’s electric vehicle infrastructure. With a combination of state and federal funding, charging stations for electric vehicles will be […]

Throughout its history, the United States has invested in infrastructure that leverages new technologies and helps society and its economy thrive. With the advent of trains in the early 1800s, four of the country’s five transcontinental railroads were built with assistance from the federal government. When cars replaced horses and [...]

The post Modern infrastructure must include analytics appeared first on Government Data Connection.

[The Conversation Africa] South Africa's finance minister, Enoch Godongwana, announced in his October mid-term budget policy statement that cabinet had approved funding for an early retirement programme to reduce the public sector wage bill. R11 billion (about US$627 million) will be allocated over the next two years to pay for the exit costs of 30,000 civil servants while retaining critical skills and promoting the entry of younger talent.

[Parliament of South Africa] Parliament, Tuesday, 12 November 2024 - The National Assembly (NA) will hold a plenary session scheduled to start at 10:00. Among the items on the agenda from 10:00 to 13:00 is the statement by the Minister of Water and Sanitation on water security in the country and a debate on 16 Days of Activism for no violence against women and children. The debate will be held under the theme, "Marking 30 years of democratic rights for women and fostering national unity to end gender-based violence".

There are opportunities for Australian companies to build sustainable resilient infrastructure in the Pacific and contribute to the region’s economic prosperity.

NVIDIA today announced that Japan cloud leaders SoftBank Corp., GMO Internet Group, Highreso, KDDI, Rutilea and SAKURA internet are building AI infrastructure with NVIDIA accelerated computing, networking and software to accelerate transformation across the nation’s robotics, automotive, healthcare and telecom industries.

The AIIB is a game changer for China in multilateral financial architecture. The Bank presents both a challenge and an opportunity for India.

Theoretical and empirical analyses of People's Republic of China's infrastructure and rural development.

South Asian private sector participation in infrastructure development is examined, and recommendations are made for future development.

The atoms within quasicrystals are arranged in repeating forms, but unlike ordinary crystals they have more complex symmetry. It turns out this makes them perfect for producing mazes

A stone wall nearly a kilometre long found under the Baltic Sea may have been built by ancient hunters to channel deer into a confined space

Title: Migraines Linked to Changes in Brain Structure
Category: Health News
Created: 8/28/2013 4:36:00 PM
Last Editorial Review: 8/29/2013 12:00:00 AM

The SARS-CoV-2 frameshifting element (FSE) has been intensely studied and explored as a therapeutic target for coronavirus diseases, including COVID-19. Besides the intriguing virology, this small RNA is known to adopt many length-dependent conformations, as verified by multiple experimental and computational approaches. However, the role these alternative conformations play in the frameshifting mechanism and how to quantify this structural abundance has been an ongoing challenge. Here, we show by DMS and dual-luciferase functional assays that previously predicted FSE mutants (using the RAG graph theory approach) suppress structural transitions and abolish frameshifting. Furthermore, correlated mutation analysis of DMS data by three programs (DREEM, DRACO, and DANCE-MaP) reveals important differences in their estimation of specific RNA conformations, suggesting caution in the interpretation of such complex conformational landscapes. Overall, the abolished frameshifting in three different mutants confirms that all alternative conformations play a role in the pathways of ribosomal transition.

PURPOSE

Meeting scholarly activity requirements continues to be a challenge in many family medicine (FM) residency programs. Studies comprehensively describing FM resident scholarship have been limited. We sought to identify institutional factors associated with increased scholarly output and meeting requirements of the Accreditation Council for Graduate Medical Education (ACGME).

A network of neurons in the brain seems to be larger in people with depression, which could change how we think about the condition's causes

In today’s rapidly evolving digital landscape, managing IP infrastructure has become increasingly complex and critical for organizations of all sizes. As networks

The post Don’t Ignore What You Can Easily Control: Your IP Infrastructure appeared first on Gigaom.

The Indian healthcare industry is looking to invest further in computational infrastructure as data integration frameworks and regulatory compliance are pivotal to ensure intelligent clinical support

May 23, 2024

Our data-centric way of seeing the world isn't serving us well. Barath Raghavan and Bruce Schneier argue that we need new socio-technical systems that leave room for the inherent messiness of reality.