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Articles by Peter Tompa
Toward a unified framework for determining conformational ensembles of disordered proteins - Nature Methods
Abstract Disordered proteins play essential roles in myriad cellular processes, yet their structural characterization remains a major challenge due to their dynamic and heterogeneous nature. Here we present a community-driven initiative to address this problem by advocating a unified framework for determining conformational ensembles of disordered proteins.
IAPN Asks Collectors to Help Protect Roman Coin Collecting
by Peter Tompa, IAPN Executive Director The US State Department has announced a proposed renewal of a cultural property Memorandum of Understanding (MOU) with the Republic of Italy. There is a danger that this will provide an excuse for US import restrictions implementing that MOU to be expanded to include late Roman Republican and Roman Imperial Coins.
Regularly updated benchmark sets for statistically correct evaluations of AlphaFold applications
Abstract AlphaFold2 changed structural biology by providing high-quality structure predictions for all possible proteins. Since its inception, a plethora of applications were built on AlphaFold2, expediting discoveries in virtually all areas related to protein science. In many cases, however, optimism seems to have made scientists forget about data leakage, a serious issue that needs to be addressed when evaluating machine learning methods.
Importance of updated benchmark sets for statistically correct AlphaFold applications
Abstract AlphaFold2 changed structural biology by providing high-quality structure prediction for all possible proteins. Since that a plethora of applications were built on AlphaFold2, expediting discoveries on virtually all fields related to protein science. In many cases it seems like optimism made scientists forget about data leakage, a serious issue that needs to be addressed when evaluating machine learning methods.
Recurrent evolution of adhesive defence systems in amphibians by parallel shifts in gene expression - Nature Communications
Abstract Natural selection can drive organisms to strikingly similar adaptive solutions, but the underlying molecular mechanisms often remain unknown. Several amphibians have independently evolved highly adhesive skin secretions (glues) that support a highly effective antipredator defence mechanism. Here we demonstrate that the glue of the Madagascan tomato frog, Dyscophus guineti, relies on two interacting proteins: a highly derived member of a widespread glycoprotein family and a galectin.
Phase-separating fusion proteins drive cancer by dysregulating transcription through ectopic condensates
Abstract Numerous cellular processes rely on biomolecular condensates formed through liquid-liquid phase separation (LLPS), thus, perturbations of LLPS underlie various diseases. We found that proteins initiating LLPS are frequently implicated in somatic cancers, even surpassing their involvement in neurodegeneration, where several such LLPS scaffolds are linked to disease emergence.
Menin regulates androgen receptor- and MLL-driven condensation, upsetting regulation of cellular AR-driven transcription.
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Customs Repatriation to Greece Raises Questions
While Customs officials claim the coins were “stolen” from Greece in a video of the event, other statements pointing to a “lack of documentation” instead suggest that the coins were seized from American citizens based on import restrictions that implement a Memorandum of Understanding (MOU) with Greece.
Minimum information guidelines for experiments structurally characterizing intrinsically disordered protein regions - Nature Methods
Abstract An unambiguous description of an experiment, and the subsequent biological observation, is vital for accurate data interpretation. Minimum information guidelines define the fundamental complement of data that can support an unambiguous conclusion based on experimental observations.
Quantification of Surface Tension Effects and Nucleation‐and‐Growth Rates during Self‐Assembly of Biological Condensates
Model Validation The general nucleation-and-growth model and its validity were tested using kinetic data of LLPS (Figure 4) and amyloid aggregation (Figure , Supporting Information), by rationalizing the formation of phase-separated condensates with large and uniform sizes under conditions where active biological processes were not present (Figure and Movies and , Supporting Information), and by comparing the predicted time evolution of droplet sizes with the measured one (Figure 5c,d).
A Lawyer’s Assessment of the Return of the Brutus Aureus
[bsa_pro_ad_space id=4] On the face of it, the Manhattan District Attorney’s Antiquities Trafficking Unit performed a service for the legitimate numismatic trade and collectors when it arrested Richard Beale, the principal at Roma Numismatics, last January for unlawfully purchasing valuable coins from Italy, Greece, and Gaza in violation of local national patrimony laws and creating false provenances to hide their illicit origins.
Under the Biden administration, can US cultural policy better reflect American values?
The seal of the US State Department AP Photo/Alex Brandon There is an opportunity for America’s cultural policy to be retooled. US President Joseph Biden has nominated Lee Satterfield, a career diplomat, to fill the role of assistant secretary for the State Department’s Bureau of Educational and Cultural Affairs. If confirmed, she will become the official who decides on memoranda of understanding (MOUs), the agreements with foreign countries that authorise US import restrictions on cultural goods.
Collecting Ancient Coins: Time to Consider a New Paradigm That Facilitates Lawful Trade
By Peter K. Tompa – Cultural Property Observer….. The following is a statement delivered at the Wednesday, July 22 meeting of the Cultural Property Advisory Committee (CPAC) by lawyer and numismatic advocate Peter K. Tompa concerning proposed updates to the 2021 renewal of the Memorandum of Understanding (MOU) with Italy. These updates threaten American collectors’ ability to collect ancient Roman coins. Tompa’s statement was originally published on his blog Cultural Property Observer.
The Trump administration’s tariffs will not hurt China but they will hurt the US art trade
President Trump talks trade with the vice premier of the People’s Republic of China, Liu He, in 2018. In a recent escalation of the US-China trade war, art and antiquities could once again be subject to tariffs, this time at a rate of 25%.
Affinity purification of human m-calpain through an intrinsically disordered inhibitor, calpastatin
Calpains are calcium-activated proteases that have biomedical and biotechnological potential. Their activity is tightly regulated by their endogenous inhibitor, calpastatin that binds to the enzyme only in the presence of calcium. Conventional approaches to purify calpain comprise multiple chromatographic steps, and are labor-intensive, leading to low yields.
A Novel Method for Assessing the Chaperone Activity of Proteins
Protein chaperones are molecular machines which function both during homeostasis and stress conditions in all living organisms. Depending on their specific function, molecular chaperones are involved in a plethora of cellular processes by playing key roles in nascent protein chain folding, transport and quality control. Among stress protein families–molecules expressed during adverse conditions, infection, and diseases–chaperones are highly abundant.
Design Principles Involving Protein Disorder Facilitate Specific Substrate Selection and Degradation by the Ubiquitin-Proteasome System
The ubiquitin-proteasome system (UPS) regulates diverse cellular pathways by the timely removal (or processing) of proteins. Here we review the role of structural disorder and conformational flexibility in the different aspects of degradation. First, we discuss post-translational modifications within disordered regions that regulate E3 ligase localization, conformation, and enzymatic activity, and also the role of flexible linkers in mediating ubiquitin transfer and reaction processivity.
The principle of conformational signaling
Signal transduction is the primary process by which cells respond to changes in their physical and chemical environments. Cellular response is initiated through a signaling protein (a receptor), which interacts with the “signal”, most often a novel molecule outside or inside the cell.
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