Challenges in describing the conformation and dynamics of proteins with ambiguous behavior.

Traditionally, our understanding of how proteins operate and how evolution shapes them is based on two main data sources: the overall protein fold and the protein amino acid sequence. However, a significant part of the proteome shows highly dynamic and/or structurally ambiguous behavior, which cannot be correctly represented by the traditional fixed set of static coordinates. Representing such protein behaviors remains challenging and necessarily involves a complex interpretation of conformational states, including probabilistic descriptions. Relating protein dynamics and multiple conformations to their function as well as their physiological context (e.g., post-translational modifications and subcellular localization), therefore, remains elusive for much of the proteome, with studies to investigate the effect of protein dynamics relying heavily on computational models. We here investigate the possibility of delineating three classes of protein conformational behavior: order, disorder, and ambiguity. These definitions are explored based on three different datasets, using interpretable machine learning from a set of features, from AlphaFold2 to sequence-based predictions, to understand the overlap and differences between these datasets. This forms the basis for a discussion on the current limitations in describing the behavior of dynamic and ambiguous proteins.

b2bTools: online predictions for protein biophysical features and their conservation.

We provide integrated protein sequence-based predictions via https://bio2byte.be/b2btools/. The aim of our predictions is to identify the biophysical behaviour or features of proteins that are not readily captured by structural biology and/or molecular dynamics approaches. Upload of a FASTA file or text input of a sequence provides integrated predictions from DynaMine backbone and side-chain dynamics, conformational propensities, and derived EFoldMine early folding, DisoMine disorder, and Agmata ß-sheet aggregation. These predictions, several of which were previously not available online, capture 'emergent' properties of proteins, i.e. the inherent biophysical propensities encoded in their sequence, rather than context-dependent behaviour (e.g. final folded state). In addition, upload of a multiple sequence alignment (MSA) in a variety of formats enables exploration of the biophysical variation observed in homologous proteins. The associated plots indicate the biophysical limits of functionally relevant protein behaviour, with unusual residues flagged by a Gaussian mixture model analysis. The prediction results are available as JSON or CSV files and directly accessible via an API. Online visualisation is available as interactive plots, with brief explanations and tutorial pages included. The server and API employ an email-free token-based system that can be used to anonymously access previously generated results.

Portal hypertension caused by acute cytomegalovirus infection with liver involvement in an immunocompetent patient.

Primary infection by cytomegalovirus in immunocompetent patients is usually unapparent. We report a case of severe acute cytomegalovirus infection in a young immunocompetent male with pulmonary and hepatic involvement and portal hypertension who recovered without specific antiviral therapy with complete resolution of sonographic signs of portal hypertension after 6 months.

Severe case of Mediterranean spotted fever in Greece with predominantly neurological features.

Rickettsia conorii is endemic in Greece, though only a few cases of infection have been published to date. The case of a 58-year-old man from northern Greece with a severe form of Mediterranean spotted fever and rapid neurological deterioration is presented here. The patient received antibiotic treatment with doxycycline, showing immediate clinical and laboratory improvement. Diagnosis was confirmed later, during the second week after disease onset, by detection of elevated titres of IgM and IgG antibodies against R. conorii using an indirect immunofluorescence assay.