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Abstract Multiple electrolyte disorders, including sodium, potassium and calcium disorders, have been associated with hypertension in pregnancy. Most of these studies failed to evaluate the combined effect of low and high sodium, potassium, calcium and chloride ion concentrations on hypertension in pregnancy. This study evaluates the combined effect of these ion categories (low, normal, high) on hypertension in pregnancy. Biochemical ion assays and blood pressure measurements were carried out on 1074 apparently healthy pregnant women in late third trimester. Serum potassium, sodium, chloride, and ionised calcium were measured by ion-selective electrode potentiometry, while total plasma calcium was measured by absorption spectrophotometry. Hypertension in pregnancy was defined as systolic blood pressure ≥ 140 mmHg and/or diastolic blood pressure ≥ 90 mmHg. The prevalence of hyponatraemia, hypokalaemia, hypochloraemia, ionised hypocalcaemia and total hypocalcaemia in late pregnancy was 1.30 [0.78–2.18]%, 3.55 [2.60–4.84]%, 1.96 [1.28–2.97]%, 1.49 [0.92–2.21]% and 43.58 [40.64–46.56]%, respectively. Hypernatraemia, hyperkalaemia, hyperchloraemia, ionised hypercalcaemia and total hypercalcaemia were found in 1.49 [0.92–2.41]%, 2.34 [1.59–3.43]%, 4.38 [3.31–5.77]%, 39.94 [37.06–42.90]%, 2.79 [1.96–3.96]% of the participants, respectively. The prevalence of hypertension in pregnancy was 7.17 [5.77–8.87]%. When ion categories were considered in multiple logistic regression, only ionised and total calcium had significant associations with hypertension in pregnancy. Women with ionised hypercalcaemia had lower odds of hypertension in pregnancy (AOR = 0.50 [0.29–0.87], p-value = 0.015), and women with total hypocalcaemia had higher odds of hypertension in pregnancy (AOR = 1.99 [1.21–3.29], p-value = 0.007), compared to women with ionised and total normocalcaemia, respectively. Increasing kalaemia was associated significantly with higher odds of hypertension in pregnancy; however, kalaemia below and above the normal concentrations had no significant association with hypertension. Nonetheless, participants with kalaemia ≤ 3.98 mmol/L, had lower odds of hypertension in pregnancy compared with those with higher kalaemia (OR = 0.40 [0.24–0.66], p-value = 0.0003). Calcium disorders remain the most frequent electrolyte disorders in pregnancy. When normal cut-offs are considered for calcium and other ions, only ionised and total calcium influence the occurrence of hypertension in pregnancy. Kalaemia seems to affect hypertension in pregnancy but primarily within its normal concentrations. Serum electrolyte follow-up is indispensable for a proper pregnancy follow-up.

With the advance of experimental procedures obtaining chemical crosslinking information is becoming a fast and routine practice. Information on crosslinks can greatly enhance the accuracy of protein structure modeling. Here, we review the current state of the art in modeling protein structures with the assistance of experimentally determined chemical crosslinks within the framework of the 13th meeting of Critical Assessment of Structure Prediction approaches. This largest-to-date blind assessment reveals benefits of using data assistance in difficult to model protein structure prediction cases. However, in a broader context, it also suggests that with the unprecedented advance in accuracy to predict contacts in recent years, experimental crosslinks will be useful only if their specificity and accuracy further improved and they are better integrated into computational workflows.

Every two years groups worldwide participate in the Critical Assessment of Protein Structure Prediction (CASP) experiment to blindly test the strengths and weaknesses of their computational methods. CASP has significantly advanced the field but many hurdles still remain, which may require new ideas and collaborations. In 2012 a web-based effort called WeFold, was initiated to promote collaboration within the CASP community and attract researchers from other fields to contribute new ideas to CASP. Members of the WeFold coopetition (cooperation and competition) participated in CASP as individual teams, but also shared components of their methods to create hybrid pipelines and actively contributed to this effort. We assert that the scale and diversity of integrative prediction pipelines could not have been achieved by any individual lab or even by any collaboration among a few partners. The models contributed by the participating groups and generated by the pipelines are publicly available at the WeFold website providing a wealth of data that remains to be tapped. Here, we analyze the results of the 2014 and 2016 pipelines showing improvements according to the CASP assessment as well as areas that require further adjustments and research.

In this paper we report the improvements and extensions of the UNRES server (https://unres-server.chem.ug.edu.pl) for physics-based simulations with the coarse-grained UNRES model of polypeptide chains. The improvements include the replacement of the old code with the recently optimized one and adding the recent scale-consistent variant of the UNRES force field, which performs better in the modeling of proteins with the β and the α+β structures. The scope of applications of the package was extended to data-assisted simulations with restraints from nuclear magnetic resonance (NMR) and chemical crosslink mass-spectroscopy (XL-MS) measurements. NMR restraints can be input in the NMR Exchange Format (NEF), which has become a standard. Ambiguous NMR restraints are handled without expert intervention owing to a specially designed penalty function. The server can be used to run smaller jobs directly or to prepare input data to run larger production jobs by using standalone installations of UNRES.

Molecular motors are essential for the movement and transportation of macromolecules in living organisms. Among them, rotatory motors are particularly efficient. In this study, we investigated the long-term dynamics of the designed left-handed alpha/alpha toroid (PDB: 4YY2), the RBM2 flagellum protein ring from Salmonella (PDB: 6SD5), and the V-type Na+-ATPase rotor in Enterococcus hirae (PDB: 2BL2) using microcanonical and canonical molecular dynamics simulations with the coarse-grained UNRES force field, including a lipid-membrane model, on a millisecond laboratory time scale. Our results demonstrate that rotational motion can occur with zero total angular momentum in the microcanonical regime and that thermal motions can be converted into net rotation in the canonical regime, as previously observed in simulations of smaller cyclic molecules. For 6SD5 and 2BL2, net rotation (with a ratcheting pattern) occurring only about the pivot of the respective system was observed in canonical simulations. The extent and direction of the rotation depended on the initial conditions. This result suggests that rotatory molecular motors can convert thermal oscillations into net rotational motion. The energy from ATP hydrolysis is required probably to set the direction and extent of rotation. Our findings highlight the importance of molecular-motor structures in facilitating movement and transportation within living organisms.

Introduction: The protein folding process is very sensitive to environmental conditions. Many possibilities in the form of numerous pathways for this process can--if an incorrect one is chosen--lead to the creation of forms described as misfolded. The aqueous environment is the natural one for the protein folding process. Nonetheless, other factors such as the cell membrane and the presence of specific molecules (chaperones) affect this process, ensuring the correct expected structural form to guarantee biological activity. All these factors can be considered components of the external force field for this process. Methods: The fuzzy oil drop-modified (FOD-M) model makes possible the quantitative evaluation of the modification of the external field, treating the aqueous environment as a reference. The FOD-M model (tested on membrane proteins) includes the component modifying the water environment, allowing the assessment of the external force field generated by prefoldin. Results: In this work, prefoldin was treated as the provider of a specific external force field for actin and tubulin. The discussed model can be applied to any folding process simulation, taking into account the changed external conditions. Hence, it can help simulate the in silico protein folding process under defined external conditions determined by the respective external force field. In this work, the structures of prefoldin and protein folded with the participation of prefoldin were analyzed. Discussion: Thus, the role of prefoldin can be treated as a provider of an external field comparable to other environmental factors affecting the protein folding process. [ABSTRACT FROM AUTHOR]

Syndecans are membrane proteoglycans regulating extracellular matrix assembly, cell adhesion and signaling. Their ectodomains can be shed from the cell surface, and act as paracrine and autocrine effectors or as competitors of full-length syndecans. We report the first biophysical characterization of the recombinant ectodomains of the four human syndecans using biophysical techniques, and show that they behave like flexible random-coil intrinsically disordered proteins, and adopt several conformation ensembles in solution. We have characterized their conformational landscapes using native mass spectrometry (MS) and ion-mobility MS, and demonstrated that the syndecan ectodomains explore the majority of their conformational landscape, from minor compact, globular-like, conformations to extended ones. We also report that the ectodomain of syndecan-4, corresponding to a natural isoform, is able to dimerize via a disulfide bond. We have generated a three-dimensional model of the C-terminus of this dimer, which supports the dimerization via a disulfide bond. Furthermore, we have mapped the NXIP adhesion motif of syndecans and their sequences involved in the formation of ternary complexes with integrins and growth factor receptors on the major conformations of their ectodomains, and shown that these sequences are not accessible in all the conformations, suggesting that only some of them are biologically active. Lastly, although the syndecan ectodomains have a far lower number of amino acid residues than their membrane partners, their intrinsic disorder and flexibility allow them to adopt extended conformations, which have roughly the same size as the cell surface receptors (e.g., integrins and growth factor receptors) they bind to.

Many proteins can fold into well-defined conformations. However, intrinsically-disordered proteins (IDPs) do not possess a defined structure. Moreover, folded multi-domain proteins often digress into alternative conformations. Collectively, the conformational dynamics enables these proteins to fulfill specific functions. Thus, most experimental observables are averaged over the conformations that constitute an ensemble. In this article, we review the recent developments in the concept and methods for the determination of the dynamic structures of flexible peptides and proteins. In particular, we describe ways to extract information from nuclear magnetic resonance small-angle X-ray scattering (SAXS), and chemical cross-linking coupled with mass spectroscopy (XL-MS) measurements. All these techniques can be used to obtain ensemble-averaged restraints or to re-weight the simulated conformational ensembles.

The UNited RESidue (UNRES) model of polypeptide chains was applied to study the association of 20 peptides with sizes ranging from 6 to 32 amino-acid residues. Twelve of those were potentially aggregating hexa- or heptapeptides excised from larger proteins, while the remaining eight contained potentially aggregating sequences, functionalized by attaching larger ends rich in charged residues. For 13 peptides, the experimental data of aggregation were used. The remaining seven were synthesized, and their properties were measured in this work. Multiplexed replica-exchange simulations of eight-chain systems were conducted at 12 temperatures from 260 to 370 K at concentrations from 0.421 to 5.78 mM, corresponding to the experimental conditions. The temperature profiles of the fractions of monomers and octamers showed a clear transition corresponding to aggregate dissociation. Low simulated transition temperatures were obtained for the peptides, which did not precipitate after incubation, as well as for the H-GNNQQNY-NH2 prion–protein fragment, which forms small fibrils. A substantial amount of inter-strand β-sheets was found in most of the systems. The results suggest that UNRES simulations can be used to assess peptide aggregation except for glutamine- and asparagine-rich peptides, for which a revision of the UNRES sidechain–sidechain interaction potentials appears necessary.

The SARS-CoV-2 virus, commonly known as COVID-19, first occurred in December 2019 in Wuhan, Hubei Province, China. Since then, it has become a tremendous threat to human health. With a pandemic threat, it is in the significant interest of the scientific world to establish its method of infection. In this manuscript, we combine knowledge of the infection mechanism with theoretical methods to answer the question of the virus’s selectivity. We proposed a two-stage infection mechanism. In the first step, the virus interacts with the ACE2 receptor, with the “proper strength”. When the interaction is too strong, the virus will remain in an “improper position”; if the interaction is too weak, the virus will “run away” from the cell. We also indicated three residues (positions 30, 31, and 353) located on the ACE2 protein-binding interface, which seems to be crucial for successful infection. Our results indicate that these residues are necessary for the initiation of the infection process.

ObjectiveAcute kidney injury (AKI) is a common complication of complex aortic surgery with high mortality, morbidity and health care expense. The current definition of AKI does not allow for structural characterization of the kidneys and utilizes functional indices with substantial limitations leading to delayed diagnosis and ineffective interventions. The aim of this study is to develop a method of early detection of structural renal abnormalities that can precede and predict the occurrence of AKI in this population. We propose a novel combined index of ultrasonography (shear wave elastography), biomarkers of renal stress (urinary insulin growth factor binding protein-7, IGFBP-7 and inhibitor of tissue metalloproteinase-2, TIMP-2) and renal injury markers (urinary neutrophil gelatinase-associated lipocalin -NGAL)- the bio-sonographic index (BSI).MethodsA prospective observational study at a tertiary referral center will be performed enrolling 80 patients undergoing elective open and endovascular repair of the visceral aorta. The BSI will be evaluated at baseline, and at 6 and 24 hours after the procedure. The primary outcome is the occurrence of AKI according to the Kidney Disease Improving Global Outcomes (KDIGO) criteria. Each patient will be his/her own control. A reference group of 15 healthy volunteers who are not undergoing interventions will be enrolled to test the feasibility of and to refine the novel SWE protocol. The BSI will be tested for its predictability of the occurrence of AKI. Comparisons will be made between individual and combined components of the BSI and traditional markers used in the KDIGO definition; serum creatinine and urine output in terms of baseline status of the kidney. Correlations will be made between the BSI and conventional indices of AKI and exploratory analyses will be conducted to identify individual disease patterns using the BSI.DiscussionWe hypothesize that the BSI will be a sensitive index of early structural abnormalities that precede and predict the occurrence of AKI as defined by KDIGO in complex vascular surgery.Trial registrationClinicalTrials.gov NCT04144894. Registered 1/6/2020.