Enzymatic turnover of macromolecules generates long-lasting protein-water-coupled motions beyond reaction steady state.

The main focus of enzymology is on the enzyme rates, substrate structures, and reactivity, whereas the role of solvent dynamics in mediating the biological reaction is often left aside owing to its complex molecular behavior. We used integrated X-ray- and terahertz- based time-resolved spectroscopic tools to study protein-water dynamics during proteolysis of collagen-like substrates by a matrix metalloproteinase. We show equilibration of structural kinetic transitions in the millisecond timescale during degradation of the two model substrates collagen and gelatin, which have different supersecondary structure and flexibility. Unexpectedly, the detected changes in collective enzyme-substrate-water-coupled motions persisted well beyond steady state for both substrates while displaying substrate-specific behaviors. Molecular dynamics simulations further showed that a hydration funnel (i.e., a gradient in retardation of hydrogen bond (HB) dynamics toward the active site) is substrate-dependent, exhibiting a steeper gradient for the more complex enzyme-collagen system. The long-lasting changes in protein-water dynamics reflect a collection of local energetic equilibrium states specifically formed during substrate conversion. Thus, the observed long-lasting water dynamics contribute to the net enzyme reactivity, impacting substrate binding, positional catalysis, and product release.

Water Dynamics from THz Spectroscopy Reveal the Locus of a Liquid-Liquid Binodal Limit in Aqueous CaCO3 Solutions.

Many phenomena depend on CaCO3 nucleation where the role of water remains enigmatic. Changes in THz absorption during the early stages of CaCO3 nucleation evidence altered coupled motions of hydrated calcium and carbonate ions. The direct link between these changes and the continuous development of the ion activity product reveals the locus of a liquid-liquid binodal limit. The data strongly suggest that proto-structured amorphous CaCO3 forms through solidification of initially liquid precursors. Furthermore, polycarboxylates, which stabilize liquid precursors of CaCO3 , significantly enhance the kinetic stability of the metastable liquid-liquid state, but they do not affect the locus of the binodal limit. The importance of water network dynamics in phase separation mechanisms can be understood based on the notions of the pre-nucleation cluster pathway, and is likely to be more general for aqueous systems.

Circular trimers of gelatinase B/matrix metalloproteinase-9 constitute a distinct population of functional enzyme molecules differentially regulated by tissue inhibitor of metalloproteinases-1.

Gelatinase B/matrix metalloproteinase-9 (MMP-9) (EC 3.4.24.35) cleaves many substrates and is produced by most cell types as a zymogen, proMMP-9, in complex with the tissue inhibitor of metalloproteinases-1 (TIMP-1). Natural proMMP-9 occurs as monomers, homomultimers and heterocomplexes, but our knowledge about the overall structure of proMMP-9 monomers and multimers is limited. We investigated biochemical, biophysical and functional characteristics of zymogen and activated forms of MMP-9 monomers and multimers. In contrast with a conventional notion of a dimeric nature of MMP-9 homomultimers, we demonstrate that these are reduction-sensitive trimers. Based on the information from electrophoresis, AFM and TEM, we generated a 3D structure model of the proMMP-9 trimer. Remarkably, the proMMP-9 trimers possessed a 50-fold higher affinity for TIMP-1 than the monomers. In vivo, this finding was reflected in a higher extent of TIMP-1 inhibition of angiogenesis induced by trimers compared with monomers. Our results show that proMMP-9 trimers constitute a novel structural and functional entity that is differentially regulated by TIMP-1.

Protein stabilization by macromolecular crowding through enthalpy rather than entropy.

The interior of the cell is a densely crowded environment in which protein stability is affected differently than in dilute solution. Macromolecular crowding is commonly understood in terms of an entropic volume exclusion effect based on hardcore repulsions among the macromolecules. We studied the thermal unfolding of ubiquitin in the presence of different cosolutes (glucose, dextran, poly(ethylene glycol), KCl, urea). Our results show that for a correct dissection of the cosolute-induced changes of the free energy into its enthalpic and entropic contributions, the temperature dependence of the heat capacity change needs to be explicitly taken into account. In contrast to the prediction by the excluded volume theory, we observed an enthalpic stabilization and an entropic destabilization for glucose, dextran, and poly(ethylene glycol). The enthalpic stabilization mechanism induced by the macromolecular crowder dextran was similar to the enthalpic stabilization mechanism of its monomeric building block glucose. In the case of poly(ethylene glycol), entropy is dominating over enthalpy leading to an overall destabilization. We propose a new model to classify cosolute effects in terms of their enthalpic contributions to protein stability.

Zn2+-Aß40 complexes form metastable quasi-spherical oligomers that are cytotoxic to cultured hippocampal neurons.

The roles of metal ions in promoting amyloid ß-protein (Aß) oligomerization associated with Alzheimer disease are increasingly recognized. However, the detailed structures dictating toxicity remain elusive for Aß oligomers stabilized by metal ions. Here, we show that small Zn(2+)-bound Aß1-40 (Zn(2+)-Aß40) oligomers formed in cell culture medium exhibit quasi-spherical structures similar to native amylospheroids isolated recently from Alzheimer disease patients. These quasi-spherical Zn(2+)-Aß40 oligomers irreversibly inhibit spontaneous neuronal activity and cause massive cell death in primary hippocampal neurons. Spectroscopic and x-ray diffraction structural analyses indicate that despite their non-fibrillar morphology, the metastable Zn(2+)-Aß40 oligomers are rich in ß-sheet and cross-ß structures. Thus, Zn(2+) promotes Aß40 neurotoxicity by structural organization mechanisms mediated by coordination chemistry.

Mild Cardiotoxicity and Continued Trastuzumab Treatment in the Context of HER2-Positive Breast Cancer.

Breast cancer is the leading cause of cancer death in women worldwide. Trastuzumab, the main HER2-targeted treatment, faces limitations due to potential cardiotoxicity. The management of patients with mild cardiotoxicity on trastuzumab remains uncertain, resulting in treatment discontinuation and negative oncological outcomes. This retrospective study analyzed 23 patients who experienced decreased left ventricular function during trastuzumab treatment. During the 18-month follow-up period, two patients (9%) had severe declines in function, leading to treatment cessation, and one patient (4%) developed heart failure symptoms. However, 21 patients showed mild, reversible myocardial dysfunction without significant differences in final ventricular function compared to a control group (58.4% vs. 61.7%, respectively; p = 0.059). The declines in function were most pronounced at nine months but improved at twelve and eighteen months. Various echocardiographic parameters changed significantly over time. As predictors of severe cardiotoxicity, we identified the following: LVEF before initial chemotherapy (p = 0.022), as well as baseline LVEF before treatment with trastuzumab (p = 0.007); initial left ventricular end systolic volume (p = 0.027); and the initial global longitudinal strain (p = 0.021) and initial velocity time integral in the left ventricular outflow track (p = 0.027). In conclusion, the continuation of trastuzumab should be considered for most patients with mild cardiotoxicity, with close cardiac monitoring and cardioprotective measures. However, identifying the patients at risk of developing severe cardiotoxicity is necessary. According to our data, the initial LVEF and GLS levels appear to be reliable predictors.

The lockdown effect: A counterfactual for Sweden.

While most countries imposed a lockdown in response to the first wave of COVID-19 infections, Sweden did not. To quantify the lockdown effect, we approximate a counterfactual lockdown scenario for Sweden through the outcome in a synthetic control unit. We find, first, that a 9-week lockdown in the first half of 2020 would have reduced infections and deaths by about 75% and 38%, respectively. Second, the lockdown effect starts to materialize with a delay of 3-4 weeks only. Third, the actual adjustment of mobility patterns in Sweden suggests there has been substantial voluntary social restraint, although the adjustment was less strong than under the lockdown scenario. Lastly, we find that a lockdown would not have caused much additional output loss.

Antifreeze glycoprotein activity correlates with long-range protein-water dynamics.

Antifreeze proteins (AFPs) and antifreeze glycoproteins (AFGPs) enable the survival of organisms living in subfreezing habitats and serve as preservatives. Although their function is known, the underlying molecular mechanism was not understood. Mutagenesis experiments questioned the previous assumption of hydrogen bonding as the dominant mechanism. We use terahertz spectroscopy to show that antifreeze activity is directly correlated with long-range collective hydration dynamics. Our results provide evidence for a new model of how AFGPs prevent water from freezing. We suggest that antifreeze activity may be induced because the AFGP perturbs the aqueous solvent over long distances. Retarded water dynamics in the large hydration shell does not favor freezing. The complexation of the carbohydrate cis-hydroxyl groups by borate suppresses the long-range hydration shell detected by terahertz absorption. The hydration dynamics shift toward bulk water behavior strongly reduces the AFGP antifreeze activity, further supporting our model.

Solvation dynamics of model peptides probed by terahertz spectroscopy. Observation of the onset of collective network motions.

We have studied the solvation of model peptides at low hydration levels by terahertz absorption spectroscopy. We have recorded the concentration-dependent terahertz absorption coefficients of N-acetyl-glycine-amide (NAGA), N-acetyl-glycine-methylamide (NAGMA), N-acetyl-leucine-amide (NALA), N-acetyl-leucine-methylamide (NALMA), and N-acetyl-tryptophan-amide (NATA) in aqueous solution. We find a dramatic decrease in the THz absorption, if the number of water molecules per solute is less than 18-20. This change is taken as a signature for the breakdown of peptide-water network motions, which supports the hypothesis that a minimum number of hydration waters is required to activate these motions. This is well below a monolayer coverage of the model peptides. It is interesting to note that the required hydration level corresponds to the number of water molecules which are required for biological functionality.

Rattling in the cage: ions as probes of sub-picosecond water network dynamics.

We present terahertz (THz) measurements of salt solutions that shed new light on the controversy over whether salts act as kosmotropes (structure makers) or chaotropes (structure breakers), which enhance or reduce the solvent order, respectively. We have carried out precise measurements of the concentration-dependent THz absorption coefficient of 15 solvated alkali halide salts around 85 cm(-1) (2.5 THz). In addition, we recorded overview spectra between 30 and 300 cm(-1) using a THz Fourier transform spectrometer for six alkali halides. For all solutions we found a linear increase of THz absorption compared to pure water (THz excess) with increasing solute concentration. These results suggest that the ions may be treated as simple defects in an H-bond network. They therefore cannot be characterized as either kosmotropes or chaotropes. Below 200 cm(-1), the observed THz excess of all salts can be described by a linear superposition of the water absorption and an additional absorption that is attributed to a rattling motion of the ions within the water network. By providing a comprehensive set of data for different salt solutions, we find that the solutions can all be very well described by a model that includes damped harmonic oscillations of the anions and cations within the water network. We find this model predicts the main features of THz spectra for a variety of salt solutions. The assumption of the existence of these ion rattling motions on sub-picosecond time scales is supported by THz Fourier transform spectroscopy of six alkali halides. Above 200 cm(-1) the excess is interpreted in terms of a change in the wing of the water network librational mode. Accompanying molecular dynamics simulations using the TIP3P water model support our conclusion and show that the fast sub-picosecond motions of the ions and their surroundings are almost decoupled. These findings provide a complete description of the solute-induced changes in the THz solvation dynamics for the investigated salts. Our results show that THz spectroscopy is a powerful experimental tool to establish a new view on the contributions of anions and cations to the structuring of water.

Hyaluronan Nanoparticles Selectively Target Plaque-Associated Macrophages and Improve Plaque Stability in Atherosclerosis.

Hyaluronan is a biologically active polymer, which can be formulated into nanoparticles. In our study, we aimed to probe atherosclerosis-associated inflammation by using hyaluronan nanoparticles and to determine whether they can ameliorate atherosclerosis. Hyaluronan nanoparticles (HA-NPs) were prepared by reacting amine-functionalized oligomeric hyaluronan (HA) with cholanic ester and labeled with a fluorescent or radioactive label. HA-NPs were characterized in vitro by several advanced microscopy methods. The targeting properties and biodistribution of HA-NPs were studied in apoe-/- mice, which received either fluorescent or radiolabeled HA-NPs and were examined ex vivo by flow cytometry or nuclear techniques. Furthermore, three atherosclerotic rabbits received 89Zr-HA-NPs and were imaged by PET/MRI. The therapeutic effects of HA-NPs were studied in apoe-/- mice, which received weekly doses of 50 mg/kg HA-NPs during a 12-week high-fat diet feeding period. Hydrated HA-NPs were ca. 90 nm in diameter and displayed very stable morphology under hydrolysis conditions. Flow cytometry revealed a 6- to 40-fold higher uptake of Cy7-HA-NPs by aortic macrophages compared to normal tissue macrophages. Interestingly, both local and systemic HA-NP-immune cell interactions significantly decreased over the disease progression. 89Zr-HA-NPs-induced radioactivity in atherosclerotic aortas was 30% higher than in wild-type controls. PET imaging of rabbits revealed 6-fold higher standardized uptake values compared to the muscle. The plaques of HA-NP-treated mice contained 30% fewer macrophages compared to control and free HA-treated group. In conclusion, we show favorable targeting properties of HA-NPs, which can be exploited for PET imaging of atherosclerosis-associated inflammation. Furthermore, we demonstrate the anti-inflammatory effects of HA-NPs in atherosclerosis.

Correlated structural kinetics and retarded solvent dynamics at the metalloprotease active site.

Solvent dynamics can play a major role in enzyme activity, but obtaining an accurate, quantitative picture of solvent activity during catalysis is quite challenging. Here, we combine terahertz spectroscopy and X-ray absorption analyses to measure changes in the coupled water-protein motions during peptide hydrolysis by a zinc-dependent human metalloprotease. These changes were tightly correlated with rearrangements at the active site during the formation of productive enzyme-substrate intermediates and were different from those in an enzyme-inhibitor complex. Molecular dynamics simulations showed a steep gradient of fast-to-slow coupled protein-water motions around the protein, active site and substrate. Our results show that water retardation occurs before formation of the functional Michaelis complex. We propose that the observed gradient of coupled protein-water motions may assist enzyme-substrate interactions through water-polarizing mechanisms that are remotely mediated by the catalytic metal ion and the enzyme active site.

The terahertz dance of water with the proteins: the effect of protein flexibility on the dynamical hydration shell of ubiquitin.

The role of water in the functioning of proteins has been a hot topic over the years. We use terahertz (THz) spectroscopy as an experimental tool to probe the protein-induced fast solvation dynamics of ubiquitin. In order to investigate the effect of protein flexibility on the changes in the solvation dynamics, we have measured the concentration-dependent THz absorption of several site-specific ubiquitin mutants. The observed non-linear dependence of absorption on concentration is a signature of a long-range hydration shell with properties distinct from bulk water. We determined a dynamical hydration shell of a thickness of at least 18 A on the protein surface. This exceeds the static hydration layer as it is typically observed by scattering methods (3 A) by far. We also conclude that any increase in flexibility obtained by side-chain truncations that decrease the structural rigidity of the protein results in more bulk-like behaviour of the dynamical hydration shell. Furthermore, our THz measurements show that a single phenylalanine-to-tryptophan substitution to introduce a fluorescent marker leads to measurable changes in the solvation dynamics.