Linked Lives: Exploring Gender and Sedentary Behaviors in Older Adult Couples

Objectives: We explored associations between co-habiting partners for sedentary behavior (type and time, via accelerometry and self-report), gender, and a surrogate health measure (inflammatory biomarker: C-reactive protein, CRP). Methods: Participants completed activity questionnaires and the Timed Up and Go (mobility), wore an accelerometer for 7 days, and provided samples for high-sensitivity (hs) CRP. We used multilevel modeling (partners within couples) to investigate associations between independent variables and (a) sedentary behavior and (b) hsCRP. Results: 112 couples (50% women) provided sedentary data and hsCRP. Sedentary behavior was significantly correlated (r = .440, p men). Gender, moderate to vigorous physical activity (MVPA), and mobility estimated 37% of the modeled variance in sedentary time, while body mass index (BMI) and MVPA estimated 10% of the modeled variance in hsCRP. Discussion: Despite differences in how activity was accumulated, there were no significant differences between women’s and men’s health biomarker.Canadian Institutes of Health Research https://doi.org/10.13039/501100000024michael smith foundation for health research https://doi.org/10.13039/501100000245social sciences and humanities research council of canada https://doi.org/10.13039/501100000155university of british columbia https://doi.org/10.13039/501100005247Peer Reviewe

QM/MM simulations as an assay for carbapenemase activity in class A β-lactamases

Carbapenemases are distinguished from carbapenem-inhibited β-lactamases with a protocol involving QM/MM free energy simulations of acyl–enzyme deacylation, requiring only the enzyme 3D structure as input.</p

QM/MM Simulations Reveal the Determinants of Carbapenemase Activity in Class A β-lactamases

[Image: see text] β-lactam antibiotic resistance in Gram-negative bacteria, primarily caused by β-lactamase enzymes that hydrolyze the β-lactam ring, has become a serious clinical problem. Carbapenems were formerly considered “last resort” antibiotics because they escaped breakdown by most β-lactamases, due to slow deacylation of the acyl-enzyme intermediate. However, an increasing number of Gram-negative bacteria now produce β-lactamases with carbapenemase activity: these efficiently hydrolyze the carbapenem β-lactam ring, severely limiting the treatment of some bacterial infections. Here, we use quantum mechanics/molecular mechanics (QM/MM) simulations of the deacylation reactions of acyl-enzyme complexes of eight β-lactamases of class A (the most widely distributed β-lactamase group) with the carbapenem meropenem to investigate differences between those inhibited by carbapenems (TEM-1, SHV-1, BlaC, and CTX-M-16) and those that hydrolyze them (SFC-1, KPC-2, NMC-A, and SME-1). QM/MM molecular dynamics simulations confirm the two enzyme groups to differ in the preferred acyl-enzyme orientation: carbapenem-inhibited enzymes favor hydrogen bonding of the carbapenem hydroxyethyl group to deacylating water (DW). QM/MM simulations of deacylation give activation free energies in good agreement with experimental hydrolysis rates, correctly distinguishing carbapenemases. For the carbapenem-inhibited enzymes, free energies for deacylation are significantly higher than for the carbapenemases, even when the hydroxyethyl group was restrained to prevent interaction with the DW. Analysis of these simulations, and additional simulations of mutant enzymes, shows how factors including the hydroxyethyl orientation, the active site volume, and architecture (conformations of Asn170 and Asn132; organization of the oxyanion hole; and the Cys69-Cys238 disulfide bond) collectively determine catalytic efficiency toward carbapenems

Using the fragment molecular orbital method to investigate agonist–orexin-2 receptor interactions

The understanding of binding interactions between any protein and a small molecule plays a key role in the rationalization of affinity and selectivity and is essential for an efficient structure-based drug discovery (SBDD) process. Clearly, to begin SBDD, a structure is needed, and although there has been fantastic progress in solving G-protein-coupled receptor (GPCR) crystal structures, the process remains quite slow and is not currently feasible for every GPCR or GPCR-ligand complex. This situation significantly limits the ability of X-ray crystallography to impact the drug discovery process for GPCR targets in 'real-time' and hence there is still a need for other practical and cost-efficient alternatives. We present here an approach that integrates our previously described hierarchical GPCR modelling protocol (HGMP) and the fragment molecular orbital (FMO) quantum mechanics (QM) method to explore the interactions and selectivity of the human orexin-2 receptor (OX2R) and its recently discovered nonpeptidic agonists. HGMP generates a 3D model of GPCR structures and its complexes with small molecules by applying a set of computational methods. FMO allowsab initioapproaches to be applied to systems that conventional QM methods would find challenging. The key advantage of FMO is that it can reveal information on the individual contribution and chemical nature of each residue and water molecule to the ligand binding that normally would be difficult to detect without QM. We illustrate how the combination of both techniques provides a practical and efficient approach that can be used to analyse the existing structure-function relationships (SAR) and to drive forward SBDD in a real-world example for which there is no crystal structure of the complex available

Perforacja odwiertów ropnych i gazowych za pomocą strumienia roztworu polimeru o dużej prędkości

The work is devoted to the development of a technological process for perforating oil and gas well casing strings by a highvelocity jet of a polymer solution. The proposed method of well perforation refers to methods for the secondary opening of productive deposits in the well by hydrojet perforation of the casing strings, annulus cement ring (stone) and rock. The new knowledge about the dynamics of polymer solutions under the conditions of flow through the jet-forming nozzles of a hydroperforator, which create a high-velocity jet, became the main scientific basis for this method of hydroperforation of oil and gas well casings. The study of the reaction of polymer solutions to the hydrodynamic effect with stretching led to the formulation of a structural concept, the “common denominator” of which is a strong deformation effect of the hydrodynamic field on macromolecular coils, which in terms of nonequilibrium thermodynamics generates a kind of rubber-like high elasticity. The peculiarities of the hydrodynamic behaviour of aqueous solutions of polyethylene oxide (PEO) during flow under the conditions of various nozzle jets were modelled, and the regularities of the influence of the resulting dynamic structures on the efficiency of hydrojet water–polymer perforation were established. The mechanism of hydrojet water–polymer perforation of casing columns in oil and gas wells was clarified. The mechanism of the large destructive capacity of a high-velocity polymer solution jet is not due to the reduction of turbulent friction by small polymer additives (the Toms effect), but consists in the destructive action of the dynamic pressure of the water–polymer jet “reinforced” by highly developed macromolecular coils and the dynamic structures formed under the action of extended flow in the inlet section of the hydroperforator nozzles. The method of perforating oil and gas well casings comprises the exact determination of the perforation zone in lowering on production tubing a hydroperforator with 2–4 jet flow-forming nozzles for directing hydrojet to the zone of perforation, sealing the inside cavity of tubing pipes and the jet operators, actuating a ball valve at the bottom of the jet operators, sealing the annulus with a self-sealing gland and supplying the working cutting fluid to the tubing – which differs in that the aqueous solution of PEO used as a working cutting fluid has a molecular weight of 6 · 106 and a concentration 0.003–0.007% by weight and a working pressure of 100–300 MPa. The PEO additives are very environmentally friendly because this polymer is not harmful to humans or the environment. Experimental and industrial testing of this method of well perforation, which was carried out during the secondary opening of a reservoir at a well in the Carpathian oil- and gas-bearing region, confirmed the practical and economic feasibility of its use.Praca poświęcona jest opracowaniu procesu technologicznego perforacji kolumn rur okładzinowych odwiertów ropnych i gazowych za pomocą strumienia roztworu polimeru o dużej prędkości. Zaproponowana metoda perforacji odwiertów odnosi się do metod wtórnego udostępniania złóż produkcyjnych za pomocą hydroperforacji kolumny rur okładzinowych, płaszcza cementowego (kamień) i skały. Uzyskana nowa wiedza na temat dynamiki roztworów polimerów w warunkach przepływu przez dysze strumieniowe hydroperforatora, które tworzą strumień o dużej prędkości, stała się główną podstawą naukową dla tej metody hydroperforacji rur okładzinowych w odwiertach ropnych i gazowych. Badanie reakcji roztworów polimerów na efekt hydrodynamiczny z naprężeniem pozwoliło na sformułowanie koncepcji strukturalnej, której podstawą jest silny wpływ odkształcenia pola hydrodynamicznego na kulki wielkocząsteczkowe, co w warunkach termodynamicznej nierównowagi generuje swego rodzaju „podobną do gumy” wysoką elastyczność. Zbadano osobliwości hydrodynamicznego zachowania się wodnych roztworów tlenku polietylenu (PEO) w modelowych warunkach podczas przepływu przez różne dysze tworzące strumień oraz ustalono prawidłowości dotyczące wpływu utworzonych struktur dynamicznych na efektywność hydroperforacji strumieniem woda–polimer. Wyjaśniono mechanizm hydroperforacji kolumn rur okładzinowych strumieniem wodno-polimerowym w odwiertach ropnych i gazowych. Mechanizm dużej zdolności niszczącej strumienia roztworu polimeru o dużej prędkości nie wynika ze zmniejszenia oporów w warunkach przepływu turbulentnego przez małe dodatki polimeru (efekt Tomsa), ale polega na niszczącym działaniu ciśnienia dynamicznego strumienia woda–polimer „wzmocnionego” przez silnie rozwinięte wiązki makromolekularne i struktury dynamiczne powstające w wyniku działania wydłużonego przepływu w sekcji wlotowej dysz hydroperforatora. Metoda perforacji rur okładzinowych odwiertów ropnych i gazowych polega na dokładnym określeniu strefy perforacji, opuszczaniu na rurach wydobywczych aparatu perforacyjnego z 2–4 dyszami formującymi strumień w celu skierowania przepływu w strefę perforacji i uszczelnieniu wnętrza rur wydobywczych. Następnie operatorzy perforatora uruchamiają zawór kulowy umieszczony w jego dolnej części, następuje uszczelnienie przestrzeni pierścieniowej samouszczelniającą dławnicą i doprowadzenie cieczy roboczej do rur. Jako płyn roboczy używany jest wodny roztwór tlenku polietylenu o masie cząsteczkowej 6 · 106 i stężeniu 0,003–0,007% wag. i pod ciśnieniem roboczym 100–300 MPa. Dodatki PEO są bardzo przyjazne dla środowiska, ponieważ polimer ten nie jest szkodliwy dla ludzi ani środowiska. Doświadczalne i przemysłowe testy tej metody perforacji odwiertów, które przeprowadzono podczas wtórnego udostępnienia złoża ropno-gazowego w jednym z odwiertów rejonu karpackiego, potwierdziły zasadność jej wykorzystania pod względem praktycznym i ekonomicznym

Using the fragment molecular orbital method to investigate agonist-orexin-2 receptor interactions

Abstract The understanding of binding interactions between any protein and a small molecule plays a key role in the rationalization of affinity and selectivity and is essential for an efficient structure-based drug discovery (SBDD) process. Clearly, to begin SBDD, a structure is needed, and although there has been fantastic progress in solving G-protein-coupled receptor (GPCR) crystal structures, the process remains quite slow and is not currently feasible for every GPCR or GPCR-ligand complex. This situation significantly limits the ability of X-ray crystallography to impact the drug discovery process for GPCR targets in &apos;real-time&apos; and hence there is still a need for other practical and cost-efficient alternatives. We present here an approach that integrates our previously described hierarchical GPCR modelling protocol (HGMP) and the fragment molecular orbital (FMO) quantum mechanics (QM) method to explore the interactions and selectivity of the human orexin-2 receptor (OX 2 R) and its recently discovered nonpeptidic agonists. HGMP generates a 3D model of GPCR structures and its complexes with small molecules by applying a set of computational methods. FMO allows ab initio approaches to be applied to systems that conventional QM methods would find challenging. The key advantage of FMO is that it can reveal information on the individual contribution and chemical nature of each residue and water molecule to the ligand binding that normally would be difficult to detect without QM. We illustrate how the combination of both techniques provides a practical and efficient approach that can be used to analyse the existing structure-function relationships (SAR) and to drive forward SBDD in a real-world example for which there is no crystal structure of the complex available

The basis for carbapenem hydrolysis by class A β-lactamases: a combined investigation using crystallography and simulations

Carbapenems are the most potent β-lactam antibiotics and key drugs for treating infections by Gram-negative bacteria. In such organisms, β-lactam resistance arises principally from β-lactamase production. Although carbapenems escape the activity of most β-lactamases, due in the class A enzymes to slow deacylation of the covalent acylenzyme intermediate, carbapenem-hydrolyzing class A β-lactamases are now disseminating in clinically relevant bacteria. The reasons why carbapenems are substrates for these enzymes, but inhibit other class A β-lactamases, remain to be fully established. Here, we present crystal structures of the class A carbapenemase SFC-1 from Serratia fonticola and of complexes of its Ser70 Ala (Michaelis) and Glu166 Ala (acylenzyme) mutants with the carbapenem meropenem. These are the first crystal structures of carbapenem complexes of a class A carbapenemase. Our data reveal that, in the SFC-1 acylenzyme complex, the meropenem 6α-1R-hydroxyethyl group interacts with Asn132, but not with the deacylating water molecule. Molecular dynamics simulations indicate that this mode of binding occurs in both the Michaelis and acylenzyme complexes of wild-type SFC-1. In carbapenem-inhibited class A β-lactamases, it is proposed that the deacylating water molecule is deactivated by interaction with the carbapenem 6α-1R-hydroxyethyl substituent. Structural comparisons with such enzymes suggest that in SFC-1 subtle repositioning of key residues (Ser70, Ser130, Asn132 and Asn170) enlarges the active site, permitting rotation of the carbapenem 6α-1R-hydroxyethyl group and abolishing this contact. Our data show that SFC-1, and by implication other such carbapenem-hydrolyzing enzymes, uses Asn132 to orient bound carbapenems for efficient deacylation and prevent their interaction with the deacylating water molecule.publishe

An Efficient Computational Assay for β-Lactam Antibiotic Breakdown by Class A β-Lactamases

Breakdown of β-lactam antibiotics by β-lactamases is one of the most common resistance mechanisms against these drugs. Here, we present a computationally efficient combined quantum mechanics/molecular mechanics simulation protocol for hydrolysis of the β-lactamase acylenzyme with meropenem, a carbapenem antibiotic. Starting from the previously published computational assay, we have successfully reduced both the conformational space and the sampling time, which leads to a more than 99% reduction on computer resources needed for this assay (less than 24 CPU hours per reaction). This simplified in silico protocol distinguishes accurately between class A β-lactamases that are able or unable to break down carbapenems. We further demonstrate that these protocols can be used to elucidate mechanistic details of β-lactam breakdown. The new efficient computational assaymay be used to predict carbapenem hydrolytic activity of new β-lactamase variants as they arise, and in identifying routes to development of new, more resilient β-lactam antibiotics or new generations of mechanism-based β-lactamase inhibitors.</div