Search results for "dynamics."

Conformational dynamics of full-length inducible human Hsp70 derived from microsecond molecular dynamics simulations in explicit solvent

2013

Human 70 kDa heat shock protein (hHsp70) is an ATP-dependent chaperone and is currently an important target for developing new drugs in cancer therapy. Knowledge of the conformations of hHsp70 is central to understand the interactions between its nucleotide-binding domain (NBD) and substrate-binding domain (SBD) and is a prerequisite to design inhibitors. The conformations of ADP-bound (or nucleotide-free) hHsp70 and ATP-bound hHsp70 was investigated by using unbiased all-atom molecular dynamics (MD) simulations of homology models of hHsp70 in explicit solvent on a timescale of .5 and 2.7 μs, respectively. The conformational heterogeneity of hHsp70 was analyzed by computing effective free-e…

Computational Modeling of Biological Systems: The LDH Story

2010

Lactate dehydrogenases, LDH, catalyzed reaction has been used in this chapter as a conductor wire to present the evolution and difficulties on computing methods to model chemical reactions in enzymes, since the early calculations based at semiempirical level carried out in gas phase to the recent sophisticated simulations based on hybrid Quantum Mechanical/Molecular Mechanics Dynamics (QM/MM MD) schemes. LDH catalyzes the reversible transformation of pyruvate into lactate. The chemical step consists in a hydride and a proton transfer from the cofactor (NADH) and a protonated histidine (His195), respectively. This fact has generated a lot of controversy about the timing of both transfers in …

Effects of heavy metals on earthworms along contamination gradients in organic rich soils.

2003

Earthworm communities and metal (bio)availability to earthworms along contamination gradients was studied in order to support chemical analyses in risk assessment of metal contaminated soils. Earthworms were sampled in three metal contaminated areas with different habitat and soil properties in Finland. Earthworm and soil samples were collected at three distances (1, 2, and 4 km) from the emission sources. Earthworms were identified as to species and analyzed for heavy metals. Total soil metal concentrations were analyzed using an ultrasound-assisted extraction method and bioavailable metal fraction was estimated by acetic acid extraction. In two of the three areas studied, heavy metal conc…

2015

Chemical ligation has been used to alter motions in specific regions of dihydrofolate reductase from E. coli and to investigate the effects of localized motional changes on enzyme catalysis. Two isotopic hybrids were prepared; one with the mobile N-terminal segment containing heavy isotopes (2H, 13C, 15N) and the remainder of the protein with natural isotopic abundance, and the other one with only the C-terminal segment isotopically labeled. Kinetic investigations indicated that isotopic substitution of the N-terminal segment affected only a physical step of catalysis, whereas the enzyme chemistry was affected by protein motions from the C-terminal segment. QM/MM studies support the idea th…

The effect of periodic bottlenecks on the competitive ability of Drosophila pseudoobscura lines.

1993

Competition experiments between several Drosophila pseudoobscura strains that were previously subjected to periodic bottlenecks of different sizes and D. willistoni have been carried out. Contrary to previous results with these two species, where stable coexistence was detected, populations of D. pseudoobscura displaced D. willistoni in a few generations. By using a relative fitness measure, the control lines (that had not gone through bottlenecks) outcompeted D. willistoni faster than bottlenecked lines. One of these, corresponding to the minimum possible bottleneck size of one pair, also shows significantly lower relative fitness than the other strains. These results are discussed in rela…

Comparison between two different cardiovascular models during a hemorrhagic shock scenario

2020

Hemorrhagic shock is a form of hypovolemic shock determined by rapid and large loss of intravascular blood volume and represents the first cause of death in the world, whether on the battlefield or in civilian traumatology. For this, the ability to prevent hemorrhagic shock remains one of the greatest challenges in the medical and engineering fields. The use of mathematical models of the cardiocirculatory system has improved the capacity, on one hand, to predict the risk of hemorrhagic shock and, on the other, to determine efficient treatment strategies. In this paper, a comparison between two mathematical models that simulate several hemorrhagic scenarios is presented. The models considere…

Empagliflozin Induces White Adipocyte Browning and Modulates Mitochondrial Dynamics in KK Cg-Ay/J Mice and Mouse Adipocytes

2021

Background: White adipose tissue (WAT) browning is a promising target for obesity prevention and treatment. Empagliflozin has emerged as an agent with weight-loss potential in clinical and in vivo studies, but the mechanisms underlying its effect are not fully understood. Here, we investigated whether empagliflozin could induce WAT browning and mitochondrial alterations in KK Cg-Ay/J (KKAy) mice, and explored the mechanisms of its effects.Methods: Eight-week-old male KKAy mice were administered empagliflozin or saline for 8 weeks and compared with control C57BL/6J mice. Mature 3T3-L1 adipocytes were treated in the presence or absence of empagliflozin. Mitochondrial biosynthesis, dynamics, a…

Experimental Analysis of bubbling dynamics in bidisperse gas-solid 2D fluidized beds

2008

Outlining the impact of intellectual capital accumulation and depletion processes on the performance of an insurance firm: a dynamic resource-based p…

2014

This paper aims to develop a conceptual framework on how Intellectual Capital (IC) accumulation and depletion processes are dynamically interrelated with firm performance. Such a framework makes explicit the relationships between policy levers, strategic resources, drivers, end-results and performance indicators through a Dynamic Resource-based perspective. Such an approach matches the Resource based perspective and the System Dynamics (SD) methodology. This paper argues that in order to explain a firm superior performance, it is not sufficient to look at the endowment of strategic resources in a given moment of time; it is instead required to investigate the dynamics of company strategic r…

Recognition of Chip Forms by Means of Dynamic Force Spectrum Analysis

1993

In this study the ability to identify chip forms occurrs in the turning of austenitic stainless steel using dynamic force spectrum analysis has been tested. For this purpose the frequency spectra obtained from various metal cutting tests were recorded along with the static cutting forces. A dual channel analysis, based on the Fast Fourier Transform (FFT), was adopted to help identify the continuous/discontinuous (favourable/unfavourable) chip forming boundary. The results showed an acceptable correlation between the types of the frequency spectra and the types of chip forms. Finally, an original classification of the spectra obtained during turning of AISI 304 (DIN 1.4301) stainless steel i…