Non-Markovian Configurational Diffusion and Reaction Coordinates for Protein Folding

The non-Markovian nature of polymer motions is accounted for in folding kinetics, using frequency-dependent friction. Folding, like many other problems in the physics of disordered systems, involves barrier crossing on a correlated energy landscape. A variational transition state theory (VTST) that reduces to the usual Bryngelson-Wolynes Kramers approach when the non-Markovian aspects are neglected is used to obtain the rate, without making any assumptions regarding the size of the barrier, or the memory time of the friction. The transformation to collective variables dependent on the dynamics of the system allows the theory to address the controversial issue of what are ``good'' reaction coordinates for folding.Comment: 9 pages RevTeX, 3 eps-figures included, submitted to PR

Computer Simulations of Supercooled Liquids and Glasses

After a brief introduction to the dynamics of supercooled liquids, we discuss some of the advantages and drawbacks of computer simulations of such systems. Subsequently we present the results of computer simulations in which the dynamics of a fragile glass former, a binary Lennard-Jones system, is compared to the one of a strong glass former, SiO_2. This comparison gives evidence that the reason for the different temperature dependence of these two types of glass formers lies in the transport mechanism for the particles in the vicinity of T_c, the critical temperature of mode-coupling theory. Whereas the one of the fragile glass former is described very well by the ideal version of mode-coupling theory, the one for the strong glass former is dominated by activated processes. In the last part of the article we review some simulations of glass formers in which the dynamics below the glass transition temperature was investigated. We show that such simulations might help to establish a connection between systems with self generated disorder (e.g. structural glasses) and quenched disorder (e.g. spin glasses).Comment: 37 pages of Latex, 11 figures, to appear as a Topical Review article in J. Phys.: Condens. Matte

Using death to one's advantage: HIV modulation of apoptosis

Infection by human immunodeficiency virus (HIV) is associated with an early immune dysfunction and progressive destruction of CD4+ T lymphocytes. This progressive disappearance of T cells leads to a lack of immune control of HIV replication and to the development of immune deficiency resulting in the increased occurrence of opportunistic infections associated with acquired immune deficiency syndrome (AIDS). The HIV-induced, premature destruction of lymphocytes is associated with the continuous production of HIV viral proteins that modulate apoptotic pathways. The viral proteins, such as Tat, Env, and Nef, are associated with chronic immune activation and the continuous induction of apoptotic factors. Viral protein expression predisposes lymphocytes, particularly CD4+ T cells, CD8+ T cells, and antigen-presenting cells, to evolve into effectors of apoptosis and as a result, to lead to the destruction of healthy, non-infected T cells. Tat and Nef, along with Vpu, can also protect HIV-infected cells from apoptosis by increasing anti-apoptotic proteins and down- regulating cell surface receptors recognized by immune system cells. This review will discuss the validity of the apoptosis hypothesis in HIV disease and the potential mechanism(s) that HIV proteins perform in the progressive T cell depletion observed in AIDS pathogenesis. Originally published Leukemia, Vol. 15, No. 3, Mar 200

Controls on short-term variations in Greenland glacier dynamics

Short-term ice-dynamical processes at Greenland’s Jakobshavn and Kangerdlugssuaq glaciers were studied using a 3 day time series of synthetic aperture radar data acquired during the 2011 European Remote-sensing Satellite-2 (ERS-2) 3 day repeat campaign together with modelled meteorological parameters. The time series spans the period March–July 2011 and captures the first 30% of the summer melting season. In both study areas, we observe velocity fluctuations at the lower 10 km of the glacier. At Jakobshavn Isbræ, where our dataset covers the first part of the seasonal calving-front retreat, we identify ten calving episodes, with a mean calving-front area loss of 1.29 0.4km2. Significant glacier speed-up was observed in the near-terminus area following all calving episodes. We identify changes in calving-front geometry as the dominant control on velocity fluctuations on both glaciers, apart from

Insights into foraging behavior from multi-day sound recording tags on goose-beaked whales (Ziphius cavirostris) in the Southern California Bight

Goose-beaked whales (Ziphius cavirostris) are deep-diving cetaceans known for their elusive nature and specialized foraging behavior. In 2019 and 2020, six telemetry tags were deployed on these whales in Southern California, resulting in 395 h of acoustic and diving data. Foraging dives were manually identified by the presence of echolocation pulses and buzzes, and generalized additive models assessed factors influencing foraging behavior. The median bathymetric depth at foraging sites was 1,419 m (IQR = 359), and the maximum dive depth was highly correlated with bathymetry depth. Individuals started echolocating on descent at a median depth of 410 m (IQR = 74); pulses were not observed shallower than 292 m. Echolocation ceased during the bottom phase for 81.6% of dives, at a median depth of 1,265 m (IQR = 472); pulses were not observed shallower than 587 m on ascent. The median depth of buzzes was 1,215 m (IQR = 479) with 63% occurring during the bottom phase. Deeper dives correlated with longer durations of diving and echolocation, greater echolocation end depths, and wider bottom phase echolocation depth inter-quartile range. The median difference between dive depth and bottom phase median echolocation depth was 98.3 m (IQR = 48.5), suggesting whales in this region forage in a narrow band close to the seafloor. In the San Nicolas Basin, individuals exhibited longer echolocation durations, produced more pulses, and started and ended echolocating at greater depths compared to adjacent regions. These records validate and expand upon previous studies, providing insights into factors influencing foraging behavior in an area with high anthropogenic disturbance

Syntheses, characterization, density functional theory calculations, and activity of tridentate SNS zinc pincer complexes

A series of tridentate SNS ligand precursors were metallated with ZnCl2 to give new tridentate SNS pincer zinc complexes. The zinc complexes serve as models for the zinc active site in liver alcohol dehydrogenase (LADH) and were characterized with single crystal X-ray diffraction, 1H, 13C, and HSQC NMR spectroscopies and electrospray mass spectrometry. The bond lengths and bond angles of the zinc complexes correlate well to those in horse LADH. The zinc complexes feature SNS donor atoms and pseudotetrahedral geometry about the zinc center, as is seen for liver alcohol dehydrogenase. The SNS ligand precursors were characterized with 1H, 13C, and HSQC NMR spectroscopies and cyclic voltammetry, and were found to be redox active. Gaussian calculations were performed and agree quite well with the experimentally observed oxidation potential for the pincer ligand. The zinc complexes were screened for the reduction of electron poor aldehydes in the presence of a hydrogen donor, 1-benzyl-1,4-dihydronicotinamide (BNAH). The zinc complexes enhance the reduction of electron poor aldehydes. Density functional theory calculations were performed to better understand why the geometry about the zinc center is pseudo-tetrahedral rather than pseudo-square planar, which is seen for most pincer complexes. For the SNS tridentate pincer complexes, the data indicate that the pseudo-tetrahedral geometry was 43.8 kcal/mol more stable than the pseudo-square planar geometry. Density functional theory calculations were also performed on zinc complexes with monodentate ligands and the data indicate that the pseudo-tetrahedral geometry was 30.6 kcal/mol more stable than pseudo-square planar geometry. Overall, the relative stabilities of the pseudo-tetrahedral and pseudo-square planar systems are the same for this coordination environment whether the ligand set is a single tridentate SNS system or is broken into three separate units. The preference of a d10 Zn center to attain a tetrahedral local environment trumps any stabilization gained by removal of constraints within the ligand set

Beaked whales respond to simulated and actual navy sonar

This article is distributed under the terms of the Creative Commons Public Domain declaration. The definitive version was published in PLoS One 6 (2011): e17009, doi:10.1371/journal.pone.0017009.Beaked whales have mass stranded during some naval sonar exercises, but the cause is unknown. They are difficult to sight but can reliably be detected by listening for echolocation clicks produced during deep foraging dives. Listening for these clicks, we documented Blainville's beaked whales, Mesoplodon densirostris, in a naval underwater range where sonars are in regular use near Andros Island, Bahamas. An array of bottom-mounted hydrophones can detect beaked whales when they click anywhere within the range. We used two complementary methods to investigate behavioral responses of beaked whales to sonar: an opportunistic approach that monitored whale responses to multi-day naval exercises involving tactical mid-frequency sonars, and an experimental approach using playbacks of simulated sonar and control sounds to whales tagged with a device that records sound, movement, and orientation. Here we show that in both exposure conditions beaked whales stopped echolocating during deep foraging dives and moved away. During actual sonar exercises, beaked whales were primarily detected near the periphery of the range, on average 16 km away from the sonar transmissions. Once the exercise stopped, beaked whales gradually filled in the center of the range over 2–3 days. A satellite tagged whale moved outside the range during an exercise, returning over 2–3 days post-exercise. The experimental approach used tags to measure acoustic exposure and behavioral reactions of beaked whales to one controlled exposure each of simulated military sonar, killer whale calls, and band-limited noise. The beaked whales reacted to these three sound playbacks at sound pressure levels below 142 dB re 1 µPa by stopping echolocation followed by unusually long and slow ascents from their foraging dives. The combined results indicate similar disruption of foraging behavior and avoidance by beaked whales in the two different contexts, at exposures well below those used by regulators to define disturbance.The research reported here was financially supported by the United States (U.S.) Office of Naval Research (www.onr.navy.mil) Grants N00014-07-10988, N00014-07-11023, N00014-08-10990; the U.S. Strategic Environmental Research and Development Program (www.serdp.org) Grant SI-1539, the Environmental Readiness Division of the U.S. Navy (http://www.navy.mil/local/n45/), the U.S. Chief of Naval Operations Submarine Warfare Division (Undersea Surveillance), the U.S. National Oceanic and Atmospheric Administration (National Marine Fisheries Service, Office of Science and Technology) (http://www.st.nmfs.noaa.gov/), U.S. National Oceanic and Atmospheric Administration Ocean Acoustics Program (http://www.nmfs.noaa.gov/pr/acoustics/), and the Joint Industry Program on Sound and Marine Life of the International Association of Oil and Gas Producers (www.soundandmarinelife.org)

Mechanical Strain Stabilizes Reconstituted Collagen Fibrils against Enzymatic Degradation by Mammalian Collagenase Matrix Metalloproteinase 8 (MMP-8)

Collagen, a triple-helical, self-organizing protein, is the predominant structural protein in mammals. It is found in bone, ligament, tendon, cartilage, intervertebral disc, skin, blood vessel, and cornea. We have recently postulated that fibrillar collagens (and their complementary enzymes) comprise the basis of a smart structural system which appears to support the retention of molecules in fibrils which are under tensile mechanical strain. The theory suggests that the mechanisms which drive the preferential accumulation of collagen in loaded tissue operate at the molecular level and are not solely cell-driven. The concept reduces control of matrix morphology to an interaction between molecules and the most relevant, physical, and persistent signal: mechanical strain.The investigation was carried out in an environmentally-controlled microbioreactor in which reconstituted type I collagen micronetworks were gently strained between micropipettes. The strained micronetworks were exposed to active matrix metalloproteinase 8 (MMP-8) and relative degradation rates for loaded and unloaded fibrils were tracked simultaneously using label-free differential interference contrast (DIC) imaging. It was found that applied tensile mechanical strain significantly increased degradation time of loaded fibrils compared to unloaded, paired controls. In many cases, strained fibrils were detectable long after unstrained fibrils were degraded.In this investigation we demonstrate for the first time that applied mechanical strain preferentially preserves collagen fibrils in the presence of a physiologically-important mammalian enzyme: MMP-8. These results have the potential to contribute to our understanding of many collagen matrix phenomena including development, adaptation, remodeling and disease. Additionally, tissue engineering could benefit from the ability to sculpt desired structures from physiologically compatible and mutable collagen