Benchmarking all-atom simulations using hydrogen exchange

Skinner, John J.,Yu, Wookyung,Gichana, Elizabeth K.,Baxa, Michael C.,Hinshaw, James R.,Freed, Karl F.,Sosnick, Tobin R. National Academy of Sciences 2014 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.111 No.45

<P><B>Significance</B></P><P>Molecular dynamics simulations have recently become capable of observing multiple protein unfolding and refolding events in a single-millisecond–long trajectory. This major advance produces atomic-level information with nanosecond resolution, a feat unmatched by experimental methods. Such simulations are being extensively analyzed to assess their description of protein folding, yet the results remain difficult to validate experimentally. We apply a combination of hydrogen exchange, NMR, and other techniques to test the simulations with a resolution of single H-bonds. Several significant discrepancies between the simulations and experimental data were uncovered for regions of the energy surface outside of the native basin. This comparison yields suggestions for improving the force fields and provides a general method for experimentally validating folding simulations.</P><P>Long-time molecular dynamics (MD) simulations are now able to fold small proteins reversibly to their native structures [Lindorff-Larsen K, Piana S, Dror RO, Shaw DE (2011) <I>Science</I> 334(6055):517–520]. These results indicate that modern force fields can reproduce the energy surface near the native structure. To test how well the force fields recapitulate the other regions of the energy surface, MD trajectories for a variant of protein G are compared with data from site-resolved hydrogen exchange (HX) and other biophysical measurements. Because HX monitors the breaking of individual H-bonds, this experimental technique identifies the stability and H-bond content of excited states, thus enabling quantitative comparison with the simulations. Contrary to experimental findings of a cooperative, all-or-none unfolding process, the simulated denatured state ensemble, on average, is highly collapsed with some transient or persistent native 2° structure. The MD trajectories of this protein G variant and other small proteins exhibit excessive intramolecular H-bonding even for the most expanded conformations, suggesting that the force fields require improvements in describing H-bonding and backbone hydration. Moreover, these comparisons provide a general protocol for validating the ability of simulations to accurately capture rare structural fluctuations.</P>

Protein dynamics viewed by hydrogen exchange.

Skinner, John J,Lim, Woon K,B?dard, Sabrina,Black, Ben E,Englander, S Walter Cambridge University Press 2012 Protein science Vol.21 No.7

<P>To examine the relationship between protein structural dynamics and measurable hydrogen exchange (HX) data, the detailed exchange behavior of most of the backbone amide hydrogens of Staphylococcal nuclease was compared with that of their neighbors, with their structural environment, and with other information. Results show that H-bonded hydrogens are protected from exchange, with HX rate effectively zero, even when they are directly adjacent to solvent. The transition to exchange competence requires a dynamic structural excursion that removes H-bond protection and allows exposure to solvent HX catalyst. The detailed data often make clear the nature of the dynamic excursion required. These range from whole molecule unfolding, through smaller cooperative unfolding reactions of secondary structural elements, and down to local fluctuations that involve as little as a single peptide group or side chain or water molecule. The particular motion that dominates the exchange of any hydrogen is the one that allows the fastest HX rate. The motion and the rate it produces are determined by surrounding structure and not by nearness to solvent or the strength of the protecting H-bond itself or its acceptor type (main chain, side chain, structurally bound water). Many of these motions occur over time scales that are appropriate for biochemical function.</P>

영국의 양육비지급정책: 운용의 3단계

Christine Skinner 한국여성정책연구원(구 한국여성개발원) 2014 한국여성정책연구원 세미나자료 Vol.2014 No.7

The Road to Sustainable Solid Waste Management in North America

( John H. Skinner ) 한국폐기물자원순환학회 2011 ISWA Vol.2011 No.0

民族文化와 世界文明의 出現

Elliott P. Skinner 세계평화교수협의회 1979 廣場 Vol.74 No.-

우주에서 충분히 방귀를 뀌면 몸을 움직일 수 있을까?

앨리스 스키너(Alice Skinner) 유니콘웨일 2024 BBC science Vol.2024 No.1

Management of Frankliniella occidentalis (Thysanoptera: Thripidae) with Entomopathogenic Fungi

Jae Su Kim,Margaret Skinner,Svetlana Gouli,Cheryl E. Frank,Jae Young Choi,Yeon Ho Je,Bruce L. Parker 한국응용곤충학회 2011 한국응용곤충학회 학술대회논문집 Vol.2011 No.05

Reported herein is the use of mycotized millet grains with entomopathogenic fungi applied to soil to control western flower thrips (WFT), Franklinella occidentalis. The majority of mature larvae move from plants to soil for pupation. Mycotized millet grains with Beauveria bassiana ERL1170 and Metarhizium anisopliae ERL1171 were mixed in the upper layer of potting soil containing a blossomed marigold as a banker plant. B. bassiana GHA, a commercial isolate, served as a control. One week post applicaion 3 mated WFT females were added per plant. At 8 wks post infestation WFT mortality in pots with ERL1170 and ERL1171 treatments was 90% and 81% respectively compared to GHA with 15% mortality. Plants in the two ERL treatments had lower levels of damage. The insecticidal activities were positively associated with the fungal soil colonization. No significant release of fungal innoculum from the potting medium was observed. These results suggest that soil applications of entomopathogenic fungi can reduce WFT populations to significantly low levels by targeting pupae. Application timing and the life cycle of WFT are important considerations.

Generating Thermotolerant Colonies by Pairing Beauveria bassiana Isolates

Jae Su Kim,Margaret Skinner,Svetlana Gouli,Jae Young Choi,Yeon Ho Je,Bruce L. Parker 한국응용곤충학회 2011 한국응용곤충학회 학술대회논문집 Vol.2011 No.10

Low thermotolerance in entomopathogenic fungi is the main impediment to their industrialization. This research, for the first time, describes the generation of a thermotolerant colony by pairing and subculturing two Beauveria bassiana isolates without sexual reproduction. A mixture of B. bassiana ERL1578 and ERL1576 was inoculated on 1/4SDAY. The paired culture was subcultured three times, followed by a heat treatment as a selection pressure. Two morphologically different colonies (BbHet1 and BbHet2) were isolated from the pairing. BbHet2 had the most rapid mycelial growth and produced sponge-like mycelial masses (the others were flat), and its conidia were darker than the non-paired colonies under a microscope. BbHet2 conidia had 60.7% germination after exposure to 45°C for 60 min (the others had <15%) without significant loss of virulence against western flower thrips, but a slight decrease in conidial yield was found. Sequencing of Bloc locus and 2-D electrophoresis were done to further clarify the phenomenon. The new phenotypes formed suggested that a genetic variation happened as a result of heterokaryosis and/or recombination, more than environmental adaptation, when mixing different conidia. This methodology seems to be very useful for enhancing thermotolerance in fungi.

Soil treatment of entomopathogenic fungus, Beauveria bassiana to control western flower thrips

Jae Su Kim,Se Jin Lee,Margaret Skinner,Bruce L. Parker 한국응용곤충학회 2015 한국응용곤충학회 학술대회논문집 Vol.2015 No.04

Western flower thrips (WFT), Franklinella occidentalis, is a major pest of ornamentals. Mycotized millet grains with entomopathogenic fungi applied to soil of potted marigold plants was tested to target pupating thrips. Two experimental fungal isolates, (Beauveria bassiana [ARS7060] and Metarhizium anisopliae [ERL1171]), were compared with the registered B.bassiana strain GHA and untreated controls in greenhouse caged trials. Mycotized millet grains were mixed into the upper surface of the potting soil in pots of flowering ‘Hero Yellow’ marigolds (4 g/pot). One week after application five mated WFT females were released onto each plant (four plants per cage). At 8 wks post-infestation, the mean total number of thrips per plant was 81 and 90% less in the ERL1171 and ARS 7060 treatments, respectively, than in the controls. The mean numbers of thrips per plant for the control and GHA treatments were not significantly different. Plant damage was 60% less on plants treated with the experimental fungi than the control and GHA treatments. At 10 wks post-application, 75-90% of WFT collected from the treatments were infected with the experimental isolates. These results demonstrate that soil applications of entomopathogenic fungi can reduce WFT populations significantly and prevent damage.

Signatures of coherent vibrational energy transfer in IR and Raman line shapes for liquid water

Yang, Mino,Skinner, J. L. Royal Society of Chemistry 2010 Physical chemistry chemical physics Vol.12 No.4

<P>We calculate theoretical IR and Raman line shapes for the OH stretch region of liquid water, using mixed quantum/classical and electronic-structure/molecular-dynamics methods. Our approach improves upon the time-averaging approximation used earlier for the same problem, and our results are in excellent agreement with experiment. Previous analysis of theoretical results for this problem considered the extent of delocalization (over local OH stretch excitations) of the instantaneous vibrational eigenstates. In this work we present a complementary analysis in the time-domain, by decomposing the appropriate response functions into diagonal and off-diagonal contributions (in the local mode basis). Our analysis indicates that all vibrational spectra show signatures of coherent vibrational energy transfer. This is manifest in different (IR, isotropic and depolarized Raman) experiments to different extents, because of the competition between coherent energy transfer and rotational disorder.</P> <P>Graphic Abstract</P><P>Time-domain analysis of theoretical line shapes calculated by mixed quantum/classical and electronic-structure/molecular-dynamics methods reveals coherent vibrational energy transfer. <IMG SRC='http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/image/GA?id=b918314k'> </P>