scholarly journals Persistent Protein Motions in a Rugged Energy Landscape Revealed by Normal Mode Ensemble Analysis

2020 ◽  
Author(s):  
Tod D. Romo ◽  
Alan Grossfield ◽  
Andrea Markelz
Keyword(s):  
Optical Absorption ◽  
Structural Variation ◽  
Biological Function ◽  
Energy Landscape ◽  
Optical Absorbance ◽  
Protein Motions ◽  
Single Protein ◽  
Specific Frequency ◽  
Experimental Challenge ◽  
Ensemble Analysis

Testing the premise of evolutionarily optimized protein dynamics has remained an experimental challenge. Most measurements fail to isolate specific structural motions. Our simulations show that the structural variation of a single protein in time results in variation in the vibrations leading to the observed broad and featureless optical absorption. However, when the thermal population of a protein’s configurations are considered, vibrations with functional displacements are concentrated in specific frequency bands. These emergent dynamics are apparent in anisotropic optical absorbance, indicating an experimental avenue for measuring these motions and their impact on biological function.

scholarly journals Persistent Protein Motions in a Rugged Energy Landscape Revealed by Normal Mode Ensemble Analysis

2020 ◽  
Author(s):  
Tod D. Romo ◽  
Alan Grossfield ◽  
Andrea Markelz
Keyword(s):  
Optical Absorption ◽  
Structural Variation ◽  
Biological Function ◽  
Energy Landscape ◽  
Optical Absorbance ◽  
Protein Motions ◽  
Single Protein ◽  
Specific Frequency ◽  
Experimental Challenge ◽  
Ensemble Analysis

Testing the premise of evolutionarily optimized protein dynamics has remained an experimental challenge. Most measurements fail to isolate specific structural motions. Our simulations show that the structural variation of a single protein in time results in variation in the vibrations leading to the observed broad and featureless optical absorption. However, when the thermal population of a protein’s configurations are considered, vibrations with functional displacements are concentrated in specific frequency bands. These emergent dynamics are apparent in anisotropic optical absorbance, indicating an experimental avenue for measuring these motions and their impact on biological function.

scholarly journals Multi-Funnel Landscape of the Fold-Switching Protein RfaH-CTD

2017 ◽  
Author(s):  
Nathan A. Bernhardt ◽  
Ulrich H.E. Hansmann
Keyword(s):  
Free Energy ◽  
Transcription Factor ◽  
Biological Function ◽  
Double Helix ◽  
Energy Landscape ◽  
Three Dimensional ◽  
Conversion Process ◽  
Free Energy Landscape ◽  
Enhanced Sampling ◽  
Helix Bundle

AbstractProteins such as the transcription factor RfaH can change biological function by switching between distinct three-dimensional folds. RfaH regulates transcription if the C-terminal domain folds into a double helix bundle, and promotes translation when this domain assumes a β-barrel form. This fold-switch has been also observed for the isolated domain, dubbed by us RfaH-CTD, and is studied here with a variant of the RET approach recently introduced by us. We use the enhanced sampling properties of this technique to map the free energy landscape of RfaH-CTD and to propose a mechanism for the conversion process.TOC Image

Electronic and optical properties of CsPb2Br5: A first-principles study

2019 ◽  
Vol 33 (22) ◽  
pp. 1950266 ◽  
Author(s):  
Mingge Jin ◽  
Zhibing Li ◽  
Feng Huang ◽  
Weiliang Wang
Keyword(s):  
Optical Properties ◽  
Optical Absorption ◽  
Visible Light ◽  
Band Gap ◽  
First Principles ◽  
First Principles Calculations ◽  
Hybrid Functional ◽  
Electronic And Optical Properties ◽  
Optical Absorbance ◽  
Indirect Band Gap

There are conflicting understandings of the electronic and optical properties of CsPb2Br5. We investigated the electronic and optical properties of CsPb2Br5 with first-principles calculations. It is confirmed that CsPb2Br5 is a semiconductor with an indirect band gap of 3.08 eV at GGA/PBE level and 3.72 eV at the HSE06 hybrid functional level. The PBE results demonstrate that the inclusion of SOC slightly reduces the band gap. We calculate the optical absorbance/emission spectrum of CsPb2Br5. It is found the optical absorption edges locate at 360–380 nm, shorter than the wavelength of visible light. Our results support the experimental results of Li et al. [Chem. Commun. 52 (2016) 11296] and Zhang et al. [J. Mater. Chem. C 6 (2018) 446].

scholarly journals Novel In Vivo Observations of Single Protein Motions Using Laboratory X-Ray Source

2018 ◽  
Vol 114 (3) ◽  
pp. 523a-524a
Author(s):  
Yuji C. Sasaki ◽  
M. Kuramochi ◽  
H. Sekiguchi ◽  
K. Mio
Keyword(s):  
X Ray ◽  
Protein Motions ◽  
Single Protein

Arotic Evans blue dye accumulation: its measurement and interpretation

1977 ◽  
Vol 232 (2) ◽  
pp. H204-H222 ◽  
Author(s):  
D. L. Fry
Keyword(s):  
Optical Absorption ◽  
Absorption Coefficient ◽  
Correlation Coefficient ◽  
Evans Blue ◽  
Vessel Wall ◽  
Optical Absorption Coefficient ◽  
Blue Dye ◽  
Optical Absorbance ◽  
Evans Blue Dye ◽  
Percentage Area

Parenteral Evans blue dye (EBD) binds to albumin and thus can indicate transvascular protein flux. A model was developed to relate the arterial surface accumulation of EBD to the light refected from the opened vessel surface. The accumulation, M (nmol cm-2), was related to the optical "absorbance" (rho) of the surface by the equation, M = 3.92 rho + 0.80 rho3, where rho = -ln(I/I0) and I and I0 are the intensities of light reflected from the surface in the stained and unstained state, respectively. The validity of the model was examined in two ways, 1) by comparing the value of the optical absorption coefficient for EBD predicted by the model to the measured value: the predicted value was 0.128 +/- SD 0.015 cm2 nmol-1, the measured value was 0.125 +/- SD 0.005 cm2 nmol-1; and 2) by comparing predicted changes in vessel wall stretch to measured values: the percentage changes (Y) in area predicted by the model from changes in M were linearly related to the directly measured percentage area changes (X) by Y = 0.09 + 1.01X, +/- SD 2.54, with a correlation coefficient of 0.994.

Knotting pathways in proteins

2013 ◽  
Vol 41 (2) ◽  
pp. 523-527 ◽  
Author(s):  
Joanna I. Sułkowska ◽  
Jeffrey K. Noel ◽  
César A. Ramírez-Sarmiento ◽  
Eric J. Rawdon ◽  
Kenneth C. Millett ◽  
...  
Keyword(s):  
Free Energy ◽  
Biological Function ◽  
Energy Landscape ◽  
Free Energy Landscape ◽  
Biological Functions ◽  
Loop Formation ◽  
Native State ◽  
Theoretical Approaches ◽  
Knotted Proteins ◽  
Comparison With Experiments

Most proteins, in order to perform their biological function, have to fold to a compact native state. The increasing number of knotted and slipknotted proteins identified suggests that proteins are able to manoeuvre around topological barriers during folding. In the present article, we review the current progress in elucidating the knotting process in proteins. Although we concentrate on theoretical approaches, where a knotted topology can be unambiguously detected, comparison with experiments is also reviewed. Numerical simulations suggest that the folding process for small knotted proteins is composed of twisted loop formation and then threading by either slipknot geometries or flipping. As the size of the knotted proteins increases, particularly for more deeply threaded termini, the prevalence of traps in the free energy landscape also increases. Thus, in the case of longer knotted and slipknotted proteins, the folding mechanism is probably supported by chaperones. Overall, results imply that knotted proteins can be folded efficiently and survive evolutionary pressure in order to perform their biological functions.

scholarly journals Optical Absorbance Sensitivity to Rugged Energy Landscape

2016 ◽  
Vol 110 (3) ◽  
pp. 513a
Author(s):  
Katherine A. Niessen ◽  
Edward Snell ◽  
Andrea G. Markelz
Keyword(s):  
Energy Landscape ◽  
Optical Absorbance

scholarly journals Characterization Studies of Reduced Graphene Oxide/Zinc Oxide Nanocomposites Synthesized by Hydrothermal Method

2019 ◽  
Vol 8 (2) ◽  
pp. 80-90
Author(s):  
A. A. Ebnalwaled ◽  
A. Abu El-Fadl ◽  
Muhammad A. Tuhamy
Keyword(s):  
Zinc Oxide ◽  
Graphene Oxide ◽  
Optical Absorption ◽  
Hydrothermal Method ◽  
Reduced Graphene Oxide ◽  
Xrd Analysis ◽  
Morphological Characterization ◽  
Optical Absorbance ◽  
Morphological Studies ◽  
Reduced Graphene

Reduced graphene oxide/zinc oxide (RGO/ZnO) nanocomposites were synthesized by facile hydrothermal method; this method consists of exfoliation of graphite with modified Hummer's method and synthesis of (RGO/ZnO) nanocomposites using hydrothermal method. X-ray diffraction, TEM and FT-IR spectroscopy were used for structure morphological characterization. Optical properties of the samples were studied by measuring their optical absorbance. It can be concluded from XRD analysis that there are improvements of crystallinity associated with the increase of the crystallite size, as well as the increase in both of the (Zn-O) bond length and unit cell volume with the increase of ZnO ratio in RGO/ZnO nanocomposites. The morphological studies confirmed that the scale of ZnO particles is large and the size distribution is not uniform in samples of RGO/ZnO and that most particles have average size of about 9 nm while some particles even have larger size. The optical absorption spectra show that the excitonic peak of the as-prepared samples is red shifted from 268 nm to 376 nm for reduced grapheme oxide (RGO) with the increase of ZnO ratio, and the optical band gap changes from 2.39 for pure RGO to 3.34 eV for pure ZnO. The effect of UV irradiation on the optical absorption nanocomposites at different UV doses was carried out using UV lamp.

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