S. Sekharan and Victor S. Batista, J. Am. Chem. Soc. 2012, 134, 19536–19539.
Melanopsin, found in the neurons of vertebrate inner retina, absorbs blue light ...
J. Am. Chem. Soc. 2013
Ana Patricia Gámiz-Hernández
Department of Chemistry University of Basel AG Meuwly
A. P. Gámiz Hernández ()
JACS
June 2013
1 / 22
Outline
1
Overview
2
Biological Clock
3
Native State Stability-crowded system
4
Three-body Binding Equilibria
5
Model of Energy Transfer in PSII
6
Beyond
A. P. Gámiz Hernández ()
JACS
June 2013
2 / 22
Overview
J. Am. Chem. Soc. Overview
Established in 1879 by the American Chemical Society. Since 2002, the journal is edited by Peter J. Stang (University of Utah). It is the most cited journal in this field and has a 2011 impact factor of 9.907
A. P. Gámiz Hernández ()
JACS
June 2013
3 / 22
Biological Clock
paper 1
The Active Site of Melanopsin: The Biological Clock Photoreceptor S. Sekharan and Victor S. Batista, J. Am. Chem. Soc. 2012, 134, 19536–19539
Melanopsin, found in the neurons of vertebrate inner retina, absorbs blue light and triggers the “biological clock”. Based on the crystal structure of squid rhodopsin (λmax = 490 nm) and shows a maximal absorbance (λmax = 447 nm) consistent with the observed absorption of the photoreceptor.
A. P. Gámiz Hernández ()
JACS
June 2013
4 / 22
Biological Clock
paper 1
QM/MM models were built by using the two-layer ONIOM scheme with electronic-embedding (EE), G09. The QM layer included the retinyl chromophore PSB11 and the side-chain N-H moiety of K305, treated according to DFT at the B3LYP/6-31G(d). MM with AMBER96 force field. Understanding the structure, wavelength sensitivity, and spectral tuning of melanopsin is the first step toward manipulating the regulation of circadian rhythms. Pave the way for converting a visual light sensor into a nonvisual sensory photoreceptor
A. P. Gámiz Hernández ()
JACS
June 2013
5 / 22
Biological Clock
paper 1
The Active Site of Melanopsin: The Biological Clock Photoreceptor S. Sekharan and Victor S. Batista, J. Am. Chem. Soc. 2012, 134, 19536–19539
First excitation energy, oscillatory strength.
A. P. Gámiz Hernández ()
Blue/red shift.
JACS
June 2013
6 / 22
Native State Stability-crowded system
paper 2
Reduced Native State Stability in Crowded Cellular Environment Due to Protein–Protein Interactions Ryuhei Harada and Michael Feig, J. Am. Chem. Soc. 2013, 135, 3696–3701
The classical view of crowding emphasizes the volume exclusion effect that generally favors compact, native states. Results from MD simulations and NMR experiments show that protein crowders may destabilize native states via protein–protein interactions. A. P. Gámiz Hernández ()
JACS
June 2013
7 / 22
Native State Stability-crowded system
paper 2
Reduced Native State Stability in Crowded Environment Methods
Simulated systems consisted of 4 protein G and 8 villin molecules, solvated with TIP3P water molecules under periodic boundary conditions.
CHARMM FF (CMAP).
Different box sizes corresponding to protein volume fractions ranging from 10 % to 43 %.
Free Energies: MMPB/SA
Production simulations were carried out over 300 ns in the NPT ensemble at 300 K and 1 bar pressure. A. P. Gámiz Hernández ()
JACS
NAMD. MMTSB tool set.
∆GMMPB/SA = ∆GMM + ∆GPB + γSASA
June 2013
8 / 22
Native State Stability-crowded system
paper 2
Reduced Native State Stability in Crowded Cellular Environment Due to Protein–Protein Interactions Ryuhei Harada and Michael Feig, J. Am. Chem. Soc. 2013, 135, 3696–3701
The largest number of non-native states was seen for the most crowded case, C5, with denatured structures denoted as LM1–LM4 In these structures, there is a loss of both tertiary and secondary structure, with RMSD values ranging from 5 to 10 Å with respect to the native state. A. P. Gámiz Hernández ()
JACS
June 2013
9 / 22
Native State Stability-crowded system
paper 2
Reduced Native State Stability in Crowded Cellular Environment Due to Protein–Protein Interactions Ryuhei Harada and Michael Feig, J. Am. Chem. Soc. 2013, 135, 3696–3701
The results challenge the classical view of crowding based on a volume exclusion effect and suggest that partially unfolded structures can become stable under crowded environments through enthalpy-driven protein–protein interactions with surrounding crowders.
A. P. Gámiz Hernández ()
JACS
June 2013
10 / 22
Three-body Binding Equilibria
paper 3
A Mathematical Model for Three-Body Binding Equilibria Eugene F. Douglass and David A. Spiegel, JACS 2013, 135, 6092–6099
Three-body (ternary complex) equilibria appear in diverse systems-level processes including coagulation, antibody-mediated phagocytosis, and supramolecular assembly. Derivation of exact mathematical models that describe ternary complex equilibria by relating concentrations of solution species to measurable parameters. A. P. Gámiz Hernández ()
JACS
June 2013
11 / 22
Three-body Binding Equilibria
paper 3
A Mathematical Model for Three-Body Binding Equilibria Eugene F. Douglass and David A. Spiegel, JACS 2013, 135, 6092–6099
Non-cooperative Equilibria (α < 1) Cooperative Equilibria (α > 1) The models can be used to explain experimental systems: cancer cell treatment.
A. P. Gámiz Hernández ()
JACS
June 2013
12 / 22
Three-body Binding Equilibria
paper 3
Model for Three-Body Binding Equilibria Eugene F. Douglass and David A. Spiegel, JACS 2013, 135, 6092–6099
Cooperative perturbation
A. P. Gámiz Hernández ()
(A) Electron Transfer (B) Antigen
JACS
June 2013
13 / 22
Model of Energy Transfer in PSII
paper 4
A Structure-Based Model of Energy Transfer Reveals the Principles of Light Harvesting in Photosystem II Supercomplexes Doran I. G. Bennett and Graham R. Fleming, J. Am. Chem. Soc. XXXX
Photosystem II (PSII) initiates photosynthesis in plants through the absorption of light and subsequent conversion of excitation energy to chemical energy via charge separation (CS). To understand the high efficiency of light harvesting in PSII requires quantitative insight into energy transfer and CS in PSII supercomplexes. A. P. Gámiz Hernández ()
JACS
June 2013
14 / 22
Model of Energy Transfer in PSII
paper 4
A Structure-Based Model of Energy Transfer Reveals the Principles of Light Harvesting in Photosystem II Supercomplexes Doran I. G. Bennett and Graham R. Fleming, J. Am. Chem. Soc. XXXX
A. P. Gámiz Hernández ()
JACS
June 2013
15 / 22
Model of Energy Transfer in PSII
paper 4
A Structure-Based Model of Energy Transfer Reveals the Principles of Light Harvesting in Photosystem II Supercomplexes Doran I. G. Bennett and Graham R. Fleming, J. Am. Chem. Soc. XXXX
A. P. Gámiz Hernández ()
JACS
June 2013
16 / 22
Model of Energy Transfer in PSII
paper 4
A Structure-Based Model of Energy Transfer Reveals the Principles of Light Harvesting in Photosystem II Supercomplexes Doran I. G. Bennett and Graham R. Fleming, J. Am. Chem. Soc. XXXX
Coarse-grained model considering electronic coupling larger than 15 cm-1. The model describes how the specific arrangement of light harvesting proteins and pigments gives rise to efficient energy capture and the fluorescence lifetimes previously measured by Caffarri and co-workers A. P. Gámiz Hernández ()
JACS
June 2013
17 / 22
Beyond
Mapping Molecular Perturbations by a New Form of Two-Dimensional Spectroscopy E. Kupce and R. Freeman, J. Am. Chem. Soc. 2013, 135, 2871–2874
New general form of 2D spectroscopy where the indirect “evolution“ dimension is derived using the Radon transform. R(p, R R α) = f (x)δ(xcosα + ysinα − p)dxdy This ”projection spectroscopy“ displays characteristic correlation peaks that highlight perturbations of chemical shifts caused by temperature, pressure, solvent, molecular binding, chemical exchange, H-bonding, pH variations or conformational changes. A. P. Gámiz Hernández ()
JACS
Figure: NMR responses for a,b, c at diff T. June 2013
18 / 22
Beyond
Spectroscopic and DFT Studies of Second-Sphere Variants of the Type 1 Copper Site in Azurin: Covalent and Nonlocal Electrostatic Contributions to Reduction Potentials
DFT calculations correlated to the experimental data allow for the fractionation of the contributions to tuning E0 into covalent and non-local electrostatic components.
A. P. Gámiz Hernández ()
JACS
June 2013
19 / 22
Beyond
Spectroscopic and DFT Studies of Co Site in Azurin: Ryan G. Hadt,and E. I. Solomon J. Am. Chem. Soc. 2012, 134, 16701–16716.
Combination of low-temperature electronic absorption and magnetic CD, EPR, resonance Raman, and S K-edge X-ray absorption spectroscopies to investigate a series of second-sphere variants which modulate hydrogen bonding to and protein-derived dipoles nearby the Cu–S(Cys) bond.
A. P. Gámiz Hernández ()
JACS
June 2013
20 / 22
Beyond
Enhanced Electron-Transfer Reactivity of Nonheme Mn(IV)–Oxo Complexes by Binding Sc Ions H. Yoon,and S. Fuhkuzumi, J. Am. Chem. Soc. XXXX, XXX, XXXâXXX
The electron-transfer reactivity of nonheme MnIV(O) complexes was enhanced as much as 107 -fold by binding of Sc3+ ions. The remarkable enhancement of the electro-transfer reactivity of MnIV(O) complexes by binding of Sc3+ ions may pave a new way to improve the catalytic reactivity of metalâoxo complexes in oxidation reactions.
A. P. Gámiz Hernández ()
JACS
June 2013
21 / 22
Beyond
A. P. Gámiz Hernández ()
JACS
June 2013
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