scholarly journals Conformational Changes and Charge Transfer in Biomolecules Resolved Using Dynamic Enhanced Raman Correlation Spectroscopy

2019 ◽  
Vol 123 (9) ◽  
pp. 1931-1938 ◽  
Author(s):  
Aymeric Leray ◽  
Jean-Emmanuel Clément ◽  
Alexandre Bouhélier ◽  
Eric Finot
Keyword(s):  
Charge Transfer ◽  
Conformational Changes ◽  
Correlation Spectroscopy ◽  
Raman Correlation Spectroscopy

Two-Dimensional Raman Correlation Spectroscopy Study of Poly[(R)-3-hydroxybutyrate-co-(R)-3-hydroxyhexanoate] Copolymers

2017 ◽  
Vol 71 (7) ◽  
pp. 1427-1431 ◽  
Author(s):  
Isao Noda ◽  
Anjan Roy ◽  
James Carriere ◽  
Brian J. Sobieski ◽  
D. Bruce Chase ◽  
...  
Keyword(s):  
Correlation Spectroscopy ◽  
Two Dimensional ◽  
Spectroscopy Study ◽  
Raman Correlation Spectroscopy

scholarly journals Microsecond and millisecond dynamics in the photosynthetic protein LHCSR1 observed by single-molecule correlation spectroscopy

2019 ◽  
Vol 116 (23) ◽  
pp. 11247-11252 ◽  
Author(s):  
Toru Kondo ◽  
Jesse B. Gordon ◽  
Alberta Pinnola ◽  
Luca Dall’Osto ◽  
Roberto Bassi ◽  
...  
Keyword(s):  
Correlation Function ◽  
Single Molecule ◽  
Conformational Changes ◽  
Protein Function ◽  
Light Harvesting ◽  
Building Blocks ◽  
Complex Stress ◽  
Correlation Spectroscopy ◽  
Light Harvesting Complex ◽  
Single Molecule Level

Biological systems are subjected to continuous environmental fluctuations, and therefore, flexibility in the structure and function of their protein building blocks is essential for survival. Protein dynamics are often local conformational changes, which allows multiple dynamical processes to occur simultaneously and rapidly in individual proteins. Experiments often average over these dynamics and their multiplicity, preventing identification of the molecular origin and impact on biological function. Green plants survive under high light by quenching excess energy, and Light-Harvesting Complex Stress Related 1 (LHCSR1) is the protein responsible for quenching in moss. Here, we expand an analysis of the correlation function of the fluorescence lifetime by improving the estimation of the lifetime states and by developing a multicomponent model correlation function, and we apply this analysis at the single-molecule level. Through these advances, we resolve previously hidden rapid dynamics, including multiple parallel processes. By applying this technique to LHCSR1, we identify and quantitate parallel dynamics on hundreds of microseconds and tens of milliseconds timescales, likely at two quenching sites within the protein. These sites are individually controlled in response to fluctuations in sunlight, which provides robust regulation of the light-harvesting machinery. Considering our results in combination with previous structural, spectroscopic, and computational data, we propose specific pigments that serve as the quenching sites. These findings, therefore, provide a mechanistic basis for quenching, illustrating the ability of this method to uncover protein function.

scholarly journals Correlated protein conformational states and membrane dynamics during attack by pore-forming toxins

2019 ◽  
Vol 116 (26) ◽  
pp. 12839-12844 ◽  
Author(s):  
Ilanila I. Ponmalar ◽  
Ramesh Cheerla ◽  
K. Ganapathy Ayappa ◽  
Jaydeep K. Basu
Keyword(s):  
Conformational Changes ◽  
Pore Formation ◽  
Bacterial Infections ◽  
Cell Lysis ◽  
Membrane Dynamics ◽  
Correlation Spectroscopy ◽  
Listeriolysin O ◽  
Conformational States ◽  
Wide Range ◽  
Membrane Bound

Pore-forming toxins (PFTs) are a class of proteins implicated in a wide range of virulent bacterial infections and diseases. These toxins bind to target membranes and subsequently oligomerize to form functional pores that eventually lead to cell lysis. While the protein undergoes large conformational changes on the bilayer, the connection between intermediate oligomeric states and lipid reorganization during pore formation is largely unexplored. Cholesterol-dependent cytolysins (CDCs) are a subclass of PFTs widely implicated in food poisoning and other related infections. Using a prototypical CDC, listeriolysin O (LLO), we provide a microscopic connection between pore formation, lipid dynamics, and leakage kinetics by using a combination of Förster resonance energy transfer (FRET) and fluorescence correlation spectroscopy (FCS) measurements on single giant unilamellar vesicles (GUVs). Upon exposure to LLO, two distinct populations of GUVs with widely different leakage kinetics emerge. We attribute these differences to the existence of oligomeric intermediates, sampling various membrane-bound conformational states of the protein, and their intimate coupling to lipid rearrangement and dynamics. Molecular dynamics simulations capture the influence of various membrane-bound conformational states on the lipid and cholesterol dynamics, providing molecular interpretations to the FRET and FCS experiments. Our study establishes a microscopic connection between membrane binding and conformational changes and their influence on lipid reorganization during PFT-mediated cell lysis. Additionally, our study provides insights into membrane-mediated protein interactions widely implicated in cell signaling, fusion, folding, and other biomolecular processes.

scholarly journals Role of active site conformational changes in photocycle activation of the AppA BLUF photoreceptor

2017 ◽  
Vol 114 (7) ◽  
pp. 1480-1485 ◽  
Author(s):  
Puja Goyal ◽  
Sharon Hammes-Schiffer
Keyword(s):  
Electron Transfer ◽  
Free Energy ◽  
Excited State ◽  
Charge Transfer ◽  
Conformational Changes ◽  
Ground State ◽  
Active Site ◽  
Locally Excited ◽  
Proton Relay ◽  
Locally Excited State

Blue light using flavin adenine dinucleotide (BLUF) proteins are essential for the light regulation of a variety of physiologically important processes and serve as a prototype for photoinduced proton-coupled electron transfer (PCET). Free-energy simulations elucidate the active site conformations in the AppA (activation of photopigment and puc expression) BLUF domain before and following photoexcitation. The free-energy profile for interconversion between conformations with either Trp104 or Met106 closer to the flavin, denoted Trpin/Metout and Trpout/Metin, reveals that both conformations are sampled on the ground state, with the former thermodynamically favorable by ∼3 kcal/mol. These results are consistent with the experimental observation of both conformations. To analyze the proton relay from Tyr21 to the flavin via Gln63, the free-energy profiles for Gln63 rotation were calculated on the ground state, the locally excited state of the flavin, and the charge-transfer state associated with electron transfer from Tyr21 to the flavin. For the Trpin/Metout conformation, the hydrogen-bonding pattern conducive to the proton relay is not thermodynamically favorable on the ground state but becomes more favorable, corresponding to approximately half of the configurations sampled, on the locally excited state. The calculated energy gaps between the locally excited and charge-transfer states suggest that electron transfer from Tyr21 to the flavin is more facile for configurations conducive to proton transfer. When the active site conformation is not conducive to PCET from Tyr21, Trp104 can directly compete with Tyr21 for electron transfer to the flavin through a nonproductive pathway, impeding the signaling efficiency.

ROLE OF ADENINE AND GUANINE SITES IN HOLE HOPPING IN DNA NANOWIRE

2009 ◽  
Vol 08 (03) ◽  
pp. 529-539
Author(s):  
INDERPREET KAUR ◽  
GIRISH S. KULKARNI ◽  
RAM AJORE ◽  
RICHA BHARADWAJ ◽  
BHANU PRAKASH KOTAMARTHI ◽  
...  
Keyword(s):  
Charge Transfer ◽  
Charge Transport ◽  
Conformational Changes ◽  
Transport Mechanism ◽  
Molecular Wire ◽  
Charge Transport Mechanism ◽  
Close Analysis ◽  
Sequence Variations ◽  
Transfer Integrals

Transfer integrals for oligos with different bases have been calculated using INDO/Koopman's approximation to unveil the charge transport mechanism in DNA. The sequences, G(A) n G , n = 1, 2, …, 10; G(A) x G(A) y G , x + y = 9; and G(A) x G(A) y G(A) z G , x + y + z = 8, were employed to interpret the Guanine (G) and Adenine(A) hopping. Adenine hopping is found to be faster in G(A) n G sequences with longer Adenine bridges (n ≥ 3). Inserting G-bases in between G(A) 10 G led to a decrease in the value of transfer integrals. Close analysis has revealed that bridge closer to 3′-end forms a hopping bottleneck; however, the presence of bridge at 5′-end enhances the charge transfer through A-hopping. Further insertion of single G sites in G(A) x G(A) y G (where x + y = 9) reduces the transfer integrals, thus explaining the hampering of A-hopping. Hence, sequences of the type G(A) n G , n > 3, are better suited for their application as molecular wire. Finally, studies on the effect of flipping of bases, i.e. flipping G:C to C:G on transfer integrals, have revealed that helical distortions and conformational changes due to sequence variations lead to changes in coupling, which is highly unpredictable.

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