Conformational Changes Combined with Charge-Transfer Interactions Are Essential for Reduction in Catalysis byp-Hydroxybenzoate Hydroxylase†

Biochemistry ◽  
2003 ◽  
Vol 42 (38) ◽  
pp. 11234-11242 ◽  
Author(s):  
Mariliz Ortiz-Maldonado ◽  
Barrie Entsch ◽  
David P. Ballou
Keyword(s):  
Charge Transfer ◽  
Conformational Changes ◽  
Hydroxybenzoate Hydroxylase

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.

Intramolecular Charge Transfer Assisted by Conformational Changes in the Excited State of Fluorene-dibenzothiophene-S,S-dioxide Co-oligomers

2006 ◽  
Vol 110 (39) ◽  
pp. 19329-19339 ◽  
Author(s):  
Fernando B. Dias ◽  
Sam Pollock ◽  
Gordon Hedley ◽  
Lars-Olof Pålsson ◽  
Andy Monkman ◽  
...  
Keyword(s):  
Excited State ◽  
Charge Transfer ◽  
Conformational Changes ◽  
Intramolecular Charge Transfer

scholarly journals Controlling the Conformational Changes in Donor-Acceptor [4]-Dendralenes through Intramolecular Charge-Transfer Processes

2009 ◽  
Vol 15 (43) ◽  
pp. 11581-11593 ◽  
Author(s):  
Alexander L. Kanibolotsky ◽  
John C. Forgie ◽  
Greg J. McEntee ◽  
M. Munsif A. Talpur ◽  
Peter J. Skabara ◽  
...  
Keyword(s):  
Charge Transfer ◽  
Conformational Changes ◽  
Intramolecular Charge Transfer ◽  
Transfer Processes ◽  
Donor Acceptor

scholarly journals Regulatory Impact of the C-Terminal Tail on Charge Transfer Pathways in Drosophila Cryptochrome

Molecules ◽  
2020 ◽  
Vol 25 (20) ◽  
pp. 4810
Author(s):  
Martin Richter ◽  
Benjamin P. Fingerhut
Keyword(s):  
Charge Transfer ◽  
Conformational Changes ◽  
Quantum Dynamics ◽  
Point Mutations ◽  
Feedback Loops ◽  
Amino Acid Residues ◽  
Linear Interaction ◽  
Regulatory Impact ◽  
Ultrafast Ct ◽  
Dynamics Simulations

Interconnected transcriptional and translational feedback loops are at the core of the molecular mechanism of the circadian clock. Such feedback loops are synchronized to external light entrainment by the blue light photoreceptor cryptochrome (CRY) that undergoes conformational changes upon light absorption by an unknown photoexcitation mechanism. Light-induced charge transfer (CT) reactions in Drosophila CRY (dCRY) are investigated by state-of-the-art simulations that reveal a complex, multi-redox site nature of CT dynamics on the microscopic level. The simulations consider redox-active chromophores of the tryptophan triad (Trp triad) and further account for pathways mediated by W314 and W422 residues proximate to the C-terminal tail (CTT), thus avoiding a pre-bias to specific W-mediated CT pathways. The conducted dissipative quantum dynamics simulations employ microscopically derived model Hamiltonians and display complex and ultrafast CT dynamics on the picosecond timescale, subtly balanced by the electrostatic environment of dCRY. In silicio point mutations provide a microscopic basis for rationalizing particular CT directionality and demonstrate the degree of electrostatic control realized by a discrete set of charged amino acid residues. The predicted participation of CT states in proximity to the CTT relates the directionality of CT reactions to the spatial vicinity of a linear interaction motif. The results stress the importance of CTT directional charge transfer in addition to charge transfer via the Trp triad and call for the use of full-length CRY models including the interactions of photolyase homology region (PHR) and CTT domains.

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