Ultrafast structural dynamics in Rydberg excited N,N,N′,N′-tetramethylethylenediamine: conformation dependent electron lone pair interaction and charge delocalization

2014 ◽  
Vol 5 (11) ◽  
pp. 4394-4403 ◽  
Author(s):  
Xinxin Cheng ◽  
Yao Zhang ◽  
Sanghamitra Deb ◽  
Michael P. Minitti ◽  
Yan Gao ◽  
...  
Keyword(s):  
Real Time ◽  
Structural Dynamics ◽  
Lone Pair ◽  
Pair Interaction ◽  
Quantum Calculations ◽  
Time Resolved ◽  
Charge Delocalization ◽  
Rydberg Fingerprint Spectroscopy

Time-resolved Rydberg fingerprint spectroscopy and quantum calculations reveal the structure dependent electron lone pair interaction and charge delocalization in real time.

scholarly journals Charge transfer and ultrafast nuclear motions: the complex structural dynamics of an electronically excited triamine

2016 ◽  
Vol 7 (1) ◽  
pp. 619-627 ◽  
Author(s):  
Xinxin Cheng ◽  
Yan Gao ◽  
Fedor Rudakov ◽  
Peter M. Weber
Keyword(s):  
Charge Transfer ◽  
Real Time ◽  
Quantum Chemical Calculations ◽  
Structural Dynamics ◽  
Quantum Chemical ◽  
Time Resolved ◽  
Electronically Excited ◽  
Rydberg Fingerprint Spectroscopy ◽  
Complex Structural

Time-resolved Rydberg fingerprint spectroscopy combined with quantum chemical calculations reveals the complex structural dynamics and charge transfer in real time.

Structural dynamics of P-type ATPase ion pumps

2019 ◽  
Vol 47 (5) ◽  
pp. 1247-1257 ◽  
Author(s):  
Mateusz Dyla ◽  
Sara Basse Hansen ◽  
Poul Nissen ◽  
Magnus Kjaergaard
Keyword(s):  
Structural Dynamics ◽  
Single Molecule ◽  
New Technologies ◽  
Atp Hydrolysis ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Time Resolved ◽  
Dynamics Simulations ◽  
Types Of Information ◽  
P Type

Abstract P-type ATPases transport ions across biological membranes against concentration gradients and are essential for all cells. They use the energy from ATP hydrolysis to propel large intramolecular movements, which drive vectorial transport of ions. Tight coordination of the motions of the pump is required to couple the two spatially distant processes of ion binding and ATP hydrolysis. Here, we review our current understanding of the structural dynamics of P-type ATPases, focusing primarily on Ca2+ pumps. We integrate different types of information that report on structural dynamics, primarily time-resolved fluorescence experiments including single-molecule Förster resonance energy transfer and molecular dynamics simulations, and interpret them in the framework provided by the numerous crystal structures of sarco/endoplasmic reticulum Ca2+-ATPase. We discuss the challenges in characterizing the dynamics of membrane pumps, and the likely impact of new technologies on the field.

scholarly journals Real-time observation of tetrapyrrole binding to an engineered bacterial phytochrome

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Yusaku Hontani ◽  
Mikhail Baloban ◽  
Francisco Velazquez Escobar ◽  
Swetta A. Jansen ◽  
Daria M. Shcherbakova ◽  
...  
Keyword(s):  
Real Time ◽  
Rational Design ◽  
Near Infrared ◽  
Fluorescent Proteins ◽  
Covalent Bond ◽  
Binding Pocket ◽  
Tissue Imaging ◽  
Covalent Attachment ◽  
Time Resolved

AbstractNear-infrared fluorescent proteins (NIR FPs) engineered from bacterial phytochromes are widely used for structural and functional deep-tissue imaging in vivo. To fluoresce, NIR FPs covalently bind a chromophore, such as biliverdin IXa tetrapyrrole. The efficiency of biliverdin binding directly affects the fluorescence properties, rendering understanding of its molecular mechanism of major importance. miRFP proteins constitute a family of bright monomeric NIR FPs that comprise a Per-ARNT-Sim (PAS) and cGMP-specific phosphodiesterases - Adenylyl cyclases - FhlA (GAF) domain. Here, we structurally analyze biliverdin binding to miRFPs in real time using time-resolved stimulated Raman spectroscopy and quantum mechanics/molecular mechanics (QM/MM) calculations. Biliverdin undergoes isomerization, localization to its binding pocket, and pyrrolenine nitrogen protonation in <1 min, followed by hydrogen bond rearrangement in ~2 min. The covalent attachment to a cysteine in the GAF domain was detected in 4.3 min and 19 min in miRFP670 and its C20A mutant, respectively. In miRFP670, a second C–S covalent bond formation to a cysteine in the PAS domain occurred in 14 min, providing a rigid tetrapyrrole structure with high brightness. Our findings provide insights for the rational design of NIR FPs and a novel method to assess cofactor binding to light-sensitive proteins.

scholarly journals Structural dynamics of the Ca2+-ATPase studied by time-resolved infrared spectroscopy

2008 ◽  
Vol 22 (2-3) ◽  
pp. 63-82 ◽  
Author(s):  
Andreas Barth
Keyword(s):  
Infrared Spectroscopy ◽  
Structural Dynamics ◽  
Ground State ◽  
Transfer Reaction ◽  
High Reactivity ◽  
Acetyl Phosphate ◽  
Time Resolved ◽  
Closed Conformation ◽  
Sarcoplasmic Reticulum Membrane ◽  
Time Resolved Infrared Spectroscopy

This review discusses the contribution of time-resolved infrared spectroscopy to the understanding of the Ca2+pump in the sarcoplasmic reticulum membrane of skeletal muscle cells (SERCA1a). The focus is on interactions of the substrate ATP with the ATPase and on the bond parameters of the phosphoenzyme phosphate group. Functional groups throughout the ATP molecule are important for stabilising the closed conformation of the ATP–ATPase complex and for fast phosphorylation of the ATPase. Dissociation of the reaction product ADP after phosphorylation leads to a more open average conformation of the enzyme and does not trigger the transition from the first phosphoenzyme Ca2E1P to the second E2P. The P–O bond between phosphate and aspartyl moieties is weaker in Ca2E1P and E2P than in acetyl phosphate in aqueous solution, which explains the high reactivity of the phosphoenzymes. This ground state property of the phosphoenzymes prepares for a phosphate transfer reaction with dissociative character.

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