Influence of basic residues on dissociation kinetics and dynamics of singly protonated peptides: time-resolved photodissociation study

2009 ◽  
Vol 44 (10) ◽  
pp. 1532-1537 ◽  
Author(s):  
So Hee Yoon ◽  
Jeong Hee Moon ◽  
Yeon Ji Chung ◽  
Myung Soo Kim
Keyword(s):  
Dissociation Kinetics ◽  
Time Resolved ◽  
Protonated Peptides ◽  
Kinetics And Dynamics

scholarly journals Real-time NMR spectroscopy in the study of biomolecular kinetics and dynamics

2021 ◽  
Author(s):  
György Pintér ◽  
Katharina F. Hohmann ◽  
J. Tassilo Grün ◽  
Julia Wirmer-Bartoschek ◽  
Clemens Glaubitz ◽  
...  
Keyword(s):  
Nmr Spectroscopy ◽  
Nuclear Polarization ◽  
Signal To Noise ◽  
Nmr Studies ◽  
Equilibrium Conditions ◽  
Time Resolved ◽  
Kinetics And Dynamics ◽  
Time Limitations ◽  
Kinetics Of ◽  
Rna And Dna

Abstract. The review describes the application of NMR spectroscopy to study kinetics of folding, refolding and aggregation of proteins, RNA and DNA. Time-resolved NMR experiments can be conducted in a reversible or an irreversible manner. In particular irreversible folding experiments pose large requirements on (i) the signal-to-noise due to the time limitations and (ii) on synchronizing the refolding steps. Thus, this contribution discusses the application of methods for signal-to-noise increases including dynamic nuclear polarization, hyperpolarization and photo-CIDNP for the study of time-resolved NMR studies. Further, methods are reviewed ranging from pressure- and temperature-jump, light induction and rapid mixing to induce rapidly non-equilibrium conditions required to initiate folding.

scholarly journals Transient kinetic studies of the antiviral Drosophila Dicer-2 reveal roles of ATP in self•nonself discrimination

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Raushan K Singh ◽  
McKenzie Jonely ◽  
Evan Leslie ◽  
Nick A Rejali ◽  
Rodrigo Noriega ◽  
...  
Keyword(s):  
Atp Hydrolysis ◽  
Kinetic Studies ◽  
Kinetic Mechanism ◽  
Helicase Domain ◽  
Dependent Manner ◽  
Time Resolved Fluorescence ◽  
Dissociation Kinetics ◽  
Time Resolved ◽  
Biologically Relevant ◽  
Dsrna Cleavage

Some RIG-I-like receptors discriminate viral and cellular dsRNA by their termini, and Drosophila melanogaster Dicer-2 (dmDcr-2) differentially processes dsRNA with blunt or 2 nucleotide 3'-overhanging termini. We investigated the transient kinetic mechanism of the dmDcr-2 reaction using a rapid reaction stopped-flow technique and time-resolved fluorescence spectroscopy. Indeed, we found that ATP binding to dmDcr-2's helicase domain impacts association and dissociation kinetics of dsRNA in a termini-dependent manner, revealing termini-dependent discrimination of dsRNA on a biologically-relevant time-scale (seconds). ATP hydrolysis promotes transient unwinding of dsRNA termini followed by slow rewinding, and directional translocation of the enzyme to the cleavage site. Time-resolved fluorescence anisotropy reveals a nucleotide-dependent modulation in conformational fluctuations (nanoseconds) of the helicase and Platform•PAZ domains that is correlated with termini-dependent dsRNA cleavage. Our study offers a kinetic framework for comparison to other Dicers, as well as all members of the RIG-I- like receptors involved in innate immunity.

scholarly journals Real-time nuclear magnetic resonance spectroscopy in the study of biomolecular kinetics and dynamics

2021 ◽  
Vol 2 (1) ◽  
pp. 291-320
Author(s):  
György Pintér ◽  
Katharina F. Hohmann ◽  
J. Tassilo Grün ◽  
Julia Wirmer-Bartoschek ◽  
Clemens Glaubitz ◽  
...  
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Resonance Spectroscopy ◽  
Signal To Noise ◽  
Nmr Studies ◽  
Time Resolved ◽  
Kinetics And Dynamics ◽  
Time Limitations ◽  
Kinetics Of ◽  
Nuclear Magnetic

Abstract. The review describes the application of nuclear magnetic resonance (NMR) spectroscopy to study kinetics of folding, refolding and aggregation of proteins, RNA and DNA. Time-resolved NMR experiments can be conducted in a reversible or an irreversible manner. In particular, irreversible folding experiments pose large requirements for (i) signal-to-noise due to the time limitations and (ii) synchronising of the refolding steps. Thus, this contribution discusses the application of methods for signal-to-noise increases, including dynamic nuclear polarisation, hyperpolarisation and photo-CIDNP for the study of time-resolved NMR studies. Further, methods are reviewed ranging from pressure and temperature jump, light induction to rapid mixing to induce rapidly non-equilibrium conditions required to initiate folding.

Microtubule nucleation sequence studied by time-resolved x-ray scattering and electron microscopy

1983 ◽  
Vol 41 ◽  
pp. 766-767
Author(s):  
Eva-Maria Mandelkow ◽  
Eckhard Mandelkow ◽  
Joan Bordas
Keyword(s):  
Electron Microscopy ◽  
Dynamic Equilibrium ◽  
Time Resolved ◽  
X Ray ◽  
Additional Information ◽  
X Ray Scattering ◽  
Low Concentrations ◽  
Microtubule Growth ◽  
Ray Patterns ◽  
Ray Scattering

When a solution of microtubule protein is changed from non-polymerising to polymerising conditions (e.g. by temperature jump or mixing with GTP) there is a series of structural transitions preceding microtubule growth. These have been detected by time-resolved X-ray scattering using synchrotron radiation, and they may be classified into pre-nucleation and nucleation events. X-ray patterns are good indicators for the average behavior of the particles in solution, but they are difficult to interpret unless additional information on their structure is available. We therefore studied the assembly process by electron microscopy under conditions approaching those of the X-ray experiment. There are two difficulties in the EM approach: One is that the particles important for assembly are usually small and not very regular and therefore tend to be overlooked. Secondly EM specimens require low concentrations which favor disassembly of the particles one wants to observe since there is a dynamic equilibrium between polymers and subunits.

Electron Channeling Patterns

1977 ◽  
Vol 35 ◽  
pp. 12-13
Author(s):  
David C. Joy
Keyword(s):  
Electron Diffraction ◽  
Incidence Angle ◽  
Photographic Plate ◽  
Diffraction Effect ◽  
Angle Of Incidence ◽  
Bulk Single Crystal ◽  
Time Resolved ◽  
Electron Channeling ◽  
Spatially Resolved ◽  
Large Bulk

Electron channeling patterns (ECP) were first found by Coates (1967) while observing a large bulk, single crystal of silicon in a scanning electron microscope. The geometric pattern visible was shown to be produced as a result of the changes in the angle of incidence, between the beam and the specimen surface normal, which occur when the sample is examined at low magnification (Booker, Shaw, Whelan and Hirsch 1967).A conventional electron diffraction pattern consists of an angularly resolved intensity distribution in space which may be directly viewed on a fluorescent screen or recorded on a photographic plate. An ECP, on the other hand, is produced as the result of changes in the signal collected by a suitable electron detector as the incidence angle is varied. If an integrating detector is used, or if the beam traverses the surface at a fixed angle, then no channeling contrast will be observed. The ECP is thus a time resolved electron diffraction effect. It can therefore be related to spatially resolved diffraction phenomena by an application of the concepts of reciprocity (Cowley 1969).

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