scholarly journals To unravel the connection between the non-equilibrium and equilibrium solvation dynamics of tryptophan: success and failure of the linear response theory of fluorescence Stokes shift

RSC Advances ◽  
2020 ◽  
Vol 10 (31) ◽  
pp. 18348-18354
Author(s):  
Xiaofang Wang ◽  
Jirui Guo ◽  
Tanping Li ◽  
Zhiyi Wei
Keyword(s):  
Excited State ◽  
Linear Response ◽  
Stokes Shift ◽  
Linear Response Theory ◽  
Solvation Dynamics ◽  
Response Theory ◽  
Gaussian Statistics ◽  
Non Equilibrium

Success and failure of linear response theory for Stokes shift correlate with the excited state Gaussian statistics.

Non-equilibrium solvation dynamics: results beyond linear response theory

2020 ◽  
Vol 118 (23) ◽  
pp. e1779365
Author(s):  
Sayantani Choudhury ◽  
Aniket Patra ◽  
Arup Kumar Pathak ◽  
Alok Kumar Samanta
Keyword(s):  
Linear Response ◽  
Linear Response Theory ◽  
Solvation Dynamics ◽  
Response Theory ◽  
Non Equilibrium

Linear response theory and optimal control for a molecular system under non-equilibrium conditions

2013 ◽  
Vol 111 (22-23) ◽  
pp. 3555-3564 ◽  
Author(s):  
Han Wang ◽  
Carsten Hartmann ◽  
Christof Schütte
Keyword(s):  
Optimal Control ◽  
Linear Response ◽  
Molecular System ◽  
Linear Response Theory ◽  
Response Theory ◽  
Equilibrium Conditions ◽  
Non Equilibrium

scholarly journals Intramolecular Communication and Allosteric Sites in Enzymes Unraveled by Time-Dependent Linear Response Theory

2019 ◽  
Author(s):  
Bang-Chieh Huang ◽  
Chi-Hong Chang-Chein ◽  
Lee-Wei Yang
Keyword(s):  
Equilibrium State ◽  
Linear Response ◽  
Signal Propagation ◽  
Linear Response Theory ◽  
Time Dependent ◽  
Response Theory ◽  
Functional Sites ◽  
Allosteric Sites ◽  
Intramolecular Communication ◽  
Non Equilibrium

ABSTRACTIt has been an established idea in recent years that protein is a physiochemically connected network. Allostery, understood in this new context, is a manifestation of residue communicating between remote sites in this network, and hence a rising interest to identify functionally relevant communication pathways and the frequent communicators within. Previous studies rationalized the coupling between functional sites and experimentally observed allosteric sites by theoretically discovered high positional/velocity/thermal correlations between these sites. However, for one to systematically discover previously unobserved allosteric sites in any receptor/enzyme providing the position of functional (orthosteric) sites, these high correlations may not be able to identify remote allosteric sites because of a number of false-positives while many of those are located in proximity to the functional site. Also, whether allosteric sites should be found in equilibrium or non-equilibrium state of a protein to be more biologically relevant is not clear, neither is the directionality preference of aforementioned propagating signals. In this study, we devised a time-dependent linear response theory (td-LRT) integrating intrinsic protein dynamics and perturbation forces that excite protein’s temporary reconfiguration at the non-equilibrium state, to describe atom-specific time responses as the propagating mechanical signals and discover that the most frequent remote communicators can be important allosteric sites, mutation of which would deteriorate the hydride transfer rate in DHFR by 2 to 3 orders. The preferred directionality of the signal propagation can be inferred from the asymmetric connection matrix (CM), where the coupling strength between a pair of residues is suggested by their communication score (CS) in the CM, which is found consistent with experimentally characterized nonadditivity of double mutants. Also, the intramolecular communication centers (ICCs), having high CSs, are found evolutionarily conserved, suggesting their biological importance.

scholarly journals Second Linear Response Theory and the Analytic Calculation of Excited-State Properties

2021 ◽  
Vol 125 (4) ◽  
pp. 1093-1102
Author(s):  
Martín A. Mosquera ◽  
Leighton O. Jones ◽  
Gyeongwon Kang ◽  
Mark A. Ratner ◽  
George C. Schatz
Keyword(s):  
Excited State ◽  
Linear Response ◽  
Linear Response Theory ◽  
Analytic Calculation ◽  
Response Theory

The breakdown of linear response theory in non-polar solvation dynamics

2005 ◽  
Vol 407 (1-3) ◽  
pp. 171-175 ◽  
Author(s):  
Edson Bernardi ◽  
Márcio Marques Martins ◽  
Hubert Stassen
Keyword(s):  
Linear Response ◽  
Linear Response Theory ◽  
Solvation Dynamics ◽  
Response Theory ◽  
Polar Solvation

Linear Response Theory for Decomposition Energies of Stokes Shift in Proteins

2020 ◽  
Vol 124 (17) ◽  
pp. 3540-3547 ◽  
Author(s):  
Jirui Guo ◽  
Xiaofang Wang ◽  
Tanping Li ◽  
Zhiyi Wei
Keyword(s):  
Linear Response ◽  
Stokes Shift ◽  
Linear Response Theory ◽  
Response Theory

scholarly journals Analysis of the window dissipation formula on the basis of linear response theory

1987 ◽  
Vol 475 (3) ◽  
pp. 557-568 ◽  
Author(s):  
Thomas Døssing ◽  
Jørgen Randrup
Keyword(s):  
Linear Response ◽  
Linear Response Theory ◽  
Response Theory
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