Biomolecular diffusional association

Gabdoulline, Razif R.; Wade, Rebecca C.

doi:10.1016/s0959-440x(02)00311-1

Cited by 180 publications

(199 citation statements)

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“…In this work, we assume a two-step model involving the formation of an EC stabilized by long-range electrostatic interactions, and a TS for the association (4,5). According to TS theory, (34) the second-order rate constant for association is related to the free-energy barrier of the TS.…”

Section: Methodsmentioning

confidence: 99%

“…Electrostatic interactions can greatly enhance the rate of protein association by providing long-range guidance in the association process (3). For fast processes assisted by electrostatic interactions, a two-step association mechanism has been proposed (4,5). The first step is the formation of a loosely bound encounter complex (EC), followed by a rate-limiting process through a transition state (TS), leading to the bound active state.…”

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confidence: 99%

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Transition state and encounter complex for fast association of cytochrome c ₂ with bacterial reaction center

Miyashita

Onuchic

Okamura

2004

Proc. Natl. Acad. Sci. U.S.A.

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Electrostatic interactions strongly enhance the electron transfer reaction between cytochrome (Cyt) c 2 and reaction center (RC) from photosynthetic bacteria, yielding a second-order rate constant, k 2 Ϸ 10 9 s ؊1 ⅐M ؊1 , close to the diffusion limit. The proposed mechanism involves an encounter complex (EC) stabilized by electrostatic interactions, followed by a transition state (TS), leading to the bound complex active in electron transfer. The effect of electrostatic interactions was previously studied by Tetreault et al. electron transfer ͉ photosynthesis ͉ electrostatics ͉ site-directed mutagenesis ͉ correlation I ntermolecular electron-transfer reactions play important roles in many biological processes such as photosynthesis and respiration (1). In these reactions, two electron-transfer proteins associate to form an electron donor-acceptor complex in which electron transfer occurs (2). Electrostatic interactions can greatly enhance the rate of protein association by providing long-range guidance in the association process (3). For fast processes assisted by electrostatic interactions, a two-step association mechanism has been proposed (4, 5). The first step is the formation of a loosely bound encounter complex (EC), followed by a rate-limiting process through a transition state (TS), leading to the bound active state. In this paper we examine the association process for the reaction center (RC) and cytochrome (Cyt) c 2 that are involved in the electron-transfer chain in bacterial photosynthesis by using electrostatic calculations and experimental data to obtain a molecular description of the TS and the EC. The results of these calculations describe the ensemble of states that represent a roadmap for the association process and the interactions likely to be important in the dynamics. This approach is complementary to Brownian dynamics simulations (5-7) that yield the diffusional rate constant.The RC is the membrane protein involved in the primary light-induced electron-transfer step in bacterial photosynthesis (8,9). Light absorbed by RC pigments activates photooxidation of the primary donor, D, a bacteriochlorophyll dimer, leading to the reduction of a quinone molecule Q, DQ 3 D ϩ Q Ϫ . The electron from Q Ϫ cycles back to D ϩ through an electron-transfer chain involving the membrane-bound Cyt bc1 complex. The last step in the cycle involves a soluble Cyt c 2 molecule that shuttles the electron back to the RC to complete the cyclic electron-transfer process. This cyclic electron transfer is coupled to proton pumping across the membrane that drives ATP synthesis.The rates of electron transfer between isolated RCs and Cyt c 2 have been measured by using laser-flash techniques and shown to be well optimized for cyclic electron transfer by using the scheme below (refs. 10-13; reviewed in ref. 14).[1]Before the laser flash, the Cyt and RC (denoted DQ) are in equilibrium between a bound state and a free state with the dissociation constant K d Ϸ 10 Ϫ6 M at low ionic strength (Ϸ5 mM) (13). After a laser flash, t...

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Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

Transition state and encounter complex for fast association of cytochrome c ₂ with bacterial reaction center

Miyashita

Onuchic

Okamura

2004

Proc. Natl. Acad. Sci. U.S.A.

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“…The diffusional association places an upper limit on the overall binding rate; so-called "perfect" enzymes operate at this diffusion-limited rate. Electrostatic forces have an important influence on biomolecular diffusional association: their long-range nature enables them to attract the substrate to its binding partner and orient the substrate properly for binding (Gabdoulline and Wade, 2002). It has been established that, for many biomolecular complexes, electrostatic interactions can significantly affect bimolecular association rates (Law et al, 2006).…”

Section: Iib Biomolecule-ligand and -Biomolecule Interactionsmentioning

confidence: 99%

Computational Methods for Biomolecular Electrostatics

Dong

Olsen

Baker

2008

Biophysical Tools for Biologists, Volume One: In Vitro Techniques

116

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An understanding of intermolecular interactions is essential for insight into how cells develop, operate, communicate and control their activities. Such interactions include several components: contributions from linear, angular, and torsional forces in covalent bonds, van der Waals forces, as well as electrostatics. Among the various components of molecular interactions, electrostatics are of special importance because of their long range and their influence on polar or charged molecules, including water, aqueous ions, and amino or nucleic acids, which are some of the primary components of living systems. Electrostatics, therefore, play important roles in determining the structure, motion and function of a wide range of biological molecules. This chapter presents a brief overview of electrostatic interactions in cellular systems with a particular focus on how computational tools can be used to investigate these types of interactions.

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“…Consequently, there has been great interest in elucidating the mechanisms through which binding partners are able to efficiently recognize each other in solution and adopt the correct conformations, relative positions, and orientations to form native stereo-specific complexes. This has been addressed theoretically (6,7), by computer simulation (8,9), and experimentally (1,5,10,11). The association process is typically broken down into at least two steps.…”

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confidence: 99%

Electrostatic Interactions in the Binding Pathway of a Transient Protein Complex Studied by NMR and Isothermal Titration Calorimetry

Meneses

Mittermaier

2014

Journal of Biological Chemistry

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Background: Electrostatic interactions are known accelerate binding in protein complexes with long lifetimes (minutes to hours). Results: NMR and calorimetry were used to characterize binding kinetics in short lived (ϳ1 ms) protein-peptide complexes. Conclusion: Electrostatic enhancement is much less and basal (electrostatic-free) association rates are greater than previously observed. Significance: Electrostatics may play different roles in short lived and long lived protein complexes.

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Biomolecular diffusional association

Cited by 180 publications

References 59 publications

Transition state and encounter complex for fast association of cytochrome c ₂ with bacterial reaction center

Transition state and encounter complex for fast association of cytochrome c ₂ with bacterial reaction center

Computational Methods for Biomolecular Electrostatics

Electrostatic Interactions in the Binding Pathway of a Transient Protein Complex Studied by NMR and Isothermal Titration Calorimetry

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Biomolecular diffusional association

Cited by 180 publications

References 59 publications

Transition state and encounter complex for fast association of cytochrome c 2 with bacterial reaction center

Transition state and encounter complex for fast association of cytochrome c 2 with bacterial reaction center

Computational Methods for Biomolecular Electrostatics

Electrostatic Interactions in the Binding Pathway of a Transient Protein Complex Studied by NMR and Isothermal Titration Calorimetry

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Product

Resources

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Transition state and encounter complex for fast association of cytochrome c ₂ with bacterial reaction center

Transition state and encounter complex for fast association of cytochrome c ₂ with bacterial reaction center