First principle study of proton transfer in the green fluorescent protein (GFP): Ab initio PES in a cluster model

Zhang, Hong; Sun, Qiao; Li, Zhen; Nanbu, Shinkoh; Smith, Sean C.

doi:10.1016/j.comptc.2012.02.035

Cited by 9 publications

(7 citation statements)

References 47 publications

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“…HBDI was systematically arranged with water, methanol (instead of Ser 205) and acetate (instead of Glu 222) and assembled to recreate the Hbonding network (as shown in Scheme 1), which has been widely used as the model to study proton transfer in GFPs. [36][37][38][39] To achieve our goal, DFT calculations, which have been well accepted to optimize the ground state structures of GFPs, 40 were carried out by a suite of Gaussian 09 programs. 41 Since a partial charge transfer (CT) can take place during the photoexcitation of FPs, 42 to account for this problem, we employed a DFT method with long-range corrected B3LYP by using the Coulomb-attenuating method (CAM-B3LYP), 43 which has been proven to perform well in describing H-bonded chains 44 and the CT state.…”

Section: Methodsmentioning

confidence: 99%

Electric field effect on the ground state proton transfer in the H-bonded HBDI complex: an implication of the green fluorescent protein

et al. 2014

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Section: Methodsmentioning

confidence: 99%

Electric field effect on the ground state proton transfer in the H-bonded HBDI complex: an implication of the green fluorescent protein

et al. 2014

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“…In contrast, spectroscopy on wildtype (wt)GFP included infrared pump probe (16), time-resolved fluorescence (17)(18)(19), transient infrared (20,21), and femtosecond Raman spectroscopy (22), as well as computational studies (23)(24)(25), providing a fairly complete picture of the photophysical and photochemical steps leading to green fluorescence (26,27). In the electronic ground state (GS), wtGFP exists as a mixture of neutral chromophore (A, ∼400 nm peak absorbance) and a small population of anionic chromophore (B, ∼475 nm peak Significance Fluorescent proteins (FPs) started their incredible, colorful journey in bioimaging and biomedicine with the extraction and purification of GFP from the Pacific jellyfish Aequorea victoria more than 50 years ago.…”

mentioning

confidence: 99%

Excited-state structural dynamics of a dual-emission calmodulin-green fluorescent protein sensor for calcium ion imaging

Oscar

Liu

Zhao

et al. 2014

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

191

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Fluorescent proteins (FPs) have played a pivotal role in bioimaging and advancing biomedicine. The versatile fluorescence from engineered, genetically encodable FP variants greatly enhances cellular imaging capabilities, which are dictated by excited-state structural dynamics of the embedded chromophore inside the protein pocket. Visualization of the molecular choreography of the photoexcited chromophore requires a spectroscopic technique capable of resolving atomic motions on the intrinsic timescale of femtosecond to picosecond. We use femtosecond stimulated Raman spectroscopy to study the excited-state conformational dynamics of a recently developed FP-calmodulin biosensor, GEM-GECO1, for calcium ion (Ca 2+ ) sensing. This study reveals that, in the absence of Ca 2+ , the dominant skeletal motion is a ∼170 cm −1 phenol-ring in-plane rocking that facilitates excited-state proton transfer (ESPT) with a time constant of ∼30 ps (6 times slower than wild-type GFP) to reach the green fluorescent state. The functional relevance of the motion is corroborated by molecular dynamics simulations. Upon Ca 2+ binding, this in-plane rocking motion diminishes, and blue emission from a trapped photoexcited neutral chromophore dominates because ESPT is inhibited. Fluorescence properties of site-specific protein mutants lend further support to functional roles of key residues including proline 377 in modulating the H-bonding network and fluorescence outcome. These crucial structural dynamics insights will aid rational design in bioengineering to generate versatile, robust, and more sensitive optical sensors to detect Ca 2+ in physiologically relevant environments.calcium-sensing fluorescent protein | femtosecond Raman spectroscopy | fluorescence modulation mechanism | molecular movie G reen fluorescent protein (GFP) first emerged as a revolutionary tool for bioimaging and molecular and cellular biology about 20 years ago (1-3), and the quest to discover and engineer biosensors with improved and expanded functionality has yielded exciting advances. Recently, the color palette of genetically encoded Ca 2+ sensors for optical imaging (the GECO series) has been expanded to include blue, improved green, red intensiometric, and emission ratiometric sensors (4-7). The GECO proteins belong to the GCaMP family of Ca 2+ sensors that are chimeras of a circularly permutated (cp)GFP, calmodulin (CaM), and a peptide derived from myosin light chain kinase (M13) (8). The CaM unit undergoes large-scale structural changes upon Ca 2+ binding as it wraps around M13. These changes, especially at the interfacial region where CaM interacts with cpGFP, allosterically alter the local environment of the tyrosine-derived chromophore and lead to dramatic fluorescence change in the presence of Ca 2+ (9, 10). Because GCaMP and GECO proteins are genetically encodable, show sensitivity to physiologically relevant Ca 2+ concentrations, and respond to Ca 2+ concentration changes rapidly, they have gained increasing popularity for in vivo imaging of Ca 2+ in neur...

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“…I 2 = = -1.0658U 2 3 -0.1179U 2 2 + 10.912U 2 + 151.84 (9) Voltage and current of T6, which is output No. 3 of the circuit, are:…”

Section: Equation Formulationmentioning

confidence: 99%

“…For certain classes of proteins, e.g. photoactive yellow protein (PYP) [8], green fluorescence protein [9], bacteriorhodopsin [10], the problem with signal formation and processing is simpler because these proteins can produce (or at least can be made to produce) a measurable response that can be sensed into the form of a signal.…”

Section: Introductionmentioning

confidence: 99%

Demonstration of protein hydrogen bonding network application to microelectronics

et al. 2014

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Model of hydrogen bonding networks in active site of -lactamase during the last intermediate EY of acylenzyme reaction semicycle is presented. The I-V characteristics of each hydrogen bond are calculated following Marcus theory and theory of protein electrostatics. Simulations showed that HBN characteristics are similar to the characteristics of microelectronic devices such as amplifier, signal modulator, triangular pulse source. The results demonstrated the analogy of HBNs in the active site of β-lactamase protein to microelectronic integrated circuit with multiple outputs each with different characteristics.

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First principle study of proton transfer in the green fluorescent protein (GFP): Ab initio PES in a cluster model

Cited by 9 publications

References 47 publications

Electric field effect on the ground state proton transfer in the H-bonded HBDI complex: an implication of the green fluorescent protein

Electric field effect on the ground state proton transfer in the H-bonded HBDI complex: an implication of the green fluorescent protein

Excited-state structural dynamics of a dual-emission calmodulin-green fluorescent protein sensor for calcium ion imaging

Demonstration of protein hydrogen bonding network application to microelectronics

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