Energetic basis of excited-state enzyme design and function

2021 ◽  
Author(s):  
Chi-Yun Lin ◽  
Matthew Romei ◽  
Irimpan Mathews ◽  
Steven Boxer
Keyword(s):  
Excited State ◽  
Protein Function ◽  
Fluorescent Protein ◽  
De Novo ◽  
Fitness Landscape ◽  
Quantitative Model ◽  
Efficient Solutions ◽  
Catalyst Design ◽  
Quantum Yields ◽  
Fluorescence Quantum Yields

The last decades have witnessed an explosion of de novo protein designs with a remarkable range of scaffolds. It remains challenging, however, to design catalytic functions that are competitive with naturally occurring counterparts as well as biomimetic or non-biological catalysts. Although directed evolution often offers efficient solutions, the fitness landscape remains opaque. Green fluorescent protein (GFP), which has revolutionized biological imaging and assays, is one of the most re-designed proteins. While not an enzyme in the conventional sense, GFPs feature competing excited-state decay pathways with the same steric and electrostatic origins as conventional ground-state catalysts, and they exert exquisite control over multiple reaction outcomes through the same principles. Thus, GFP is an “excited-state enzyme”. Herein we show that rationally designed mutants and hybrids that contain environmental mutations and substituted chromophores provide the basis for a quantitative model and prediction that describes the influence of sterics and electrostatics on excited-state catalysis of GFPs. As both perturbations can selectively bias photoisomerization pathways, GFPs with fluorescence quantum yields (FQYs) and photoswitching characteristics tailored for specific applications could be predicted and then demonstrated. The underlying energetic landscape, readily accessible via spectroscopy for GFPs, offers an important missing link in the design of protein function that is generalizable to catalyst design.

scholarly journals Energetic basis of excited-state enzyme design and function

2021 ◽  
Author(s):  
Chi-Yun Lin ◽  
Matthew Romei ◽  
Irimpan Mathews ◽  
Steven Boxer
Keyword(s):  
Excited State ◽  
Protein Function ◽  
Fluorescent Protein ◽  
De Novo ◽  
Fitness Landscape ◽  
Quantitative Model ◽  
Efficient Solutions ◽  
Catalyst Design ◽  
Quantum Yields ◽  
Fluorescence Quantum Yields

The last decades have witnessed an explosion of de novo protein designs with a remarkable range of scaffolds. It remains challenging, however, to design catalytic functions that are competitive with naturally occurring counterparts as well as biomimetic or non-biological catalysts. Although directed evolution often offers efficient solutions, the fitness landscape remains opaque. Green fluorescent protein (GFP), which has revolutionized biological imaging and assays, is one of the most re-designed proteins. While not an enzyme in the conventional sense, GFPs feature competing excited-state decay pathways with the same steric and electrostatic origins as conventional ground-state catalysts, and they exert exquisite control over multiple reaction outcomes through the same principles. Thus, GFP is an “excited-state enzyme”. Herein we show that rationally designed mutants and hybrids that contain environmental mutations and substituted chromophores provide the basis for a quantitative model and prediction that describes the influence of sterics and electrostatics on excited-state catalysis of GFPs. As both perturbations can selectively bias photoisomerization pathways, GFPs with fluorescence quantum yields (FQYs) and photoswitching characteristics tailored for specific applications could be predicted and then demonstrated. The underlying energetic landscape, readily accessible via spectroscopy for GFPs, offers an important missing link in the design of protein function that is generalizable to catalyst design.

scholarly journals Visualization of Intracellular Transport of Vesicular Stomatitis Virus Nucleocapsids in Living Cells

2006 ◽  
Vol 80 (13) ◽  
pp. 6368-6377 ◽  
Author(s):  
Subash C. Das ◽  
Debasis Nayak ◽  
You Zhou ◽  
Asit K. Pattnaik
Keyword(s):  
Vesicular Stomatitis Virus ◽  
Protein Function ◽  
Intracellular Transport ◽  
Fluorescent Protein ◽  
De Novo ◽  
Virus Production ◽  
Hinge Region ◽  
Cell Periphery ◽  
P Protein ◽  
Vesicular Stomatitis

ABSTRACT The phosphoprotein (P) of vesicular stomatitis virus (VSV) is a subunit of the viral RNA polymerase. In previous studies, we demonstrated that insertion of 19 amino acids in the hinge region of the protein had no significant effect on P protein function. In the present study, we inserted full-length enhanced green fluorescent protein (eGFP) in frame into the hinge region of P and show that the fusion protein (PeGFP) is functional in viral genome transcription and replication, albeit with reduced activity. A recombinant vesicular stomatitis virus encoding PeGFP in place of the P protein (VSV-PeGFP), which possessed reduced growth kinetics compared to the wild-type VSV, was recovered. Using the recombinant VSV-PeGFP, we show that the viral replication proteins and the de novo-synthesized RNA colocalize to sites throughout the cytoplasm, indicating that replication and transcription are not confined to any particular region of the cytoplasm. Real-time imaging of the cells infected with the eGFP-tagged virus revealed that, following synthesis, the nucleocapsids are transported toward the cell periphery via a microtubule (MT)-mediated process, and the nucleocapsids were seen to be closely associated with mitochondria. Treatment of cells with nocodazole or Colcemid, drugs known to inhibit MT polymerization, resulted in accumulation of the nucleocapsids around the nucleus and also led to inhibition of infectious-virus production. These findings are compatible with a model in which the progeny viral nucleocapsids are transported toward the cell periphery by MT and the transport may be facilitated by mitochondria.

Steric Effects in the Electronic Spectra of the 3,5-Diarylaminobenzene Derivatives

1986 ◽  
Vol 41 (11) ◽  
pp. 1311-1314 ◽  
Author(s):  
A. Balter ◽  
W. Nowak ◽  
P. Milart ◽  
J. Sepioł
Keyword(s):  
Excited State ◽  
Electronic Spectra ◽  
Fluorescence Properties ◽  
Steric Effects ◽  
Quantum Yields ◽  
Spectroscopic Behaviour ◽  
Fluorescence Quantum Yields ◽  
Excited State Lifetimes ◽  
Methyl Phenyl

Absorption and fluorescence properties, excited state lifetimes and fluorescence quantum yields were determined for a series of 3,5-diarylaminobenzene derivatives in solvents of different polarities. The role of the nitrile, methyl, phenyl and naphthyl substituents is discussed. Especially the steric effects on the spectroscopic behaviour of the investigated molecules are studied.

Exceptional Near-Infrared Fluorescence Quantum Yields and Excited-State Absorptivity of Highly Conjugated Porphyrin Arrays

2006 ◽  
Vol 128 (28) ◽  
pp. 9000-9001 ◽  
Author(s):  
Timothy V. Duncan ◽  
Kimihiro Susumu ◽  
Louise E. Sinks ◽  
Michael J. Therien
Keyword(s):  
Excited State ◽  
Near Infrared ◽  
Quantum Yields ◽  
Near Infrared Fluorescence ◽  
Fluorescence Quantum Yields

Excited state acid–base equilibrium of tyrosine

1978 ◽  
Vol 56 (9) ◽  
pp. 1238-1245 ◽  
Author(s):  
David Michael Rayner ◽  
Donald Theodore Krajcarski ◽  
Arthur Gustav Szabo
Keyword(s):  
Excited State ◽  
Proton Transfer ◽  
Quantum Yields ◽  
Acid Base ◽  
Large Shift ◽  
Fluorescence Quantum Yields ◽  
Base Equilibrium ◽  
Tyrosine Fluorescence ◽  
Acid Base Equilibrium ◽  
Buffer Base

Fluorescence attributable to the tyrosinate form of the amino acid tyrosine, previously only observed at pH > pK(S0) = 10.3 where tyrosinate exists in the ground state, has been observed at neutral pH in the presence of high buffer base concentrations. This observation is consistent with the large shift in pK(Sl) predicted from absorption measurements and confirms that proton transfer is indeed a mechanism by which carboxylate ions quench tyrosine fluorescence. The dependence of the fluorescence quantum yields of tyrosine and tyrosinate on pH does not fit a simple excited state acid–base equilibrium model but a more complicated system where carboxylate is also capable of simultaneously quenching tyrosine fluorescence by a mechanism not involving proton transfer. Kinetic analysis of the system allows calculation of pK(S1) = 4.2 for tyrosine. The quantum yield of tyrosinate fluorescence can be appreciably higher than that normally measured at alkaline pH where a separate quenching mechanism must operate. These results have significance in the interpretation of the fluorescence properties of proteins.

The influence of phenylethynyl linkers on the photo-physical properties of metal-free porphyrins

2000 ◽  
Vol 04 (07) ◽  
pp. 669-683 ◽  
Author(s):  
GARY A. BAKER ◽  
FRANK V. BRIGHT ◽  
MICHAEL R. DETTY ◽  
SIDDHARTH PANDEY ◽  
COREY E. STILTS ◽  
...  
Keyword(s):  
Excited State ◽  
Radiative Decay ◽  
Phenyl Group ◽  
Quantum Yields ◽  
Fluorescence Lifetimes ◽  
Strongly Coupled ◽  
Metal Free ◽  
Fluorescence Quantum Yields ◽  
Porphyrin Core ◽  
Absorbance Spectra

Series of 5,10,15,20-tetraarylporphyrins 1 and 5,10,15,20-tetrakis[4-(arylethynyl)phenyl]porphyrins 2 were prepared via condensation of pyrrole with the appropriate benzaldehyde or 4-(arylethynyl)benzaldehyde derivative (3). Condensation of meso-phenyldipyrromethane with mixtures of benzaldehyde and 4-(trimethylsilyl-ethynyl)benzaldehyde gave a separable mixture of mono- (6), bis- (both cis-7 and trans-8) and tris[4-(trimethylsilylethynyl)phenyl]porphyrin (9). Following removal of the trimethylsilyl groups of 6–9, the 4-ethynylphenyl groups of 11–14 were coupled to 1-iodo-3,5-di(trifluoromethyl)benzene with Pd ( OAc )2 to give 15–18 bearing one, two (both cis- and trans-) and three 4-[bis-3,5-(trifluoromethyl)phenylethynyl]phenyl groups respectively. Coupling of 11 and 1-iodo-4-nitrobenzene with Pd ( OAc )2 gave porphyrin 19 with one 4-(4-nitrophenylethynyl)phenyl group. Porphyrin 24 with a p-quinone linked to the porphyrin core via a phenylethynyl group was prepared via similar chemistry. The absorbance spectra, emission maxima, excited-state fluorescence lifetimes, quantum yields of fluorescence, rates of fluorescence and rates of non-radiative decay were measured for each of the porphyrins. Absorbance spectra and emission maxima were nearly identical for all the porphyrins of this study, which suggests that the aryl groups and 4-(arylethynyl)phenyl groups are not strongly coupled to the porphyrin core in these metal-free compounds. Fluorescence quantum yields and rates of radiative decay were larger for porphyrins bearing 4-(arylethynyl)phenyl groups, while excited-state fluorescence lifetimes were somewhat shorter. These effects were additive for each additional 4-(arylethynyl)phenyl group.

scholarly journals Functional Interaction between the pp71 Protein of Human Cytomegalovirus and the PML-Interacting Protein Human Daxx

2002 ◽  
Vol 76 (11) ◽  
pp. 5769-5783 ◽  
Author(s):  
Heike Hofmann ◽  
Hilde Sindre ◽  
Thomas Stamminger
Keyword(s):  
Human Cytomegalovirus ◽  
Protein Function ◽  
Fluorescent Protein ◽  
De Novo ◽  
Human Fibroblasts ◽  
Specific Interaction ◽  
Immediate Early ◽  
Regulatory Function ◽  
Viral Protein Synthesis ◽  
Interacting Protein

ABSTRACT The tegument protein pp71 (UL82) of human cytomegalovirus (HCMV) has previously been shown to transactivate the major immediate-early enhancer-promoter of HCMV. Furthermore, this protein is able to enhance the infectivity of viral DNA and to accelerate the infection cycle, suggesting an important regulatory function during viral replication. To gain insight into the underlying mechanisms that are used by pp71 to exert these pleiotropic effects, we sought for cellular factors interacting with pp71 in a yeast two-hybrid screen. Here, we report the isolation of the human Daxx (hDaxx) protein as a specific interaction partner of HCMV pp71. hDaxx, which was initially described as an adapter protein involved in apoptosis regulation, has recently been identified as a nuclear protein that interacts and colocalizes with PML in the nuclear domain ND10. In order to assess whether pp71 can also be detected in ND10 structures, a vector expressing pp71 in fusion with the green fluorescent protein was used for transfection of human fibroblasts. This revealed a colocalization of pp71 with the ND10 proteins PML and Sp100. In addition, cotransfection of a hDaxx expression vector resulted in an enhanced recruitment of pp71 to ND10. Targeting of pp71 to nuclear dots could also be observed in infected human fibroblasts in the absence of de novo viral protein synthesis. Moreover, cotransfection experiments revealed that pp71-mediated transactivation of the major immediate-early enhancer-promoter was synergistically enhanced in the presence of hDaxx. These results suggest an important role of hDaxx for pp71 protein function.

scholarly journals Toward machine-guided design of proteins

2018 ◽  
Author(s):  
Surojit Biswas ◽  
Gleb Kuznetsov ◽  
Pierce J. Ogden ◽  
Nicholas J. Conway ◽  
Ryan P. Adams ◽  
...  
Keyword(s):  
Directed Evolution ◽  
High Throughput ◽  
Protein Design ◽  
Protein Function ◽  
High Throughput Screening ◽  
Fluorescent Protein ◽  
Fitness Landscape ◽  
Optimization Strategy ◽  
Local Maxima ◽  
Green Fluorescent

AbstractProteins—molecular machines that underpin all biological life—are of significant therapeutic and industrial value. Directed evolution is a high-throughput experimental approach for improving protein function, but has difficulty escaping local maxima in the fitness landscape. Here, we investigate how supervised learning in a closed loop with DNA synthesis and high-throughput screening can be used to improve protein design. Using the green fluorescent protein (GFP) as an illustrative example, we demonstrate the opportunities and challenges of generating training datasets conducive to selecting strongly generalizing models. With prospectively designed wet lab experiments, we then validate that these models can generalize to unseen regions of the fitness landscape, even when constrained to explore combinations of non-trivial mutations. Taken together, this suggests a hybrid optimization strategy for protein design in which a predictive model is used to explore difficult-to-access but promising regions of the fitness landscape that directed evolution can then exploit at scale.

scholarly journals Remarkable Increase of Fluorescence Quantum Efficiency by Cyano Substitution on an ESIPT Molecule 2-(2-Hydroxyphenyl)benzothiazole: A Highly Photoluminescent Liquid Crystal Dopant

Crystals ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 1105
Author(s):  
Tsuneaki Sakurai ◽  
Masaya Kobayashi ◽  
Hiroyuki Yoshida ◽  
Masaki Shimizu
Keyword(s):  
Liquid Crystal ◽  
Excited State ◽  
Solid State ◽  
Room Temperature ◽  
Cyano Group ◽  
Stokes Shift ◽  
Phenyl Group ◽  
Intramolecular Proton Transfer ◽  
Quantum Yields ◽  
Fluorescence Quantum Yields

Fluorescent molecules with excited-state intramolecular proton transfer (ESIPT) character allow the efficient solid-state luminescence with large Stokes shift that is important for various applications, such as organic electronics, photonics, and bio-imaging fields. However, the lower fluorescence quantum yields (ΦFL) in the solution or viscous media, due to their structural relaxations in the excited state to reach the S0/S1 conical intersection, shackle further applications of ESIPT-active luminophores. Here we report that the introduction of a cyano group (-CN) into the phenyl group of 2-(2-hydroxyphenyl)benzothiazole (HBT), a representative ESIPT compound, remarkably increase its fluorescence quantum yield (ΦFL) from 0.01 (without -CN) to 0.49 (with -CN) in CH2Cl2, without disturbing its high ΦFL (=0.52) in the solid state. The large increase of the solution-state ΦFL of the cyano-substituted HBT (CN-HBT) is remarkable, comparing with our previously reported ΦFL values of 0.05 (with 4-pentylphenyl), 0.07 (with 1-hexynyl), and 0.15 (with 4-pentylphenylethynyl). Of interest, the newly-synthesized compound, CN-HBT, is miscible in a conventional room-temperature nematic liquid crystal (LC), 4-pentyl-4′-cyano biphenyl (5CB), up to 1 wt% (~1 mol%), and exhibits a large ΦFL of 0.57 in the viscous LC medium. A similar ΦFL value of ΦFL = 0.53 was also recorded in another room-temperature LC, trans-4-(4-pentylcyclohexyl)benzonitrile (PCH5), with a doping ratio of 0.5 wt% (~0.5 mol%). These 5CB/CN-HBT and PCH5/CN-HBT mixtures serve as light-emitting room-temperature LCs, and show anisotropic fluorescence with the dichroic ratio of 3.1 upon polarized excitation, as well as electric field response of luminescence intensity changes.

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