Design and Synthesis of Photochemically Controllable Restriction EndonucleaseBamHI by Manipulating the Salt-Bridge Network in the Dimer Interface

Recent Advances in Protein Caging Tools for Protein Photoactivation

In biosciences and biotechnologies, it is recently critical to promote research regarding the regulation of the dynamic functions of proteins of interest. Light-induced control of protein activity is a strong tool for a wide variety of applications because light can be spatiotemporally irradiated in high resolutions. Therefore, synthetic, semi-synthetic, and genetic engineering techniques for photoactivation of proteins have been actively developed. In this review, the conventional approaches will be outlined. As a solution for overcoming barriers in conventional ones, our recent approaches in which proteins were chemically modified with biotinylated caging reagents are introduced to photo-activate a variety of proteins without genetic engineering and elaborate optimization. This review mainly focuses on protein caging and describes the concepts underlying the development of reported approaches that can contribute to the emergence of both novel protein photo-regulating methods and their killer applications.

A simple and general approach to generate photoactivatable DNA processing enzymes

DNA processing enzymes, such as DNA polymerases and endonucleases, have found many applications in biotechnology, molecular diagnostics, and synthetic biology, among others. The development of enzymes with controllable activity, such as hot-start or light-activatable versions, has boosted their applications and improved the sensitivity and specificity of the existing ones. However, current approaches to produce controllable enzymes are experimentally demanding to develop and case-specific. Here, we introduce a simple and general method to design light-start DNA processing enzymes. In order to prove its versatility, we applied our method to three DNA polymerases commonly used in biotechnology, including the Phi29 (mesophilic), Taq, and Pfu polymerases, and one restriction enzyme. Light-start enzymes showed suppressed polymerase, exonuclease, and endonuclease activity until they were re-activated by an UV pulse. Finally, we applied our enzymes to common molecular biology assays and showed comparable performance to commercial hot-start enzymes.

Stimulus-Responsive Regulation of Enzyme Activity for One-Step and Multi-Step Syntheses

Multi-step biocatalytic reactions have gained increasing importance in recent years because the combination of different enzymes enables the synthesis of a broad variety of industrially relevant products. However, the more enzymes combined, the more crucial it is to avoid cross-reactivity in these cascade reactions and thus achieve high product yields and high purities. The selective control of enzyme activity, i.e., remote on-/off-switching of enzymes, might be a suitable tool to avoid the formation of unwanted by-products in multi-enzyme reactions. This review compiles a range of methods that are known to modulate enzyme activity in a stimulus-responsive manner. It focuses predominantly on in vitro systems and is subdivided into reversible and irreversible enzyme activity control. Furthermore, a discussion section provides indications as to which factors should be considered when designing and choosing activity control systems for biocatalysis. Finally, an outlook is given regarding the future prospects of the field.

Catalytic activity control of restriction endonuclease--triplex forming oligonucleotide conjugates

Targeting of individual genes in complex genomes requires endonucleases of extremely high specificity. To direct cleavage at the unique site(s) in the genome, both naturally occurring and artificial enzymes have been developed. These include homing endonucleases, zinc-finger nucleases, transcription activator-like effector nucleases, and restriction or chemical nucleases coupled to a triple-helix forming oligonucleotide (TFO). The desired cleavage has been demonstrated both in vivo and in vitro for several model systems. However, to limit cleavage strictly to unique sites and avoid undesired reactions, endonucleases with controlled activity are highly desirable. In this study we present a proof-of-concept demonstration of two strategies to generate restriction endonuclease-TFO conjugates with controllable activity. First, we combined the restriction endonuclease caging and TFO coupling procedures to produce a caged MunI-TFO conjugate, which can be activated by UV-light upon formation of a triple helix. Second, we coupled TFO to a subunit interface mutant of restriction endonuclease Bse634I which shows no activity due to impaired dimerization but is assembled into an active dimer when two Bse634I monomers are brought into close proximity by triple helix formation at the targeted site. Our results push the restriction endonuclease-TFO conjugate technology one step closer to potential in vivo applications.

Restriction endonuclease SsoII with photoregulated activity--a "molecular gate" approach

A novel method for regulating the activity of homodimeric proteins--"molecular gate" approach--was proposed and its usefulness illustrated for the type II restriction endonuclease SsoII (R.SsoII) as a model. The "molecular gate" approach is based on the modification of R.SsoII with azobenzene derivatives, which allows regulating DNA binding and cleavage via illumination with light. R.SsoII variants with single cysteine residues introduced at selected positions were obtained and modified with maleimidoazobenzene derivatives. A twofold change in the enzymatic activity after illumination with light of wavelengths of 365 and 470 nm, respectively, was demonstrated when one or two molecules of azobenzene derivatives were attached to the R.SsoII at the entrance of or within the DNA-binding site.

Photocaged variants of the MunI and PvuII restriction enzymes

Regulation of proteins by light is a new and promising strategy for the external control of biological processes. In this study, we demonstrate the ability to regulate the catalytic activity of the MunI and PvuII restriction endonucleases with light. We used two different approaches to attach a photoremovable caging compound, 2-nitrobenzyl bromide (NBB), to functionally important regions of the two enzymes. First, we covalently attached a caging molecule at the dimer interface of MunI to generate an inactive monomer. Second, we attached NBB at the DNA binding site of the single-chain variant of PvuII (scPvuII) to prevent binding and cleavage of the DNA substrate. Upon removal of the caging group by UV irradiation, nearly 50% of the catalytic activity of MunI and 80% of the catalytic activity of PvuII could be restored.

Illuminating the chemistry of life: design, synthesis, and applications of "caged" and related photoresponsive compounds

Biological systems are characterized by a level of spatial and temporal organization that often lies beyond the grasp of present day methods. Light-modulated bioreagents, including analogs of low molecular weight compounds, peptides, proteins, and nucleic acids, represent a compelling strategy to probe, perturb, or sample biological phenomena with the requisite control to address many of these organizational complexities. Although this technology has created considerable excitement in the chemical community, its application to biological questions has been relatively limited. We describe the challenges associated with the design, synthesis, and use of light-responsive bioreagents; the scope and limitations associated with the instrumentation required for their application; and recent chemical and biological advances in this field.

Spatial control of protein binding on lipid bimembrane using photoeliminative linker

Protein adsorption and dissociation on cell membrane surfaces is a topic of important study to reveal biological processes including signal transduction and protein trafficking. We demonstrated here the establishment of a mimic model system for the spatial control of protein adsorption/elimination on a lipid bimembrane using a photochemical technique. The novel photoeliminative linker that we synthesized here consists of three distinct components: a substrate (biotin), a photoeliminative group (4-(4-(1-hydroxyethyl)-2-methoxy-5-nitrophenoxy)butanoic acid), and a lipid bimembrane-adsorbent group (farnesyl). The photoeliminative linker was inserted on the entire surface of the lipid bimembrane and two-dimensionally eliminated by spatial UV irradiation onto the membrane to create a biotin pattern. A target protein, streptavidin was selectively immobilized on the patterned biotin, although it was almost not attached on the nonirradiated region. The streptavidin array was selectively dissociated by UV irradiation onto the entire membrane.

Protein recording material: photorecord/erasable protein array using a UV-eliminative linker

Protein patterning on solid surfaces is a topic of significant importance in the fields of biosensors, diagnostic assays, cell adhesion technologies, and biochip microarrays. In this letter, we have established a novel, rapid method for the fabrication of a "protein recording material", which enables us to spatiotemporally regulate the recording, reading, and erasing of a fluorescent protein array as information by a photochemical technique. A photolinker that we synthesized here was used to control the protein array spatiotemporally. The recording process was almost completed after 1 min of photoirradiation to read a clear pattern consisting of a specific protein-ligand complex with high spatiotemporal resolution. The erasing of the protein array was then achieved by photoirradiation onto the entire patterned surface.

Molecular tools for cell and systems biology

The sequencing of the genomes of key organisms and the subsequent identification of genes merely leads us to the next real challenge in modern biology-revealing the precise functions of these genes. Further, detailed knowledge of how the products of these genes behave in space and time is required, including their interactions with other molecules. In order to tackle these considerable tasks, a large and continuously expanding toolbox is required to probe the functions of proteins on a cellular level. Here, the currently available tools are described and future developments are projected. There is no doubt that only the close interplay between the life science disciplines in addition to advances in engineering will be able to meet the challenge.

Biologically active molecules with a "light switch"

Biologically active compounds which are light-responsive offer experimental possibilities which are otherwise very difficult to achieve. Since light can be manipulated very precisely, for example, with lasers and microscopes rapid jumps in concentration of the active form of molecules are possible with exact control of the area, time, and dosage. The development of such strategies started in the 1970s. This review summarizes new developments of the last five years and deals with "small molecules", proteins, and nucleic acids which can either be irreversibly activated with light (these compounds are referred to as "caged compounds") or reversibly switched between an active and an inactive state.

Reversible inactivation of the CG specific SssI DNA (cytosine-C5)-methyltransferase with a photocleavable protecting group

Caging of proteins by conjugation with a photocleavable group is a powerful approach for reversibly blocking enzymatic activity. Here we describe the covalent modification of the bacterial SssI DNA methyltransferase (M.SssI) with the cysteine-specific reagent 4,5-dimethoxy-2-nitrobenzylbromide (DMNBB). M.SssI contains two cysteine residues; replacement of the active-site Cys141 with Ser resulted in an approximately 100-fold loss of enzymatic activity; this indicates an important role for this residue in catalysis. However, replacement of Cys368 with Ala did not affect methyltransferase activity. Treatment of the Cys368Ala mutant enzyme with DMNBB led to an almost complete loss of activity. Irradiation of the inactivated enzyme with near-ultraviolet light (320-400 nm) restored 60 % of the catalytic activity. This indicates that caging by DMNBB can be used for the reversible inactivation of M.SssI.

Monitoring of three distinct structures of restriction enzyme complexes using characteristic fluorescence from site-selectively incorporated solvatochromic probe

The local change in the three different structures of restriction enzyme BamHI, which include DNA-free dimer and non-specific and specific complexes with DNA, were detected by the fluorescence from a site-selectively introduced solvatochromic fluorophore Nbeta-L-alanyl-5-(N,N-dimethylamino)naphthalene-1-sulfonamide (DanAla). According to the crystal structure, alpha-helices of the non-specific complex containing Ile82, Glu86 and Trp206 residues are converted into random coil by the formation of specific complex with a substrate. To understand the microenvironmental change caused by the structural transition around these positions, the DanAla probe was site-specifically introduced into the positions, and steady-state and time-resolved fluorescence was observed. The steady-state fluorescence gave us information that the rigidity of the polypeptide chains would be enhanced by the formation of the specific complex. The time-resolved fluorescence supported that the change in a water molecule-accessible space was induced by DNA-binding. We revealed that the change in rigidity and solvation around the specific positions was detected by the characteristic fluorescence using the combination of steady-state and time-resolved fluorescence techniques.

Detection of the Local Structural Changes in the Dimer Interface of BamHI Initiated by DNA Binding and Dissociation Using a Solvatochromic Fluorophore

To detect the local structural change in an interface between proteins induced by the substrate binding and dissociation, a solvatochromic fluorescent N(beta)-L-alanyl-5-(N,N-dimethylamino)-naphthalene-1-sulfonamide (DanAla) was introduced into 132 position of the dimer interface in BamHI. Before addition of the substrate, the fluorescence from the normal planer excited state of DanAla moiety was observed as a main emission, and thereby the DanAla in the dimer interface is located in the hydrophobic microenvironment. The incubation with the substrate for 20 min induced the gradual increase in fluorescence intensity around 430 nm. The fact reflects that the polarity is reduced by the slight structural change initiated by the formation of the complex with the substrate. Furthermore, the incubation for more than 20 min caused the slight decrease in fluorescence around 430 nm and an appearance of fluorescence (560 nm) due to twisted intramolecular charge transfer (TICT) excited state. Therefore, the DanAla is exposed to comparative polar environment after the dissociation of the substrate. The fluorescence lifetime as a minor component, which is attributed to the TICT excited state, was reduced by addition of the substrate. The results provide that the hydrophobicity in the dimer interface is increased by the substrate binding. Interestingly, we found that the structure of an initial form is different from that of a refolded form after the dissociation of the substrate using a spectral subtraction technique. We have achieved detection of the changing structure induced by the substrate binding and dissociation using a steady-state and time-resolved fluorescence.

A simple procedure for the photoregulation of chymotrypsin activity

A convenient and rapid method for the photo-regulation of the proteolytic enzyme alpha-chymotrypsin is described. When alpha-chymotrypsin is coated with photolytic 1-(2-nitrophenyl)ethanol residues this not only markedly reduces the capability of the enzyme to digest both of the small substrates N-benzoyl-L-tyrosine ethyl ester and N-succinyl-L-phenylalanine p-nitroanilide, but also completely inhibits the enzyme's proteolytic activity. The inactivated alpha-chymotrypsin can then be reactivated under physiological conditions, when and where it is required, by exposure to UV-A light. These results further demonstrate that 1-(2-nitrophenyl)ethanol coated proteins can often be used as light sensitive biological switches as a simple alternative to site directed procedures.

The preparation and in vivo applications of caged peptides and proteins

Cellular behavior, such as mitosis and motility, are controlled by both when and where specific intracellular signaling pathways are activated in response to environmental cues. Analogous temporally and spatially controlled events occur throughout the lifetime of an organism (e.g. embryogenesis). Consequently, reagents that can be switched on (or off) at any time or at any place in a cell, a tissue, or a living animal, represent the means by which the biochemical basis of spatially and temporally sensitive biological behavior can be evaluated. This review summarizes recent advances in the design and synthesis of light-activated ('caged') peptides and proteins as well as the application of these caged reagents to unanswered questions in biology.

A Hydrophilic Azobenzene-Bearing Amino Acid for Photochemical Control of a Restriction Enzyme BamHI

A novel hydrophilic and negatively charged azobenzene-bearing amino acid, 4'-carboxyphenylazophenylalanine (azoAla 1), has been designed and synthesized for investigation of the photochemical regulation of the enzyme activity. The properties of photoisomerization and thermal stability of the cis-isomer were similar to those of a commonly used phenylazophenylalanine (azoAla 2). For photochemical control of the enzyme, these two azobenzene-bearing amino acids were incorporated into the specific position at the dimer interface of a restriction enzyme BamHI. These trans-azobenzene derivatives in the BamHI suppressed the enzymatic activity, and the following photoirradiation at 366 nm induced the recovery of its activity. Although the activities of both azoAla-BamHI mutants were same level after a long time irradiation, the recovery of the activity of azoAla 1-BamHI was faster than that of azoAla 2-BamHI with a short time irradiation. This result suggests that the negatively charged carboxylate group introduced into an azobenzene moiety affects the behavior of azoAla in the protein scaffold during the trans-cis photoisomerization.