Site-to-site diffusion in proteins as observed by energy transfer and frequency-domain fluorometry

An improved fluorescent noncanonical amino acid for measuring conformational distributions using time-resolved transition metal ion FRET

With the recent explosion in high-resolution protein structures, one of the next frontiers in biology is elucidating the mechanisms by which conformational rearrangements in proteins are regulated to meet the needs of cells under changing conditions. Rigorously measuring protein energetics and dynamics requires the development of new methods that can resolve structural heterogeneity and conformational distributions. We have previously developed steady-state transition metal ion fluorescence resonance energy transfer (tmFRET) approaches using a fluorescent noncanonical amino acid donor (Anap) and transition metal ion acceptor to probe conformational rearrangements in soluble and membrane proteins. Here, we show that the fluorescent noncanonical amino acid Acd has superior photophysical properties that extend its utility as a donor for tmFRET. Using maltose-binding protein (MBP) expressed in mammalian cells as a model system, we show that Acd is comparable to Anap in steady-state tmFRET experiments and that its long, single-exponential lifetime is better suited for probing conformational distributions using time-resolved FRET. These experiments reveal differences in heterogeneity in the apo and holo conformational states of MBP and produce accurate quantification of the distributions among apo and holo conformational states at subsaturating maltose concentrations. Our new approach using Acd for time-resolved tmFRET sets the stage for measuring the energetics of conformational rearrangements in soluble and membrane proteins in near-native conditions.

Short-distance probes for protein backbone structure based on energy transfer between bimane and transition metal ions

The structure and dynamics of proteins underlies the workings of virtually every biological process. Existing biophysical methods are inadequate to measure protein structure at atomic resolution, on a rapid time scale, with limited amounts of protein, and in the context of a cell or membrane. FRET can measure distances between two probes, but depends on the orientation of the probes and typically works only over long distances comparable with the size of many proteins. Also, common probes used for FRET can be large and have long, flexible attachment linkers that position dyes far from the protein backbone. Here, we improve and extend a fluorescence method called transition metal ion FRET that uses energy transfer to transition metal ions as a reporter of short-range distances in proteins with little orientation dependence. This method uses a very small cysteine-reactive dye monobromobimane, with virtually no linker, and various transition metal ions bound close to the peptide backbone as the acceptor. We show that, unlike larger fluorophores and longer linkers, this donor-acceptor pair accurately reports short-range distances and changes in backbone distances. We further extend the method by using cysteine-reactive metal chelators, which allow the technique to be used in protein regions of unknown secondary structure or when native metal ion binding sites are present. This improved method overcomes several of the key limitations of classical FRET for intramolecular distance measurements.

Förster energy transfer from nonexponentially decaying donors

Necessary modifications to the expression for the Förster energy transfer rate are discussed when fluorescence decay of the donor in the absence of acceptor is nonexponential. Discrete and continuous models of the nonexponentiality are taken into account. No general solution of the problem is found. It is, however, suggested that in many of the biochemical problems the most appropriate modification of the transfer rate can be that which is based on the assumption of the same constant value of the radiative decay rate for all donor molecules. The effect of the assumed form of the Förster energy transfer rate on the recovered values of the distance distribution and dynamics parameters of some exemplary bichromophoric systems is examined.

Site-to-site distance distribution in flexible molecules: theoretical evaluation of the donor and/or acceptor fluorescence decay function

We present the theoretical expression describing dependence of the fluorescence intensity decays on the distance distribution P(r)between energy donors and acceptors in flexible bichromophoric molecules. The expression allows for multiexponential fluorescence decay of the donor- and acceptor-only molecules and takes into account the possibility of incomplete labeling of the molecules by acceptors. It is assumed that the donors and acceptors are static in space and do not move relative to each other during the excited-state lifetime. The potential application of the obtained expression is evaluation of the parameters of the function P(r).

DNA dynamics: a fluorescence resonance energy transfer study using a long-lifetime metal-ligand complex

Fluorescent probes bound to DNA typically display nanosecond decay times and reveal only nanosecond motions. We extend the time range of measurable DNA dynamics using [Ru(bpy)2(dppz)]2+ (bpy=2,2'-bipyridine, dppz=dipyrido[3,2-a:2',3'-c]phenazine) (RuBD) which displays a mean lifetime near 90 ns. To test the usefulness of RuBD as a probe for diffusive processes in calf thymus DNA, we compared the efficiencies of fluorescence resonance energy transfer (FRET) using three donors which display lifetimes near 5 ns for acridine orange (AO), 22 ns for ethidium bromide (EB) and 92 ns for RuBD, with nile blue (NB) as the acceptor. The Forster distances for AO-NB, EB-NB and RuBD-NB donor-acceptor pairs were 42.3, 52.3, and 30.6 A, respectively. All three donors showed dramatic decreases in fluorescence intensities and more rapid intensity decays with increasing NB concentrations. The intensity decays of AO and EB in the presence of varying concentrations of NB were satisfactorily described by the one-dimensional FRET model without diffusion (Blumen and Manz, 1979). In the case of the long-lifetime donor RuBD, the experimental phase and modulation somewhat deviated from the recovered values computed from this model. The recovered NB concentrations and FRET efficiencies from the model were slightly larger than the expected values, however, the recovered and expected values did not show a significant difference. Thus, it is suggested that the lifetime of RuBD is too short to measure diffusive processes in calf thymus DNA.

Calcium-induced flexibility changes in the troponin C-troponin I complex

The contraction of vertebrate striated muscle is modulated by Ca(2+) binding to the regulatory protein troponin C (TnC). Ca(2+) binding causes conformational changes in TnC which alter its interaction with the inhibitory protein troponin I (TnI), initiating the regulatory process. We have used the frequency domain method of fluorescence resonance energy transfer (FRET) to measure distances and distance distributions between specific sites in the TnC-TnI complex in the presence and absence of Ca(2+) or Mg(2+). Using sequences based on rabbit skeletal muscle proteins, we prepared functional, binary complexes of wild-type TnC and a TnI mutant which contains no Cys residues and a single Trp residue at position 106 within the TnI inhibitory region. We used TnI Trp-106 as the FRET donor, and we introduced energy acceptor groups into TnC by labeling at Met-25 with dansyl aziridine or at Cys-98 with N-(iodoacetyl)-N'-(1-sulfo-5-naphthyl)ethylenediamine. Our distance distribution measurements indicate that the TnC-TnI complex is relatively rigid in the absence of Ca(2+), but becomes much more flexible when Ca(2+) binds to regulatory sites in TnC. This increased flexibility may be propagated to the whole thin filament, helping to release the inhibition of actomyosin ATPase activity and allowing the muscle to contract. This is the first report of distance distributions between TnC and TnI in their binary complex.

End-to-end diffusion on the microsecond timescale measured with resonance energy transfer from a long-lifetime rhenium metal-ligand complex

We measured the end-to-end diffusion coefficient of an alkyl chain-linked donor-acceptor pair using the time-resolved frequency-domain decay of the donor. The donor was a rhenium metal-ligand complex with a mean decay time ranging from 2.1 to 7.9 microseconds in the absence of the Texas red acceptor. The decay time was used to measure the donor-to-acceptor distance distribution and the mutual diffusion coefficient. Using this long lifetime donor, it was easily possible to determine a diffusion coefficient near 2 x 10(-8) cm2/s and diffusion coefficients as low as 1.3 x 10(-9) cm2/s were measurable. Such long lifetime donors should be valuable for measuring the flexing of peptides on the microsecond timescale, domain motions of proteins and lateral diffusion in membranes. The availability of microsecond decay time luminophores now allows luminescence spectroscopy to be useful generally for studies of microsecond dynamics of biological macromolecules.

Long-lifetime Ru(II) complexes as labeling reagents for sulfhydryl groups

We report the synthesis and spectral properties of two long-lifetime highly luminescent Ru(II) complexes containing either a sulfhydryl reactive iodoacetamido group or a less reactive choloroacetamido group, [Ru(bpy)2(5-iodoacetamido-1,10-phenanthroline)] (PF6)2 and [Ru(bpy)2(5-chloroacetamido-1,10-phenanthroline)](PF6) 2, respectively, where bpy is 2,2'-bipyridine. Ru(bpy)2(phen-IA)](PF6)2 was covalently linked to human serum albumin (HSA) and human immunoglobulin G (IgG). The photoluminescence lifetime of protein-bound probes approaches 1 microsecond under ambient conditions. In the absence of rotational motions, this probe displayed an anisotropy of 0.18 for excitation at 472 nm. Anisotropy decay data were used to determine the overall rotational correlation times of HSA and IgG. These long-lifetime sulfhydryl-reactive probes can be used to recover microsecond rotational motions and/or domain motions of proteins and/or macromolecular complexes.

Synthesis and spectral characterization of a thiol-reactive long-lifetime Ru(II) complex

We report the synthesis and spectral properties of a long-lifetime luminescent Ru complex containing a sulfhydryl-reactive maleimide group, [Ru (2,2'-bipyridine)2(1, 10-phenanthroline-5-maleimide)](PF6)2. [Ru(bpy)2(phen-mi)]2+ was covalently linked to human serum albumin, immunoglobulin G, and beta-galactosidase. The lifetimes for probe bound to proteins were near 1.1 micros. In the absence of rotational motions, the probe displayed an anisotropy near 0.17 for excitation near 475 nm. Anisotropy decay data were used to determine rotational correlation times of the proteins, which showed local probe motions in addition to overall rotational diffusion. This long-lifetime sulfhydryl-reactive probe can be used to recover microsecond rotational motions and/or domain motions of proteins and/or macromolecular complexes.

Long-Lifetime Metal-Ligand Complexes as Luminescent Probes for DNA. J Fluoresc 1997;7:107-112. [PMID: 31903017 DOI: 10.1007/bf02760501]

We examined the intensity and anisotropy decays of DNA labeled with two ruthenium metal-ligand complexes, [Ru(bpy)₂(dppz)]²⁺ and [Ru(phe)₂(dppz)]²⁺. Both complexes display high emission anisotropies in the absence of rotational diffusion, making them suitable probes for rotational motions. When bound to DNA, these complexes display decay times as long as 294 ns, providing long-lived probes of DNA dynamics. The decay times of both complexes were rather insensitive to dissolved oxygen. We examined anisotropy decays of these complexes bound to B-form DNA. The anisotropy decays revealed correlation times near 10, 50, and several hundred nanoseconds, suggesting that these probes are sensitive to a wide range of DNA motions. The use of metal-ligand complexes should allow resolution of both the torsional and bending motions of DNA, the latter of which has been mostly inaccessible using shorter-lived fluorescent probes bound to DNA.

Calcium-induced troponin flexibility revealed by distance distribution measurements between engineered sites

The contraction of vertebrate striated muscle is regulated by Ca2+ binding to troponin C (TnC). This causes conformational changes which alter the interaction of TnC with the inhibitory protein TnI and the tropomyosin-binding protein TnT. We have used the frequency domain method of fluorescence resonance energy transfer to measure TnT-TnC and TnT-TnI distances and distance distributions, in the presence of Ca2+, Mg2+, or EGTA, in TnC.TnI.TnT complexes. We reconstituted functional, ternary troponin complexes using the following recombinant subunits whose sequences were based on those of rabbit skeletal muscle: wild-type TnC; TnT25, a mutant C-terminal 25-kDa fragment of TnT containing a single Trp212 which was used as the sole donor for fluorescence energy transfer measurements; Trp-less TnI mutants which contained either no Cys or a single Cys at position 9, 96, or 117. Energy acceptor groups were introduced into TnC or TnI by labeling with dansyl aziridine or N-(iodoacetyl)-N'-(1-sulfo-5-naphthyl)ethylenediamine. Our results indicate that the troponin complex is relatively rigid in relaxed muscle, but becomes much more flexible when Ca2+ binds to regulatory sites in TnC. This increased flexibility may be propagated to the whole thin filament, releasing the inhibition of actomyosin ATPase activity and allowing the muscle to contract. This is the first report of distance distribution measurements between troponin subunits.

Metal-ligand complexes as a new class of long-lived fluorophores for protein hydrodynamics

We describe the use of asymmetric Ru-ligand complexes as a new class of luminescent probes that can be used to measure rotational motions of proteins. These complexes are known to display luminescent lifetimes ranging from 10 to 4000 ns. In this report, we show that the asymmetric complex Ru(bpy)2(dcbpy) (PF6)2 displays a high anisotropy value when excited in the long wavelength absorption band. For covalent linkage to proteins, we synthesized the N-hydroxy succinimide ester of this metal-ligand complex. To illustrate the usefulness of these probes, we describe the intensity and anisotropy decays of [Ru(bpy)2(dcbpy)] when covalently linked to human serum albumin, concanavalin A (ConA), human immunoglobulin G (IgG), and Ferritin, and measured in solutions of increased viscosity. These data demonstrate that the probes can be used to measure rotational motions on the 10 ns to 1.5 microseconds timescale, which so far has been inaccessible using luminescence methods. The present probe [Ru(bpy)2(dcbpy)] can be regarded as the first of a class of metal-ligand complexes, each with different chemical reactivity and spectral properties, for studies of macromolecular dynamics.

Distribution of distances between the tryptophan and the N-terminal residue of melittin in its complex with calmodulin, troponin C, and phospholipids

We used frequency-domain measurements of fluorescence resonance energy transfer to measure the distribution of distances between Trp-19 of melittin and a 1-dimethylamino-5-sulfonylnaphthalene (dansyl) residue on the N-terminal-alpha-amino group. Distance distributions were obtained for melittin free in solution and when complexed with calmodulin (CaM), troponin C (TnC), or palmitoyloleoyl-L-alpha-phosphatidylcholine (POPC) vesicles. A wide range of donor (Trp-19)-to-acceptor (dansyl) distances was found for free melittin, which is consistent with that expected for the random coil state, characterized by a Gaussian width (full width at half maxima) of 28.2 A. In contrast, narrow distance distributions were found for melittin complexed with CaM, 8.2 A, or with POPC vesicles, 4.9 A. A somewhat wider distribution was found for the melittin complex with TnC, 12.8 A, suggesting the presence of heterogeneity in the mode of binding between melittin and TnC. For all the complexes the mean Trp-19 to dansyl distance was near 20 A. This value is somewhat smaller than expected for the free alpha-helical state of melittin, suggesting that binding with CaM or TnC results in a modest decrease in the length of the melittin molecule.