Illuminating the mechanistic roles of enzyme conformational dynamics.

Many enzymes mold their structures to enclose substrates in their active sites such that conformational remodeling may be required during each catalytic cycle. In adenylate kinase (AK), this involves a large-amplitude rearrangement of the enzyme's lid domain. Using our method of high-resolution single-molecule FRET, we directly followed AK's domain movements on its catalytic time scale.

Detection of intensity change points in time-resolved single-molecule measurements.

We present a method for the analysis of optical single molecule emission data that exhibit discrete intensity jumps. This new method uses a generalized likelihood ratio test that determines the location of an intensity change point based on individual photon arrival times. This test is applied recursively to an entire single molecule intensity trajectory, thus finding each change points.

Quantitative single-molecule conformational distributions: a case study with poly-(L-proline).

Precise measurement of the potential of mean force is necessary for a fundamental understanding of the dynamics and chemical reactivity of a biological macromolecule. The unique advantage provided by the recently developed constant-information approach to analyzing time-dependent single-molecule fluorescence measurements was used with maximum entropy deconvolution to create a procedure for the accurate determination of molecular conformational distributions, and analytical expressions for the errors in these distributions were derived. This new method was applied to a derivatized poly(L-proline) series, P(n)CG3K(biotin) (n = 8, 12, 15, 18, and 24), using a modular, server-based single-molecule spectrometer that is capable of registering photon arrival times with a continuous-wave excitation source.

Information bounds and optimal analysis of dynamic single molecule measurements.

Time-resolved single molecule fluorescence measurements may be used to probe the conformational dynamics of biological macromolecules. The best time resolution in such techniques will only be achieved by measuring the arrival times of individual photons at the detector. A general approach to the estimation of molecular parameters based on individual photon arrival times is presented.

Biindanylidenes: role of central bond torsion in nonvertical triplet excitation transfer to the stilbenes.

The stilbenes were proposed to function as nonvertical triplet excitation (NVET) acceptors for energy-deficient donors because rotation about the central bond diminishes the energy gap between ground and triplet energy surfaces. Recently, the role of central bond torsion in facilitating NVET to cis-stilbene (c-St) was questioned because the behavior of 2,3-diphenylnorbornene as a triplet energy acceptor is similar to that of cis-stilbene. On the basis of the assumption that the rigidity of the norbornene skeleton precludes torsional displacement of the phenyl rings in the triplet state, an alternative mechanism was proposed involving phenyl-vinyl torsion as the key reaction coordinate for NVET to c-St.