RESUMEN

Protein surfaces have pivotal roles in interactions between proteins and other biological molecules. However, the structural dynamics of protein surfaces have rarely been explored and are poorly understood. Here, the surface of a single-stranded DNA (ssDNA) binding protein (SSB) with four DNA binding domains that bind ssDNA in binding site sizes of 35, 56, and 65 nucleotides per tetramer is investigated. Using oligonucleotides as probes to sense the charged surface, NaCl induces a two-state structural transition on the SSB surface even at moderate concentrations. Chelation of sodium ions with charged amino acids alters the network of hydrogen bonds and/or salt bridges on the surface. Such changes are associated with changes in the electrostatic potential landscape and interaction mode. These findings advance the understanding of the molecular mechanism underlying the enigmatic salt-induced transitions between different DNA binding site sizes of SSBs. This work demonstrates that monovalent salt is a key regulator of biomolecular interactions that not only play roles in non-specific electrostatic screening effects as usually assumed but also may configure the surface of proteins to contribute to the effective regulation of biomolecular recognition and other downstream events.

RESUMEN

Doppler-free spectroscopy of 40Ca+ on the transition 3D3/2 → 4P1/2 known as the frequency standard for repumping beam of Calcium ion trap was performed by means of optogalvanic detection. This reference signal was applied to measure the frequency stability of laser locked to the resonance of an ultra-low expansion (ULE) glass made cavity. Lamb dip spectrum fitting of this Calcium ion spectra revealed that the long-term drift of our laser system is below 2 MHz per hour. A simple setup for frequency locking of dual colour of lasers at 866 nm and 780 nm was also demonstrated. Consistencies of the frequency difference between these two lasers were measured less than 2 MHz in a hour after stabilizing both lasers to the cavity.

RESUMEN

We demonstrate a tunable external cavity tapered amplifier laser (ECTAL) using a narrowband interference filter as the wavelength discriminator. The laser is tunable over a wavelength range from 1006 to 1031 nm with an output power of ∼1 W. The amplified stimulated emission of the laser system is suppressed to better than 32 dB. The laser is applied to study the saturation spectroscopy on the R(39) 57-0 line of iodine molecule, which, to our best knowledge, is the first measurement of this line close to the dissociation limit. The linewidth of the a1 component is ∼2 MHz at the iodine vapor pressure of ∼11 Pa, and the pressure-broadening coefficient is ∼156 kHz/Pa. This laser system is also used for the injection seeding of a 1030 nm disk laser to perform hyperfine spectroscopy of muonic hydrogen. To reach a satisfactory condition for disk laser use, the ECTAL is successfully stabilized to the iodine Doppler-free spectroscopy of the P(26) 43-0 line near 515 nm, with continuous locking over 48 h.

RESUMEN

Given the importance of peptide-mediated protein interactions in cellular processes, protein-peptide docking has received increasing attention. Here, we have developed a Hierarchical flexible Peptide Docking approach through fast generation and ensemble docking of peptide conformations, which is referred to as HPepDock. Tested on the LEADS-PEP benchmark data set of 53 diverse complexes with peptides of 3-12 residues, HPepDock performed significantly better than the 11 docking protocols of five small-molecule docking programs (DOCK, AutoDock, AutoDock Vina, Surflex, and GOLD) in predicting near-native binding conformations. HPepDock was also evaluated on the 19 bound/unbound and 10 unbound/unbound protein-peptide complexes of the Glide SP-PEP benchmark and showed an overall better performance than Glide SP-PEP+MM-GBSA and FlexPepDock in both bound and unbound docking. HPepDock is computationally efficient, and the average running time for docking a peptide is ∼15 min with the range from about 1 min for short peptides to around 40 min for long peptides.

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RESUMEN

We report absolute frequency measurements of molecular iodine P(46) 5-4 a1, a10, and a15 hyperfine transitions at 647 nm with a fiber-based frequency comb. The light source is based on a Littrow-type external-cavity diode laser. A frequency stability of 5×10-12 at a 200 s integration time is achieved when the light source is stabilized to the P(46) 5-4 a15 line. The pressure shift is determined to be -8.3(7) kHz/Pa. Our determination of the line centers reached a precision of 21 kHz. The light source can serve as a reference laser for lithium spectroscopy (2S→3P).

RESUMEN

In our previous work on the Lamb-dips of the ν2 fundamental band transitions of H3+, the saturated absorption spectrum was obtained by third-derivative spectroscopy using frequency modulation with an optical parametric oscillator (OPO). However, frequency modulation also caused errors in the absolute frequency determination. To solve this problem, we built a tunable offset locking system to lock the pump frequency of the OPO to an iodine-stabilized Nd:YAG laser. With this improvement, we were able to scan the OPO idler frequency precisely and obtain the saturated absorption profile using intensity modulation. Furthermore, ion concentration modulation was employed to subtract the background noise and increase the signal-to-noise ratio. To determine the absolute frequency of the idler wave, the OPO signal frequency was locked to an optical frequency comb. The absolute frequency accuracy of our spectrometer was better than 7 kHz, demonstrated by measuring the wavelength standard transition of methane at 3.39 µm. Finally, we measured 16 transitions of H3+ and our results agree very well with other precision measurements. This work successfully resolved the discrepancies between our previous measurements and other precision measurements.

RESUMEN

We report a precision frequency measurement of the (4)He 2(1)S(0)→2(1)P(1) transition at 2058 nm. The saturated absorption spectroscopy is performed in a rf discharge sealed-off cell with a volume Bragg grating-based Tm:Ho:YLF laser. The absolute transition frequency measured using a fiber optical frequency comb is 145 622 892 822 (183) kHz with a relative uncertainty of 1.3×10(-9). Our result is ten times more precise than current best theoretical calculations and is in reasonable agreement with the calculated values. However, the ionization energy of the 2(1)P(1) state, derived from our result and other precisely measured transitions, shows a discrepancy of approximately 3.5σ with the most precise atomic theory. We have also determined the isotope shift between (3)He and (4)He to be 4248.7 (5.3) MHz, which is more precise than the previous measurement by one order of magnitude.

RESUMEN

We report absolute frequency measurements on the a(1), a(10), and a(15) hyperfine components of the R(78) 4-6 line of (127)I(2). An external-cavity diode laser system at 671 nm is frequency-stabilized to the saturated absorption center obtained by modulation transfer spectroscopy in an iodine vapor cell. Its absolute frequency is measured by an optical frequency comb. The effect of pressure shift is investigated to obtain the absolute transition frequency at zero pressure. Our determination of the line centers reaches a precision of better than 40 kHz and will provide useful input for theoretical calculations. This frequency-stabilized laser can be used as a reference laser for the spectroscopy of lithium D lines.

RESUMEN

The probability of two-photon transition (TPT) under a control field to inhibit the quantum interference and enhance the nonlinear optical cross section is observed. Essentially, this is a V-type electromagnetically induced transparency (EIT) with TPT instead of one photon transition. Numerical simulation based on solving the steady state density matrix can qualitatively fit the experimental data. A model of double-Lorentzian profile is used to fit the observed spectrum and give the de-convolution information of the inhibition of TPT spectrum due to EIT and enhancement on the wings of TPT. The frequency shift of the inhibit center is linear to the intensity of the control field (one-photon) and quadratic to the intensity of probe field (two-photon). Under the control field, a factor of 10 enhancements on the wings of the TPT is observed.

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