Andrea M. Nagy

Plant Peptides Govern Terminal Differentiation of Bacteria in Symbiosis

Legume Symbiosome Leguminous plants (peas and beans) are major players in global nitrogen cycling by virtue of their symbioses with nitrogen-fixing bacteria that are harbored in specialized structures, called nodules, on the plants roots. Van de Velde et al. (p. 1122) show that the host plant, Medicago truncatula produces nodule-specific cysteine-rich peptides, resembling natural plant defense peptides. The peptides enter the bacterial cells and promote its development into the mature symbiont. In a complementary study, D. Wang et al. (p. 1126), have identified the signal peptidase, also encoded by the plant, that is required for processing these specialized peptides into their active form. Products encoded by the leguminous plant Medicago direct the differentiation of the bacterial partner in symbiosis. Legume plants host nitrogen-fixing endosymbiotic Rhizobium bacteria in root nodules. In Medicago truncatula, the bacteria undergo an irreversible (terminal) differentiation mediated by hitherto unidentified plant factors. We demonstrated that these factors are nodule-specific cysteine-rich (NCR) peptides that are targeted to the bacteria and enter the bacterial membrane and cytosol. Obstruction of NCR transport in the dnf1-1 signal peptidase mutant correlated with the absence of terminal bacterial differentiation. On the contrary, ectopic expression of NCRs in legumes devoid of NCRs or challenge of cultured rhizobia with peptides provoked symptoms of terminal differentiation. Because NCRs resemble antimicrobial peptides, our findings reveal a previously unknown innovation of the host plant, which adopts effectors of the innate immune system for symbiosis to manipulate the cell fate of endosymbiotic bacteria.

Coherent Control of Retinal Isomerization in Bacteriorhodopsin

Optical control of the primary step of photoisomerization of the retinal molecule in bacteriorhodopsin from the all-trans to the 13-cis state was demonstrated under weak field conditions (where only 1 of 300 retinal molecules absorbs a photon during the excitation cycle) that are relevant to understanding biological processes. By modulating the phases and amplitudes of the spectral components in the photoexcitation pulse, we showed that the absolute quantity of 13-cis retinal formed upon excitation can be enhanced or suppressed by ±20% of the yield observed using a short transform-limited pulse having the same actinic energy. The shaped pulses were shown to be phase-sensitive at intensities too low to access different higher electronic states, and so these pulses apparently steer the isomerization through constructive and destructive interference effects, a mechanism supported by observed signatures of vibrational coherence. These results show that the wave properties of matter can be observed and even manipulated in a system as large and complex as a protein.

Coherent control of the population transfer in complex solvated molecules at weak excitation. An experimental study

We performed a series of successful experiments for the optimization of the population transfer from the ground to the first excited state in a complex solvated molecule (rhodamine 101 in methanol) using shaped excitation pulses at very low intensities (1 absorbed photon per 100-500 molecules per pulse). We found that the population transfer can be controlled and significantly enhanced by applying excitation laser pulses with crafted pulse shapes. The optimal shape was found in feedback-controlled experiments using a genetic search algorithm. The temporal profile of the optimal excitation pulse corresponds to a comb of subpulses regularly spaced by approximately 150 fs, whereas its spectrum consists of a series of well-resolved peaks spaced apart by approximately 6.5 nm corresponding to a frequency of 220 cm(-1). This frequency matches very well with the frequency modulation of the population kinetics (period of approximately 150 fs), observed by excitation with a short (approximately 20 fs) transform-limited laser pulse directly after excitation. In addition, an antioptimization experiment was performed under the same conditions. The difference in the population of the excited state for the optimal and antioptimal pulses reaches approximately 30% even at very weak excitation. The results of optimization are reproducible and have clear physical meaning.

Observation of the cascaded atomic-to-global length scales driving protein motion

Model studies of the ligand photodissociation process of carboxymyoglobin have been conducted by using amplified few-cycle laser pulses short enough in duration (<10 fs) to capture the phase of the induced nuclear motions. The reaction-driven modes are observed directly in real time and depict the pathway by which energy liberated in the localized reaction site is efficiently channeled to functionally relevant mesoscale motions of the protein.

Optimal control of the isomerization yield in bacteriorhodopsin using tailored light pulses

The all-trans to 13-cis isomerization of the retinal chromophore in bacteriorhodopsin (bR) plays an essential role in Nature (e.g., in photosynthesis of halobacteria). bR is a candidate for optical nanodevices driven by laser pulses, and a prospective material for optical memory storage devices and photoswitches. From the viewpoint of possible applications of bR in nanodevices we performed an experimental study of the isomerization yield by excitation with tailored laser pulses, using a coherent control approach. With specially shaped excitation pulses (found in optimization experiments) we are able to manipulate the 13-cis yield in bR over an absolute range of 60% (30% enhancement as well as 30% suppression in comparison to excitation with a transform-limited pulse) while keeping the absorbed excitation energy at a constant level.

Chapter 77 - Reaction driven modes in carboxymyoglobin: pathway of force transduction for functionally relevant protein motions

Heme proteins form the cornerstone for our understanding of the general phenomena of molecular cooperativity; where the binding affinity of diatomic ligands in hemoglobin and associated changes in quaternary structure with ligation state is the best-characterized example. At the heart of this problem is an understanding how the initially localized reaction forces couple to the global protein coordinate to execute these functionally relevant motions. The energetics for this process are derived from one or a few chemical bonds and at the instant the bond is formed or broken, the motions are necessarily localized over atomic length scales at the active site and subject to quantum effects. From a practical standpoint, the heme proteins provide ideal model systems for studying the relationship between protein structure and function since they are well-characterized and their ligands can be photo-dissociated with unit quantum efficiency on the truly femtosecond timescale. This chapter discusses the results of ultrafast pump-probe spectroscopy of carboxymyoglobin (MbCO) to determine the initial structure changes of the ligand dissociation process using pulses of less than 10 fs in the 500-600 nm spectral regions.