Long-distance effects of site-directed mutations on backbone conformation in bacteriorhodopsin from solid state NMR of [1-13C]Val-labeled proteins

Dynamic Coupling of Tyrosine 185 with the Bacteriorhodopsin Photocycle, as Revealed by Chemical Shifts, Assisted AF-QM/MM Calculations and Molecular Dynamic Simulations

Aromatic residues are highly conserved in microbial photoreceptors and play crucial roles in the dynamic regulation of receptor functions. However, little is known about the dynamic mechanism of the functional role of those highly conserved aromatic residues during the receptor photocycle. Tyrosine 185 (Y185) is one of the highly conserved aromatic residues within the retinal binding pocket of bacteriorhodopsin (bR). In this study, we explored the molecular mechanism of its dynamic coupling with the bR photocycle by automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) calculations and molecular dynamic (MD) simulations based on chemical shifts obtained by 2D solid-state NMR correlation experiments. We observed that Y185 plays a significant role in regulating the retinal cis–trans thermal equilibrium, stabilizing the pentagonal H-bond network, participating in the orientation switch of Schiff Base (SB) nitrogen, and opening the F42 gate by interacting with the retinal and several key residues along the proton translocation channel. Our findings provide a detailed molecular mechanism of the dynamic couplings of Y185 and the bR photocycle from a structural perspective. The method used in this paper may be applied to the study of other microbial photoreceptors.

Human cytidine deaminase: a biochemical characterization of its naturally occurring variants

Human cytidine deaminase is an enzyme of the pyrimidine salvage pathways that metabolizes several cytosine nucleoside analogs used as prodrugs in chemotherapy. We carried out a characterization of the cytidine deaminase 79A>C and 208G>A Single Nucleotide Polymorphisms, in order to highlight their functional role and provide data that could help fine-tune the chemotherapic use of cytosine nucleosides in patients carrying the above mentioned SNPs. The 79A>C SNP results in a K27Q change in a protein region not involved in the catalytic event. The 208G>A SNP produces an alanine to threonine substitution (A70T) within the conserved catalytic domain. Q27 variant is endowed with a greater catalytic efficiency toward the natural substrates and the antileukemic agent cytarabine (Ara-C), when compared to K27 variant. Molecular modeling, protein stability experiments and site-directed mutagenesis suggest that K27 variant may have an increased stability with respect to Q27 due to an ionic interaction between a lysine residue at position 27 and a glutamate residue at position 24. The T70 variant has a lower catalytic efficiency toward the analyzed substrates when compared to the A70 variant, suggesting that patients carrying the 208G>A SNP may have a greater exposure to cytosine based pro drugs, with possible toxicity consequences.

Generation and analysis of bacteriorhodopsin mutants with the potential for biotechnological applications

The properties of bacteriorhodopsin (BR) can be manipulated by genetic engineering. Therefore, by the methods of gene engineering, Asp85 was replaced individually by two other amino acids (D85V, D85S). The resulting recombinant proteins were assembled into soybean vesicles retinylated to form functional BR-like nano-particles. Proton translocation was almost completely abrogated by the mutant D85S, while the D85V mutant was partially active in pumping protons. Compared with wild type, maximum absorption of the mutants, D85V and D85S, were 563 and 609 nm, which illustrated 5 nm reductions (blue shift) and 41 nm increases (red shift), respectively. Since proton transport activity and spectroscopic activities of the mutants are different, a wide variety of membrane bioreactors (MBr) have been developed. Modified proteins can be utilized to produce unique photo/Electro-chromic materials and tools.

Significance of low-frequency local fluctuation motions in the transmembrane B and C alpha-helices of bacteriorhodopsin, to facilitate efficient proton uptake from the cytoplasmic surface, as revealed by site-directed solid-state 13C NMR

13C NMR spectra of [1-13C]Val- or -Pro-labeled bacteriorhodopsin (bR) and its single or double mutants, including D85N, were recorded at various pH values to reveal conformation and dynamics changes in the transmembrane alpha-helices, in relation to proton release and uptake between bR and the M-like state caused by modified charged states at Asp85 and the Schiff base (SB). It was found that the D85N mutant acquired local fluctuation motion with a frequency of 10(4) Hz in the transmembrane B alpha-helix, concomitant with deprotonation of SB in the M-like state at pH 10, as manifested from a suppressed 13C NMR signal of the [1-13C]-labeled Val49 residue. Nevertheless, local dynamics at Pro50 neighboring with Val49 turned out to be unchanged, irrespective of the charged state of SB as viewed from the 13C NMR of [1-13C]-labeled Pro50. This means that the transmembrane B alpha-helix is able to acquire the fluctuation motion with a frequency of 10(4) Hz beyond the kink at Pro50 in the cytoplasmic side. Concomitantly, fluctuation motion at the C helix with frequency in the order of 10(4) Hz was found to be prominent, due to deprotonation of SB at pH 10, as viewed from the 13C NMR signal of Pro91. Accordingly, we have proposed here a novel mechanism as to proton uptake and transport based on a dynamic aspect that a transient environmental change from a hydrophobic to hydrophilic nature at Asp96 and SB is responsible for the reduced p Ka value which makes proton uptake efficient, as a result of acquisition of the fluctuation motion at the cytoplasmic side of the transmembrane B and C alpha-helices in the M-like state. Further, it is demonstrated that the presence of a van der Waals contact of Val49 with Lys216 at the SB is essential to trigger this sort of dynamic change, as revealed from the 13C NMR data of the D85N/V49A mutant.

Dynamic aspect of bacteriorhodopsin as a typical membrane protein as revealed by site-directed solid-state 13C NMR

We demonstrate here a general feature of dynamic aspect of membrane proteins as revealed by site-directed 13C NMR studies on bacteriorhodopsin (bR) as a typical membrane protein and a variety of mutants at ambient temperature. 13C NMR signals of [3-13C]Ala- or [1-13C]Val-labeled proteins were assigned regio-specifically with reference to the data of the conformation-dependent 13C chemical shifts from model polypeptides, followed by site-specific assignment based on site-directed mutants. Revealed picture of membrane protein at ambient temperature is not static in contrast to anticipation from crystalline structures but flexible enough to undergo a variety of local fluctuations with frequencies from 10(2) to 10(8)Hz, as pointed out already. This picture was further refined by taking into account of residue-specific dynamics of interfacial domains between the surface and inner part of the transmembrane helices and conformational fluctuation induced by the presence of a kinked structure. The residue-specific dynamics of the former was revealed by observation of broadened or suppressed peaks from the interfacial domains caused by acquisition of internal fluctuation motions interfered with frequencies of proton decoupling or magic angle spinning. The presence of such suppressed peaks due to molecular fluctuations in the interfacial domains was further confirmed by insensitivity of the peak-intensities from the interfacial domains in spite of the presence of accelerated relaxation rate to nearby residues from surface bound Mn2+ ion. Further, conformational change of the transmembrane alpha-helix F due to a plausible kinked structure at Pro 186 was confirmed in view of specific displacements of Ala 184 and Val 187 13C NMR peaks from chemically synthesized [3-13C]Ala(184)-, [1-13C]Val(187)-labeled wild type and P186L mutant of transmembrane fragment F(164-194) incorporated into lipid bilayer. It is emphasized that the observed displacement of [3-13C]-labeled Ala 184 peak at 17.4 ppm in the presence of kinked structure in this model peptide is consistent with that of intact protein at 17.27 ppm.

Structure and dynamics of the phospholipase C-delta1 pleckstrin homology domain located at the lipid bilayer surface

Despite the importance of signal transduction pathways at membrane surfaces, there have been few means of investigating their molecular mechanisms based on the structural information of membrane-bound proteins. We applied solid state NMR as a novel method to obtain structural information about the phospholipase C-delta1 (PLC-delta1) pleckstrin homology (PH) domain at the lipid bilayer surface. NMR spectra of the alanine residues in the vicinity of the beta5/beta6 loop in the PH domain revealed changes in local conformations due to the membrane localization of the protein. We propose that these conformational changes originate from a hydrophobic interaction between the amphipathic alpha-helix located in the beta5/beta6 loop and the hydrophobic layer of the membrane and contribute to the membrane binding affinity, interdomain interactions and intermolecular interactions of PLC-delta1.

Residue-specific millisecond to microsecond fluctuations in bacteriorhodopsin induced by disrupted or disorganized two-dimensional crystalline lattice, through modified lipid-helix and helix-helix interactions, as revealed by 13C NMR

We have recorded 13C NMR spectra of [3-13C]-, [1-13C]Ala-, and [1-13C]Val-labeled bacteriorhodopsin (bR), W80L and W12L mutants and bacterio-opsin (bO) from retinal-deficient E1001 strain, in order to examine the possibility of their millisecond to microsecond local fluctuations with correlation time in the order of 10(-4) to 10(-5) s, induced or prevented by disruption or assembly of two-dimensional (2D) crystalline lattice, respectively, at ambient temperature. The presence of disrupted or disorganized 2D lattice for W12L, W80L and bO from E1001 strain was readily visualized by increased relative proportions of surrounding lipids per protein, together with their broadened 13C NMR signals of transmembrane alpha-helices and loops in [3-13C]Ala-labeled proteins, with reference to those of wild-type. In contrast, 13C CP-MAS NMR spectra of [1-13C]Ala- and Val-labeled these mutants were almost completely suppressed, owing to the presence of fluctuations with time scale of 10(-4) s interfered with magic angle spinning. In particular, 13C NMR signals of [1-13C]Ala-labeled transmembrane alpha-helices of wild-type were almost completely suppressed at the interface between the surface and inner part (up to 8.7 A deep from the surface) with reference to those of the similarly suppressed peaks by Mn(2+)-induced accelerated spin-spin relaxation rate. Such fluctuation-induced suppression of 13C NMR peaks from the interfacial regions, however, was less significant for [1-13C]Val-labeled proteins, because fluctuation motions in Val residues with bulky side-chains at the C(alpha) moiety were modified to those of longer correlation time (>10(-4) s), if any, by residue-specific manner. To support this view, we found that such suppressed 13C NMR signals of [1-13C]Ala-labeled peaks in the wild-type were recovered for D85N and bO in which correlation times of fluctuations were shifted to the order of 10(-5) s due to modified helix-helix interactions as previously pointed out [Biochemistry, 39 (2000) 14472; J. Biochem. (Tokyo) 127 (2000) 861].

Multisite fluorescence in proteins with multiple tryptophan residues. Apomyoglobin natural variants and site-directed mutants

Time-resolved fluorescence experiments were carried out on a variety of apomyoglobins with one or two tryptophan (Trp) residues located at invariant positions 7 and 14 in the primary sequence. In all cases, the Trp fluorescence kinetics were resolved adequately into two discrete lifetime domains, and decay-associated spectra (DAS) were obtained for each decay component. The DAS resolved for unfolded proteins were indistinguishable by position of the emission maxima and the spectral shapes. The folded proteins revealed noticeable differences in the DAS, which relate to the diverse local environments around the Trp residues in the individual proteins. Furthermore, the DAS of wild-type protein possessing two Trp residues were simulated well by that of one Trp mutants either in the native, molten globule, or unfolded states. Overall, employing Trp fluorescence and site-directed mutagenesis allowed us to highlight the conformational changes induced by the single amino acid replacement and generate novel structural information on equilibrium folding intermediates. Specifically, it was found that conformational fluctuations in the local cluster around the evolutionarily conserved Trp(14) are very similar in the native and molten globule states of apomyoglobins. This result indicates that residues in the E and B helices contributing to this cluster are most likely involved in the stabilization of the overall architecture of the structured molten globule intermediate.

Reconciling crystallography and mutagenesis: a synthetic approach to the creation of a comprehensive model for proton pumping by bacteriorhodopsin

As a result of the number of new high-resolution structures of the pigment and some of its photointermediates, a realistic model for the functioning of bacteriorhodopsin seems to be finally emerging. However, lack of structural information for some of the key functional states, and contradictions between some published structural models, argue for the use of the synthetic approach, one that includes use of data from both crystallographic and mutagenesis studies. The role of mutagenesis in this synthetic approach falls into two categories. First, to provide additional structural information, and second, to test the predictions of structural models by studying mutant phenotypes. This review urges critical comparisons of the structural and mutagenesis data, as there are problems with their selective and indiscriminate use.

Conformation and backbone dynamics of bacteriorhodopsin revealed by (13)C-NMR

It is demonstrated here how the secondary structure and dynamics of transmembrane helices, as well as surface residues, such as interhelical loops and N- or C-terminus of bacteriorhodopsin (bR) in purple membrane, can be determined at ambient temperature based on very simple (13)C-NMR measurements, together with a brief experimental background. In contrast to the static picture of bR, currently available from X-ray diffraction or cryo-electron microscopy, the structure consists of dynamically heterogeneous domains which undergo various types of local fluctuations with a frequency range of 10(2)--10 (8) Hz. The significance of this picture is discussed in relation to the biological function of this protein.

Conformational changes of bacteriorhodopsin along the proton-conduction chain as studied with (13)C NMR of [3-(13)C]Ala-labeled protein: arg(82) may function as an information mediator

We have recorded (13)C NMR spectra of [3-(13)C]Ala-labeled wild-type bacteriorhodopsin (bR) and its mutants at Arg(82), Asp(85), Glu(194), and Glu(204) along the extracellular proton transfer chain. The upfield and downfield displacements of the single carbon signals of Ala(196) (in the F-G loop) and Ala(126) (at the extracellular end of helix D), respectively, revealed conformational differences in E194D, E194Q, and E204Q from the wild type. The same kind of conformational change at Ala(126) was noted also in the Y83F mutant, which lacks the van der Waals contact between Tyr(83) and Ala(126) present in the wild type. The absence of a negative charge at Asp(85) in the site-directed mutant D85N induced global conformational changes, as manifested in displacements or suppression of peaks from the transmembrane helices, cytoplasmic loops, etc., as well as the local changes at Ala(126) and Ala(196) seen in the other mutants. Unexpectedly, no conformational change at Ala(126) was observed in R82Q (even though Asp(85) is protonated at pH 6) or in D85N/R82Q. The changes induced in the Ala(126) signal when Asp(85) is uncharged could be interpreted therefore in terms of displacement of the positive charge of Arg(82) toward Tyr(83), where Ala(126) is located. It is possible that disruption of the proton transfer chain after protonation of Asp(85) in the photocycle could cause the same kind of conformational change we detect at Ala(196) and Ala(126). If so, the latter change would be also the result of rearrangement of the side chain of Arg(82).