Lactose permease H+-lactose symporter: mechanical switch or Brownian ratchet?

Molecular Ratchets and Kinetic Asymmetry: Giving Chemistry Direction

Over the last two decades ratchet mechanisms have transformed the understanding and design of stochastic molecular systems-biological, chemical and physical-in a move away from the mechanical macroscopic analogies that dominated thinking regarding molecular dynamics in the 1990s and early 2000s (e.g. pistons, springs, etc), to the more scale-relevant concepts that underpin out-of-equilibrium research in the molecular sciences today. Ratcheting has established molecular nanotechnology as a research frontier for energy transduction and metabolism, and has enabled the reverse engineering of biomolecular machinery, delivering insights into how molecules 'walk' and track-based synthesisers operate, how the acceleration of chemical reactions enables energy to be transduced by catalysts (both motor proteins and synthetic catalysts), and how dynamic systems can be driven away from equilibrium through catalysis. The recognition of molecular ratchet mechanisms in biology, and their invention in synthetic systems, is proving significant in areas as diverse as supramolecular chemistry, systems chemistry, dynamic covalent chemistry, DNA nanotechnology, polymer and materials science, molecular biology, heterogeneous catalysis, endergonic synthesis, the origin of life, and many other branches of chemical science. Put simply, ratchet mechanisms give chemistry direction. Kinetic asymmetry, the key feature of ratcheting, is the dynamic counterpart of structural asymmetry (i.e. chirality). Given the ubiquity of ratchet mechanisms in endergonic chemical processes in biology, and their significance for behaviour and function from systems to synthesis, it is surely just as fundamentally important. This Review charts the recognition, invention and development of molecular ratchets, focussing particularly on the role for which they were originally envisaged in chemistry, as design elements for molecular machinery. Different kinetically asymmetric systems are compared, and the consequences of their dynamic behaviour discussed. These archetypal examples demonstrate how chemical systems can be driven inexorably away from equilibrium, rather than relax towards it.

A β-barrel for oil transport through lipid membranes: Dynamic NMR structures of AlkL

Here we show how AlkL, a minimalistic outer-membrane protein from oil-consuming bacteria, exploits dynamics of extracellular loops to channel substrate across the polysaccharide barrier and into the hydrophobic interior of the outer membrane. This work represents a unique example of a side-by-side atomic-level structure determination by solution NMR in detergents and by solid-state NMR in lipid bilayers, which critically demonstrates the importance of a lipid environment to investigate function. Corroborating our experimental measurements, molecular-dynamics simulations capture substrate transit via lateral openings. The capacity to unravel membrane protein function under near-native conditions, fueled by the latest method developments, opens up a new frontier for their investigation, and provides thereby for improved fundamental insights into biological processes.

The protein AlkL is known to increase permeability of the outer membrane of bacteria for hydrophobic molecules, yet the mechanism of transport has not been determined. Differing crystal and NMR structures of homologous proteins resulted in a controversy regarding the degree of structure and the role of long extracellular loops. Here we solve this controversy by determining the de novo NMR structure in near-native lipid bilayers, and by accessing structural dynamics relevant to hydrophobic substrate permeation through molecular-dynamics simulations and by characteristic NMR relaxation parameters. Dynamic lateral exit sites large enough to accommodate substrates such as carvone or octane occur through restructuring of a barrel extension formed by the extracellular loops.

Transport cycle of Escherichia coli lactose permease in a nonhomogeneous random walk model

We present Monte Carlo simulations for the transport cycle of Escherichia coli lactose permease (LacY), using as a starting point the model proposed by Kaback et al. [Nat. Rev. Mol. Cell Biol. 2, 610 (2001)NRMCBP1471-007210.1038/35085077], which is based on functional properties of mutants and x-ray structures. Kaback's model suggests the existence of six states for the whole cycle of lactose-H^{+} symport. However, the free-energy differences between these states have not yet been reported in the literature. Here, we analyzed the biochemical structure of each state and determined a range of possible values for each one of the five free-energy variations. Then, using the Metropolis algorithm in a nonhomogeneous random walk model, we tested all the possible combinations with these values to find the free-energy curve that best reproduces the dynamics of LacY. The agreement between our model predictions and the experimental data suggests that our free-energy curve is appropriate for describing the lactose-H^{+} symport. We found not only this curve, but also the time of occupancy of the permease at each conformation. In addition, we paved the way in this work to solve an open question related to this transport mechanism, which is the importance of protonation for lactose binding.

Membrane Transport

Every living cell has to exchange molecules across the membrane for cellular functions. The hydrophobic or lipophilic molecules do not require energy for crossing the membrane. They can diffuse freely from higher to lower concentration till equilibrium is established. This process is called passive transport or diffusion.

Peptide Probes Reveal a Hydrophobic Steric Ratchet in the Anthrax Toxin Protective Antigen Translocase

Anthrax toxin is a tripartite virulence factor produced by Bacillus anthracis during infection. Under acidic endosomal pH conditions, the toxin's protective antigen (PA) component forms a transmembrane channel in host cells. The PA channel then translocates its two enzyme components, lethal factor and edema factor, into the host cytosol under the proton motive force. Protein translocation under a proton motive force is catalyzed by a series of nonspecific polypeptide binding sites, called clamps. A 10-residue guest/host peptide model system, KKKKKXXSXX, was used to functionally probe polypeptide-clamp interactions within wild-type PA channels. The guest residues were Thr, Ala, Leu, Phe, Tyr, and Trp. In steady-state translocation experiments, the channel blocked most tightly with peptides that had increasing amounts of nonpolar surface area. Cooperative peptide binding was observed in the Trp-containing peptide sequence but not the other tested sequences. Trp substitutions into a flexible, uncharged linker between the lethal factor amino-terminal domain and diphtheria toxin A chain expedited translocation. Therefore, peptide-clamp sites in translocase channels can sense large steric features (like tryptophan) in peptides, and while these steric interactions may make a peptide translocate poorly, in the context of folded domains, they can make the protein translocate more rapidly presumably via a hydrophobic steric ratchet mechanism.

Role of ComEA in DNA uptake during transformation of competent Bacillus subtilis

The role of the competence protein ComEA in DNA uptake during transformation of competent Bacillus subtilis was analyzed by lysed-protoplast transformation (LP transformation). A comEA deletion mutant was constructed by a fusion polymerase chain reaction. Transformants of the mutant were obtained by LP transformation at a frequency of 1.1 × 10(2) transformants per μg DNA, representing a low relative efficiency of transformation [RET (mutant/wild type)] of 2.7 × 10(-6). This implied an important role of the protein during DNA uptake. When analyzing LP transformation of comEA with a plasmid (5.7 kb), a similar RET (mutant/wild type) of 5.6 × 10(-5) was obtained. Following addition of DNA into the comEA mutant culture, the number of transformants increased at a rate of 0.5 transformants/min, which was very low compared with the wild-type (6.9×10(4) transformants/min). However, even in the comEA mutant, DNA uptake began immediately after addition of DNA. Using co-transformation analysis of the comEA mutant, short linkages at distances of 2-156 kb could be detected, but not long linkages at distances of 671-1662 kb. Taken together, the results indicate that ComEA plays an important role in the transfer of transforming DNA into the DNA channel and in controlling the rate of DNA uptake.

Role of ComFA in controlling the DNA uptake rate during transformation of competent Bacillus subtilis

The roles of ComFA and ComEC in DNA uptake by competent Bacillus subtilis were analyzed by transformation with DNA in protoplast lysates (LP transformation). Deletion mutants of comFA and comEC and putative Walker A mutants (K152N, K152Q, K152E) of comFA were constructed by fusion polymerase chain reaction. Transformants of comEC mutant with purified DNA and DNA in protoplast lysate were not obtained, which shows a lack of transformation ability and backwards recombination of the mutant. Transformants of the comFA mutant were obtained by LP transformation (1.8 × 10(4) transformants/μg DNA). Low relative efficiency of transformation (RET) of comFA compared to wild type (4.3 × 10(-4)) showed an important role for comFA in DNA uptake. Walker A mutants showed 1.8-19 × 10(-4) RET, suggesting a dependence on ATPase activity for transformation. Co-transformation between short linkages was only detected in comFA mutants. The results demonstrated that ComFA controlled the DNA uptake rate. The interpretation was further supported by analyzing the plasmid used in LP transformation of the comFA mutant. The RET of comFA compared to the wild type was 2.7 × 10(-2), 60-fold higher than that with chromosomal DNA (4.3 × 10(-4)). Following addition of DNA into comFA culture, transformants were obtained after 15 min, with the number of transformants increasing over time. The kinetics strongly suggested that in comFA mutants, formation of another DNA uptake complex without ComFA would be a lengthy process.

Structural basis of substrate selectivity in the glycerol-3-phosphate: phosphate antiporter GlpT

Major facilitators represent the largest superfamily of secondary active transporter proteins and catalyze the transport of an enormous variety of small solute molecules across biological membranes. However, individual superfamily members, although they may be architecturally similar, exhibit strict specificity toward the substrates they transport. The structural basis of this specificity is poorly understood. A member of the major facilitator superfamily is the glycerol-3-phosphate (G3P) transporter (GlpT) from the Escherichia coli inner membrane. GlpT is an antiporter that transports G3P into the cell in exchange for inorganic phosphate (P(i)). By combining large-scale molecular-dynamics simulations, mutagenesis, substrate-binding affinity, and transport activity assays on GlpT, we were able to identify key amino acid residues that confer substrate specificity upon this protein. Our studies suggest that only a few amino acid residues that line the transporter lumen act as specificity determinants. Whereas R45, K80, H165, and, to a lesser extent Y38, Y42, and Y76 contribute to recognition of both free P(i) and the phosphate moiety of G3P, the residues N162, Y266, and Y393 function in recognition of only the glycerol moiety of G3P. It is the latter interactions that give the transporter a higher affinity to G3P over P(i).

Integration of evolutionary features for the identification of functionally important residues in major facilitator superfamily transporters

The identification of functionally important residues is an important challenge for understanding the molecular mechanisms of proteins. Membrane protein transporters operate two-state allosteric conformational changes using functionally important cooperative residues that mediate long-range communication from the substrate binding site to the translocation pathway. In this study, we identified functionally important cooperative residues of membrane protein transporters by integrating sequence conservation and co-evolutionary information. A newly derived evolutionary feature, the co-evolutionary coupling number, was introduced to measure the connectivity of co-evolving residue pairs and was integrated with the sequence conservation score. We tested this method on three Major Facilitator Superfamily (MFS) transporters, LacY, GlpT, and EmrD. MFS transporters are an important family of membrane protein transporters, which utilize diverse substrates, catalyze different modes of transport using unique combinations of functional residues, and have enough characterized functional residues to validate the performance of our method. We found that the conserved cores of evolutionarily coupled residues are involved in specific substrate recognition and translocation of MFS transporters. Furthermore, a subset of the residues forms an interaction network connecting functional sites in the protein structure. We also confirmed that our method is effective on other membrane protein transporters. Our results provide insight into the location of functional residues important for the molecular mechanisms of membrane protein transporters.

Major Facilitator Superfamily (MFS) transporters are one of the largest families of membrane protein transporters and are ubiquitous to all three kingdoms of life. Structural studies of MFS transporters have revealed that the members of this superfamily share structural homology; however, due to weak sequence similarity, their structural similarity has only been found after structural determination. Even after the structures were solved, painstaking efforts were needed to detect functionally important residues. The identification of functionally important cooperative residues from sequences may provide an alternative way to understanding the function of this important class of proteins. Here, we show that it is possible to identify functionally important residues of MFS transporters by integrating two different evolutionary features, sequence conservation and co-evolutionary information. Our results suggest that the conserved cores of evolutionarily coupled residues are involved in specific substrate recognition and translocation of membrane protein transporters. Also, a subset of the identified residues comprises an interaction network connecting functional sites in the protein structure. The ability to identify functional residues from protein sequences may be helpful for locating potential mutagenesis targets in mechanistic studies of membrane protein transporters.

Alternating carrier models of asymmetric glucose transport violate the energy conservation laws

Alternating access transporters with high-affinity externally facing sites and low-affinity internal sites relate substrate transit directly to the unliganded asymmetric "carrier" (Ci) distribution. When both bathing solutions contain equimolar concentrations of ligand, zero net flow of the substrate-carrier complex requires a higher proportion of unliganded low-affinity inside sites (proportional, variant 1/KD(in)) and slower unliganded "free" carrier transit from inside to outside than in the reverse direction. However, asymmetric rates of unliganded carrier movement, kij, imply that an energy source, DeltaGcarrier = RT ln (koi/kio) = RT ln (Cin/Cout) = RT ln (KD(in)/KD(out)), where R is the universal gas constant (8.314 Joules/M/K degrees), and T is the temperature, assumed here to be 300 K degrees , sustains the asymmetry. Without this invalid assumption, the constraints of carrier path cyclicity, combined with asymmetric ligand affinities and equimolarity at equilibrium, are irreconcilable, and any passive asymmetric uniporter or cotransporter model system, e.g., Na-glucose cotransporters, espousing this fundamental error is untenable. With glucose transport via GLUT1, the higher maximal rate and Km of net ligand exit compared to net ligand entry is only properly simulated if ligand transit occurs by serial dissociation-association reactions between external high-affinity and internal low-affinity immobile sites. Faster intersite transit rates occur from lower-affinity sites than from higher-affinity sites and require no other energy source to maintain equilibrium. Similar constraints must apply to cotransport.

Amino acids that confer transport of raffinose and maltose sugars in the raffinose permease (RafB) of Escherichia coli as implicated by spontaneous mutations at Val-35, Ser-138, Ser-139, Gly-389 and Ile-391

In order to identify amino acid residues in the Escherichia coli raffinose-H(+) permease (RafB) that play a role in sugar selection and transport, we first incubated E. coli HS4006 containing plasmid pRU600 (expresses inducible raffinose permease and alpha-galactosidase) on maltose MacConkey indicator plates overnight. Initially, all colonies were white, indicating no fermentation of maltose. Upon further incubation, 100 mutants appeared red. pRU600 DNA was prepared from 55 mutants. Five mutants transferred the phenotype for fermentation of maltose (red). Plasmid DNA from five maltose-positive phenotype transformants was prepared and sequenced, revealing three distinct types of mutations. Two mutants exhibited Val-35-->Ala (MT1); one mutant had Ile-391-->Ser (MT2); and two mutants had Ser-138-->Asp, Ser-139-->Leu and Gly-389-->Ala (MT3). Transport studies of [(3)H]-maltose showed that cells harboring MT1, MT2 and MT3 had greater uptake (P <or= 0.05) than cells harboring wild-type RafB. However, [(14)C]-raffinose uptake was reduced in all mutant cells (P <or= 0.05) with MT1, MT2 and MT3 mutants compared to cells harboring wild-type RafB. Kinetic analysis showed enhanced apparent K (m) values for maltose and reduced V (max)/ K (m) ratios for raffinose compared to wild-type values. The apparent K (i) value of maltose for RafB indicates a competitive relationship between maltose and raffinose. Maltose "uphill" accumulation was greater for mutants (P <or= 0.05) than for cells with wild-type RafB. Thus, we implicate residues in RafB that are responsible for raffinose transport and suggest that the substituted residues in RafB dictate structures that enhance transport of maltose.

Design principles for Brownian molecular machines: how to swim in molasses and walk in a hurricane

Protein molecular motors-perfected over the course of millions of years of evolution-play an essential role in moving and assembling biological structures. Recently chemists have been able to synthesize molecules that emulate in part the remarkable capabilities of these biomolecular motors (for extensive reviews see the recent papers: E. R. Kay, D. A. Leigh and F. Zerbetto, Angew. Chem., Int. Ed., 2006, 46, 72-191; W. R. Browne and B. L. Feringa, Nat. Nanotechnol., 2006, 1, 25-35; M. N. Chatterjee, E. R. Kay and D. A. Leigh, J. Am. Chem. Soc., 2006, 128, 4058-4073; G. S. Kottas, L. I. Clarke, D. Horinek and J. Michl, Chem. Rev., 2005, 105, 1281-1376; M. A. Garcia-Garibay, Proc. Natl. Acad. Sci., U. S. A., 2005, 102, 10771-10776)). Like their biological counterparts, many of these synthetic machines function in an environment where viscous forces dominate inertia-to move they must "swim in molasses". Further, the thermal noise power exchanged reversibly between the motor and its environment is many orders of magnitude greater than the power provided by the chemical fuel to drive directed motion. One might think that moving in a specific direction would be as difficult as walking in a hurricane. Yet biomolecular motors (and increasingly, synthetic motors) move and accomplish their function with almost deterministic precision. In this Perspective we will investigate the physical principles that govern nanoscale systems at the single molecule level and how these principles can be useful in designing synthetic molecular machines.