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Stephen H White

Publications and source records attributed to Stephen H White.

18 recordsLinked to original sources

Interface connections of a transmembrane voltage sensor.

Voltage-sensitive ion channels open and close in response to changes in transmembrane (TM) potential caused by the motion of the S4 voltage sensors. These sensors are alpha-helices that include four or more positively charged amino acids, most commonly arginine. The so-called paddle model, based on the high-resolution structure of the KvAP K+ channel [Jiang, et al. (2003) Nature 423, 33-41], posits that the S4 sensors move within the membrane bilayer in response to TM voltage changes. Direct exposure of S4 sensors to lipid is contrary to the classical expectation that the dielectric contrast between the membrane hydrocarbon core and water presents an insurmountable energetic penalty to burial of electric charges. Nevertheless, recent experiments have shown that a helix with the sequence of KvAP S4 can be inserted across the endoplasmic reticulum membrane. To reconcile this result with the classical energetics argument, we have carried out a molecular dynamics simulation of an isolated TM S4 helix in a lipid bilayer. The simulation reveals a stabilizing hydrogen-bonded network of water and lipid phosphates around the arginines that reduces the effective thickness of the bilayer hydrocarbon core to approximately 10 A in the vicinity of the helix. It suggests that bilayer phospholipids can adapt locally to strongly perturbing protein elements, causing the phospholipids to become a structural extension of the protein.

Hydrogen Bonding↗

An experiment-based algorithm for predicting the partitioning of unfolded peptides into phosphatidylcholine bilayer interfaces.

Knowing the partitioning free energy of unfolded polypeptides into membrane interfaces is necessary for understanding membrane protein stability and for designing antimicrobial and other peptides. Experiment-based whole-residue free-energy (hydropathy) scales for amino acids in unfolded peptides, derived from the partitioning of host-guest pentapeptides (Ac-WLXLL) into the interfaces of phosphatidylcholine bilayers and into n-octanol, have been determined by W. C. Wimley, S. H. White, and colleagues [(1996) Nat. Struc. Biol. 3, 842; Wimley, W. C. et al. (1996) Biochemistry 35, 5109]. These scales offer the possibility of computing absolute partitioning free energies of unfolded peptides given only their amino acid sequences. However, the scales are incomplete, because partitioning free energies of N- and C-terminal groups are missing. To complete the scales, we have measured the pH-dependent partitioning of the host-guest pentapeptide variants AcWL-X-LL-NH(2) and WL-X-LL-NH(2) (X = G or W) into palmitoyloleoylphosphatidylcholine (POPC) bilayer interfaces and n-octanol. These measurements, in combination with the earlier ones, lead to hydrophobicity scale values for protonation, deprotonation, or acetylation of the N terminus and protonation, deprotonation, or amidation of the C terminus. A surprising finding is that a charged N terminus has a much smaller effect on bilayer partitioning than a charged C terminus. We present a simple algorithm for computing the absolute partitioning free energies of unfolded peptides into the phosphatidylcholine bilayer interface.

Algorithms↗

A comprehensive classification system for lipids.

Lipids are produced, transported, and recognized by the concerted actions of numerous enzymes, binding proteins, and receptors. A comprehensive analysis of lipid molecules, "lipidomics," in the context of genomics and proteomics is crucial to understanding cellular physiology and pathology; consequently, lipid biology has become a major research target of the postgenomic revolution and systems biology. To facilitate international communication about lipids, a comprehensive classification of lipids with a common platform that is compatible with informatics requirements has been developed to deal with the massive amounts of data that will be generated by our lipid community. As an initial step in this development, we divide lipids into eight categories (fatty acyls, glycerolipids, glycerophospholipids, sphingolipids, sterol lipids, prenol lipids, saccharolipids, and polyketides) containing distinct classes and subclasses of molecules, devise a common manner of representing the chemical structures of individual lipids and their derivatives, and provide a 12 digit identifier for each unique lipid molecule. The lipid classification scheme is chemically based and driven by the distinct hydrophobic and hydrophilic elements that compose the lipid. This structured vocabulary will facilitate the systematization of lipid biology and enable the cataloging of lipids and their properties in a way that is compatible with other macromolecular databases.

Database Management Systems↗

Predicting in vivo clinical performance of anterior cruciate ligament fixation methods from in vitro analysis: industrial tests of fatigue life and tolerance limits are more useful than other cyclic loading parameters.

BACKGROUND: Anterior cruciate ligament graft fixations experience cyclic loads in vivo. Present cyclic loading studies testing fixation use "incremental cycling," "residual strength" protocols, or a combination. Industrial standards, however, rely on fatigue life testing and use tolerance limits to determine guaranteed minimum levels of cycles to failure. HYPOTHESIS: Industrial standards of fatigue life and lower tolerance limits provide a more conservative assessment of cycles to failure than do currently used cyclic loading models, and they facilitate interpretation of data toward clinical performance. STUDY DESIGN: Descriptive laboratory study. METHODS: Fatigue life curves and lower tolerance limits were calculated for porcine patellar tendon graft fixations that were tested to failure in single pulls or cycled to failure at 2 different load levels. A log curve was constructed so that the expected values at other load levels could be calculated. Comparison of a metal and a composite resorbable interference screw design was used as an example. RESULTS: Cycles to failure of both screw designs varied widely at each load level. The guaranteed minimum number of cycles calculated by tolerance limits was therefore much lower than the mean cycles to failure at any given load level. For example, at a load of 250 N, the predicted mean life for the composite screw and the metal screw was 2513 and 1490 cycles, respectively, whereas the 80/80 tolerance limits (the value that 80% could be expected to achieve with 80% confidence) were only 63 and 68 cycles, respectively. Small reductions in load level gave very large increases in minimally expected life. CONCLUSIONS: Fatigue testing of anterior cruciate ligament reconstructions better shows the wide variation between specimens and the large effect of load levels on expected life. Wide scatter makes mean levels over-optimistic and difficult to interpret. Tolerance limits give estimates that are more conservative and facilitate data interpretation. CLINICAL RELEVANCE: A method for testing and analyzing fatigue properties was presented, results of which are more readily interpreted to clinical practice.

Animals↗

Recognition of transmembrane helices by the endoplasmic reticulum translocon.

Membrane proteins depend on complex translocation machineries for insertion into target membranes. Although it has long been known that an abundance of nonpolar residues in transmembrane helices is the principal criterion for membrane insertion, the specific sequence-coding for transmembrane helices has not been identified. By challenging the endoplasmic reticulum Sec61 translocon with an extensive set of designed polypeptide segments, we have determined the basic features of this code, including a 'biological' hydrophobicity scale. We find that membrane insertion depends strongly on the position of polar residues within transmembrane segments, adding a new dimension to the problem of predicting transmembrane helices from amino acid sequences. Our results indicate that direct protein-lipid interactions are critical during translocon-mediated membrane insertion.

Amino Acid Sequence↗

Membrane insertion of a potassium-channel voltage sensor.

The mechanism of voltage gating in K+ channels is controversial. The paddle model posits that highly charged voltage-sensor domains move relatively freely across the lipid bilayer in response to membrane depolarization; competing models picture the charged S4 voltage-sensor helix as being shielded from lipid contact by other parts of the protein. We measured the apparent free energy of membrane insertion of a K+-channel S4 helix into the endoplasmic reticulum membrane and conclude that S4 is poised very near the threshold of efficient bilayer insertion. Our results suggest that the paddle model is not inconsistent with the high charge content of S4.

Arginine↗

Transmembrane helices before, during, and after insertion.

The transmembrane (TM) helix is the fundamental structural unit of helix-bundle membrane proteins. Recent biophysical studies provide new insights into the interactions of TM helices with each other and with membrane lipid bilayers. The biological process of helix insertion is carried out by translocon complexes acting in concert with ribosomes. An electron cryo-microscopic reconstruction of these complexes reveals their architecture in new detail, and shows that the complex is constructed from four SecY/Sec61 heterotrimers and two TRAP complexes. A disulfide bridge study shows that elongating polypeptide chains pass through the pore previously identified in the X-ray structure of an archaeal SecY heterotrimer. The fundamental code used by the translocon to select polypeptide segments for insertion as TM helices has been broken. A detailed analysis of the TM amino acid distributions of helix-bundle membrane proteins of known structure recapitulates this code.

Animals↗

How hydrogen bonds shape membrane protein structure.

The energetic cost of partitioning peptide bonds into membrane bilayers is prohibitive unless the peptide bonds participate in hydrogen bonds. However, even then there is a significant free energy penalty for dehydrating the peptide bonds that can only be overcome by favorable hydrophobic interactions. Membrane protein structure formation is thus dominated by hydrogen bonding interactions, which is the subject of this review.

Hydrogen↗

Experimental validation of molecular dynamics simulations of lipid bilayers: a new approach.

A novel protocol has been developed for comparing the structural properties of lipid bilayers determined by simulation with those determined by diffraction experiments, which makes it possible to test critically the ability of molecular dynamics simulations to reproduce experimental data. This model-independent method consists of analyzing data from molecular dynamics bilayer simulations in the same way as experimental data by determining the structure factors of the system and, via Fourier reconstruction, the overall transbilayer scattering-density profiles. Multi-nanosecond molecular dynamics simulations of a dioleoylphosphatidylcholine bilayer at 66% RH (5.4 waters/lipid) were performed in the constant pressure and temperature ensemble using the united-atom GROMACS and the all-atom CHARMM22/27 force fields with the GROMACS and NAMD software packages, respectively. The quality of the simulated bilayer structures was evaluated by comparing simulation with experimental results for bilayer thickness, area/lipid, individual molecular-component distributions, continuous and discrete structure factors, and overall scattering-density profiles. Neither the GROMACS nor the CHARMM22/27 simulations reproduced experimental data within experimental error. The widths of the simulated terminal methyl distributions showed a particularly strong disagreement with the experimentally observed distributions. A comparison of the older CHARMM22 with the newer CHARMM27 force fields shows that significant progress is being made in the development of atomic force fields for describing lipid bilayer systems empirically.

Computer Simulation↗

Reversible unfolding of beta-sheets in membranes: a calorimetric study.

The hexapeptide acetyl-Trp-Leu(5) (AcWL(5)) has the remarkable ability to assemble reversibly and spontaneously into beta-sheets on lipid membranes as a result of monomer partitioning followed by cooperative assembly. This system provides a unique opportunity to study the thermodynamics of protein folding in membranes, which we have done using isothermal titration calorimetry (ITC) and differential scanning calorimetry (DSC). The results, which may represent the first example of reversible thermal unfolding of peptides in membranes, help to define the contribution of hydrogen bonding to the extreme thermal stability of membrane proteins. ITC revealed that the enthalpy change for partitioning of monomeric, unstructured AcWL(5) from water into membranes was zero within experimental error over the temperature range of 5 degrees C to 75 degrees C. DSC showed that the beta-sheet aggregates underwent a reversible, endothermic, and very asymmetric thermal transition with a concentration-dependent transition temperature (T(m)) in the range of 60 degrees C to 80 degrees C. A numerical model of nucleation and growth-dependent assembly of oligomeric beta-sheets, proposed earlier to describe beta-sheet formation in membranes, recreated remarkably well the unusual shape and concentration-dependence of the transition peaks. The enthalpy for thermal unfolding of AcWL(5) beta-sheets in the membrane was found to be about 8(+/-1)kcal mol(-1), or about 1.3(+/-0.2)kcal mol(-1) per residue.

Calorimetry↗

Reversible refolding of the diphtheria toxin T-domain on lipid membranes.

The catalytic domain of diphtheria toxin (DT) is translocated across endosomal membranes by the T-domain (DTT) in response to acidification. Understanding the energetics of translocation, besides clarifying the mechanism of translocation, should provide insights into general principles of membrane protein stability and assembly. As a first step, we have evaluated the energetics of DTT binding to lipid vesicles using three single-cysteine mutants (L350C, Q369C, and Y280C) labeled with a 7-nitrobenz-2-oxa-1,3-diazol-4-yl (NBD) fluorophore sensitive to polarity changes. Remarkably strong association with the vesicles was detected for all mutants, even at pH 7 at which DTT is believed to be in a fully folded membrane-incompetent state. Lowering the pH in the presence of anionic membranes resulted in a strong but reversible increase in emission of NBD-labeled mutants, consistent with reversible membrane insertion. This reversibility permitted free energies of DTT interactions with vesicles to be determined for the first time. Free energy values for the three mutants ranged from -8 to -10 kcal mol(-1) at pH 4.3 and from -7 to -8 kcal mol(-1) at pH 7. Insights into the disposition of DTT on membranes were obtained using a novel hydropathy analysis that considers the relative free energies of transmembrane and interfacial interactions as a function of pH. This analysis suggests that interactions at the membrane interface dominate pH-triggered insertion of DTT, implying that the folding pathway involves interfacial intermediates.

Diphtheria Toxin↗

Interfacial folding and membrane insertion of a designed helical peptide.

Nonconstitutive membrane-active proteins, such as diphtheria toxin, must refold on membrane interfaces in the course of membrane penetration. A useful step in deciphering this process is to understand quantitatively the energetics of interface-mediated insertion of model transmembrane helices. A difficulty is that peptides that are sufficiently hydrophobic to span a lipid bilayer have a strong tendency to aggregate in the aqueous phase. To learn how to control the aqueous and membrane behavior of model peptides, we designed a 31-residue peptide (TMX-3) whose properties are described here. TMX-3 has two important structural features: a proline residue in the hydrophobic core that discourages the formation of highly helical aggregates in solution and two histidine residues that allow control of membrane and solution interactions by means of pH changes. The partitioning of TMX-3 into membranes followed complex kinetics, induced helicity, and shifted the histidine pK(a) from 6.8 to approximately 6. Topology measurements disclosed two general modes of TMX-3 binding: interfacial (IF) at low peptide concentrations and partial transmembrane (TM) insertion at higher concentrations. Both modes were reversible and, consequently, suitable for thermodynamic analysis. The free energies of IF partitioning of TMX-3 with deprotonated (pH 7.6) and protonated histidines (pH 4.5) were estimated by fluorescence titration to be -6.7 and -5.0 kcal/mol, respectively. These results show that histidine titration is likely to be important in the pH-dependent refolding of toxins on membrane interfaces and that the most favored state of TMX-3 under any conditions is the IF folded state, which emphasizes the importance of such states in the spontaneous refolding and insertion of diphtheria and other membrane toxins.

Buffers↗

The machinery of membrane protein assembly.

The SecY (bacteria) and Sec61 (eukaryotes) translocon complexes, or protein-conducting channels, work in concert with bound ribosomes to insert proteins into membranes during the first step of membrane protein assembly. The crystallographic structure of an archaeal SecY translocon provides dramatic new insights into the mechanism of translocon function. This structure suggests an explanation for how the translocon can aid in establishing membrane protein topology via the positive-inside rule. The folding of membrane proteins may begin in the ribosome exit tunnel, before entering the translocon, according to cryo-electron microscopy and biophysical studies.

Archaea↗

The progress of membrane protein structure determination.

The rate of membrane protein (MP) structure determination has been examined for the 18-year period following the publication of the first high-resolution crystal structure. The growth is solidly exponential, but lags behind the rate for soluble proteins during the equivalent time period.

Animals↗

Translocons, thermodynamics, and the folding of membrane proteins.

Recent three-dimensional structures of helical membrane proteins present new challenges for the prediction of structure from amino acid sequence. Membrane proteins reside stably in a thermodynamic free energy minimum after release into the membrane's bilayer fabric from the translocon complex. This means that structure prediction is primarily a problem of physical chemistry. But the folding processes within the translocon must also be considered. A distilled overview of the physical principles of membrane protein stability is presented, and extended to encompass translocon-assisted folding.

Calcium-Binding Proteins↗

Determining the membrane topology of proteins: insertion pathway of a transmembrane helix of annexin 12.

We describe a sensitive method for determining the bilayer topology of single-site cysteine-linked NBD fluorescent labels on membrane proteins. Based upon a method developed for peptides [W. C. Wimley and S. H. White (2000) Biochemistry 39, 161-170], it utilizes a novel fluorescence quencher, lysoUB, comprised of a single acyl chain attached to a UniBlue chromophore. The enhanced sensitivity of the method arises from the brightness of the NBD fluorescence and the quenching efficiency of lysoUB, which is not fluorescent. In the course of validating the method, we examined the insertion topology of the D-E helical region of repeat 2 of annexin 12, known to adopt a transbilayer orientation at mildly acidic pH [Langen et al. (1998) Proc. Natl. Acad. Sci. USA 95, 14060-14065]. In the final membrane-inserted state, an NBD label attached to the single-cysteine mutant D134C was found to be in the outer (cis) leaflet, while the one attached to D162C was found in the trans leaflet. But kinetic measurements of NBD fluorescence suggested the existence of a transient intermediate insertion state whose lifetime could be increased by increasing the fraction of anionic lipids in the vesicles. Indeed, the lifetime could be increased for times sufficient for the completion of lysoUB-NBD topology measurements. Such measurements revealed that the D-E region adopts an interfacial topology in the intermediate state with both ends on the cis side of the membrane, consistent with the general concept of interface-directed membrane insertion of proteins [White et al. (2001) J. Biol. Chem. 276, 32395-32398].

4-Chloro-7-nitrobenzofurazan↗

Bucket handle tear of medial plica.

A case of locking of the knee due to a 'bucket handle tear' of the medial plica is described. The sign of clunking could be relieved by pushing the patella medially, so reducing the plica from the trochlea into the medial gutter. Arthroscopic resection cured the condition. There may be association with patellar instability, possibly the lesion is more common than previously recognised.

Adult↗