Erythematous Plaques and Tense Bullae in an Infant.

Although often thought of as a disease of the elderly, bullous pemphigoid is the second most common bullous disease in infants. Infantile bullous pemphigoid is extremely rare and may be easily confused with other skin diseases such as epidermolysis bullosa and chronic bullous disease of childhood. There appears to be a paucity of literature on unique clinical presentations of infantile bullous pemphigoid. In this report, we describe a case of infantile bullous pemphigoid, which presented with tense bullae in a widespread distribution, including many labial bullae. The rash initially began on this patient's temples and ears four days prior. We believe this case will be of interest as it demonstrates a rare infantile disease with an unusual clinical presentation. It is important to consider infantile bullous pemphigoid in a patient presenting with tense bullae and initiate appropriate diagnostic studies.

Changes in Disease Activity and Damage Over Time in Patients With Morphea.

Importance: Prospective studies of the disease course in patients with morphea are lacking, particularly those comparing adults and children. Objective: To investigate the disease course in patients with morphea treated with standard-of-care therapy using validated clinical outcome measures. Design, Setting, and Participants: Prospective cohort study of 130 adults and children from the Morphea in Adults and Children cohort with at least 2 years of clinical follow-up and Localized Scleroderma Cutaneous Assessment Tool scores recorded at each study visit. Study patients were seen at a tertiary referral center (UT Southwestern Medical Center, Dallas, Texas) from November 1, 2008, through April 1, 2016. The dates of analysis were May 2016 through July 2019. Exposures: All patients received standard-of-care therapy. Main Outcomes and Measures: Patterns in disease activity and recurrence were examined. The time to recurrence of morphea disease activity from the first visit with inactive disease was assessed using survival analysis with the log-rank test to compare differences between morphea subtypes. Results: In total, 130 adults and children (663 study visits) were included in this study. The mean (SD) age of patients was 34.4 (23.8) years, and 101 of 130 (78%) were female. The mean (SD) follow-up was 4.3 (1.7) years. Fifty patients had at least 5 years of follow-up. Most patients were white individuals (96 of 130 [74%]) and had linear subtype (72 of 130 [55%]) or generalized subtype (40 of 130 [31%]). Overall, 13 of 30 (43%) with generalized subtype had recurrence of disease activity compared with 14 of 66 (21%) with linear subtype (hazard ratio, 3.28; 95% CI, 1.38-7.79). The median (interquartile range) time to first recurrence of disease activity after initial resolution of disease activity was 1.1 (0.8-1.9) years for generalized subtype and 2.3 (1.0-3.3) years for linear subtype. Of the 50 patients followed up for at least 5 years, 18 (36%) had recurrence of disease activity. Conclusions and Relevance: Disease activity appeared to improve in most patients with morphea over 6 to 12 months using previously published treatment plans, underscoring their effectiveness. Sclerosis improved more slowly (over 2-5 years), often after discontinuation of treatment, but atrophy increased slightly as sclerosis subsided. Standard-of-care therapy appears to improve disease activity, which allows sclerosis to improve, and provides relative stability of other features of disease damage. A substantial number of patients, particularly those with generalized subtype, have a relapsing-remitting course over many years. Patients with morphea should be monitored for recurrent disease activity over extended periods.

Serial tempering without exchange.

Serial tempering is a computational method that turns the temperature T (or more generally any independent λ parameter) into a dynamical variable. It is shown that, under conditions for which this variable is fast, serial tempering is equivalent to the umbrella sampling method with a single effective potential. This equivalence is demonstrated using both a small one-dimensional system and a small solvated peptide. The suggestion is then made to replace the serial tempering protocol with the equivalent umbrella sampling calculation. This approach, serial tempering without exchange (STeWiE), has the same performance as serial tempering in the limit that exchanges are frequent, is simpler to implement, and has fewer adjustable parameters than conventional serial tempering. The equivalence of serial tempering and STeWiE also provides a convenient route for estimating and optimizing the performance of serial tempering simulations and other generalized-ensemble methods.

Energy landscape of the trpzip2 peptide.

Replica exchange simulations are used to study the energy landscape of trpzip2, a model beta-hairpin system, using the AMBER99sb force field and explicit solvent. The total simulation time is 300 ns per replica (approximately 10 mus total). The trp side chains are observed to adopt multiple packing arrangements with a freezing temperature below 273 K in the simulated system. The secondary structure and native hydrogen bonds melt out cooperatively around 273 K. The residual beta-strand structure and antiparallel bonding persist at high temperature. These results provide a model for the three apparent melting transitions observed experimentally in this system. The dominant folding mechanism of trpzip2 in this model appears to be zipping, which is consistent with recent measurements on similar hairpins. Structures for which the turn is native-like and the termini are non-native-like collectively form a metastable intermediate. Most of the stabilizing enthalpy is gained after the formation of the turn. Equilibrium thermodynamic quantities are compared against experiment. Although the AMBER99sb force field reproduces the native structure with good fidelity, the stability of the native state is significantly underpredicted with a melting temperature near 273 K, and the relative heat capacity is only about one tenth of its experimental value.

Test of the Gouy-Chapman theory for a charged lipid membrane against explicit-solvent molecular dynamics simulations.

A wealth of experimental data has verified the applicability of the Gouy-Chapman (GC) theory to charged lipid membranes. Surprisingly, a validation of GC by molecular dynamics (MD) simulations has been elusive. Here, we report a test of GC against extensive MD simulations of an anionic lipid bilayer solvated by water at different concentrations of NaCl or KCl. We demonstrate that the ion distributions from the simulations agree remarkably well with GC predictions when information on the adsorption of counterions to the bilayer is incorporated.

Quantitative computer simulations of biomolecules: a snapshot.

A recent workshop titled "Quantitative Computational Biophysics" at Florida State University provided an overview of the state of the art in quantitative modeling of biomolecular systems. The presentations covered a wide range of interrelated topics, including the development and validation of force fields, the modeling of protein-protein interactions, the sampling of conformational space, and the assessment of equilibration and statistical errors. Substantial progress in all these areas was reported.

Determining the solution conformational entropy of O-linked oligosaccharides at quasi-physiological conditions: size-exclusion chromatography and molecular dynamics.

The physiological functions of oligosaccharides are influenced by a number of structural parameters such as anomeric configuration, glycosidic linkage, and degree of polymerization. These parameters affect the conformation of the oligosaccharides which, in turn, is responsible for characteristics such as aptameric and enzymatic binding, chiral recognition, and the structural targeting of bacterial and parasitic recognition events. Here, we measure the solution conformational entropy (DeltaS) of two series of oligosaccharides, linear malto- and cellooligosaccharides, using size-exclusion chromatography (SEC). For each series, we have determined DeltaS as a function of degree of polymerization (DP). The choice of oligosaccharides studied also allowed us to compare the influence of anomeric configuration on DeltaS, and to do so as a function of DP. Studies were conducted in water at physiological temperature and pH in order to resemble conditions within the human body. Experimental results were augmented with results from molecular dynamics computer modeling simulations in aqueous solvent. A comparison between experimental and computational data showed how the techniques can complement each other. An example of the latter is the considerable enthalpic contribution to the chromatographic separation of alpha- and gamma-cyclodextrin, which may have gone unnoticed if not for the large discrepancy between the results obtained by the separate techniques.

A method to determine dielectric constants in nonhomogeneous systems: application to biological membranes.

Continuum electrostatic models have had quantitative success in describing electrostatic-mediated phenomena on atomistic scales; however, there continues to be significant disagreement about how to assign dielectric constants in mixed, nonhomogeneous systems. We introduce a method for determining a position-dependent dielectric profile from molecular dynamics simulations. In this method, the free energy of introducing a test charge is computed two ways: from a free energy perturbation calculation and from a numerical solution to Poisson's Equation. The dielectric profile of the system is then determined by minimizing the discrepancy between these two calculations simultaneously for multiple positions of the test charge. We apply this method to determine the dielectric profile of a lipid bilayer surrounded by water. We find good agreement with dielectric models for lipid bilayers obtained by other approaches. The free energy of transferring an ion from bulk water to the lipid bilayer computed from the atomistic simulations indicates that large errors are introduced when the bilayer is represented as a single slab of low dielectric embedded in the higher-dielectric solvent. Significant improvement results from introducing an additional layer of intermediate dielectric ( approximately 3) on each side of the low dielectric core extending from approximately 12 A to 18 A. A small dip in transfer free energy just outside the lipid headgroups indicates the presence of a very high dielectric. These results have implications for the design of implicit membrane models and our understanding of protein-membrane interactions.

How Efficient Is Replica Exchange Molecular Dynamics? An Analytic Approach.

Replica exchange molecular dynamics (REMD) has become a standard technique for accelerating relaxation in biosimulations. Despite its widespread use, questions remain about its efficiency compared with conventional, constant temperature molecular dynamics (MD). An analytic approach is taken to describe the relative efficiency of REMD with respect to MD. This is applied to several simple two-state models and to several real proteins-protein L and the B domain of protein A-to predict the relative efficiency of REMD with respect to MD in actual applications. In agreement with others, we find the following: as long as there is a positive activation energy for folding, REMD is more efficient than MD; the effectiveness of REMD is strongly dependent on the activation enthalpy; and the efficiency of REMD for actual proteins is a strong function of the maximum temperature. Choosing the maximum temperature too high can result in REMD becoming significantly less efficient than conventional MD. A good rule of thumb appears to be to choose the maximum temperature of the REMD simulation slightly above the temperature at which the enthalpy for folding vanishes. Additionally, we find that the number of replicas in REMD, while important for simulations shorter than one or two relaxation times, has a minimal effect on the asymptotic efficiency of the method.

Replica exchange simulation of reversible folding/unfolding of the Trp-cage miniprotein in explicit solvent: on the structure and possible role of internal water.

We simulate the folding/unfolding equilibrium of the 20-residue miniprotein Trp-cage. We use replica exchange molecular dynamics simulations of the AMBER94 atomic detail model of the protein explicitly solvated by water, starting from a completely unfolded configuration. We employ a total of 40 replicas, covering the temperature range between 280 and 538 K. Individual simulation lengths of 100 ns sum up to a total simulation time of about 4 micros. Without any bias, we observe the folding of the protein into the native state with an unfolding-transition temperature of about 440 K. The native state is characterized by a distribution of root mean square distances (RMSD) from the NMR data that peaks at 1.8A, and is as low as 0.4A. We show that equilibration times of about 40 ns are required to yield convergence. A folded configuration in the entire extended ensemble is found to have a lifetime of about 31 ns. In a clamp-like motion, the Trp-cage opens up during thermal denaturation. In line with fluorescence quenching experiments, the Trp-residue sidechain gets hydrated when the protein opens up, roughly doubling the number of water molecules in the first solvation shell. We find the helical propensity of the helical domain of Trp-cage rather well preserved even at very high temperatures. In the folded state, we can identify states with one and two buried internal water molecules interconnecting parts of the Trp-cage molecule by hydrogen bonds. The loss of hydrogen bonds of these buried water molecules in the folded state with increasing temperature is likely to destabilize the folded state at elevated temperatures.

Indole localization in lipid membranes revealed by molecular simulation.

It is commonly known that the amino acid residue tryptophan and its side-chain analogs, e.g., indole, are strongly attracted to the interfacial region of lipid bilayers. Phenylalanine and its side-chain analogs, e.g., benzene, do not localize in the interface but are distributed throughout the lipid bilayer. We use molecular dynamics to investigate the details of indole and benzene localization and orientation within a POPC bilayer and the factors that lead to their different properties. We identify three sites in the bilayer at which indole is localized: 1), a site in the interface near the glycerol moiety; 2), a weakly bound site in the interface near the choline moiety; and 3), a weakly bound site in the center of the bilayer's hydrocarbon core. Benzene is localized in the same three positions, but the most stable position is the hydrocarbon core followed by the site near the glycerol moiety. Transfer of indole from water to the hydrocarbon core shows a classic hydrophobic effect. In contrast, interfacial binding is strongly enthalpy driven. We use several different sets of partial charges to investigate the factors that contribute to indole's and benzene's orientational and spatial distribution. Our simulations show that a number of electrostatic interactions appear to contribute to localization, including hydrogen bonding to the lipid carbonyl groups, cation-pi interactions, interactions between the indole dipole and the lipid bilayer's strong interfacial electric field, and nonspecific electrostatic stabilization due to a mismatch in the variation of the nonpolar forces and local dielectric with position in the bilayer.

Folding is not required for bilayer insertion: replica exchange simulations of an alpha-helical peptide with an explicit lipid bilayer.

We implement the replica exchange molecular dynamics algorithm to study the interactions of a model peptide (WALP-16) with an explicitly represented DPPC membrane bilayer. We observe the spontaneous, unbiased insertion of WALP-16 into the DPPC bilayer and its folding into an alpha-helix with a transbilayer orientation. The free energy surface suggests that the insertion of the peptide into the DPPC bilayer precedes secondary structure formation. Although the peptide has some propensity to form a partially helical structure in the interfacial region of the DPPC/water system, this state is not a productive intermediate but rather an off-pathway trap for WALP-16 insertion. Equilibrium simulations show that the observed insertion/folding pathway mirrors the potential of mean force (PMF). Calculation of the enthalpic and entropic contributions to this PMF show that the surface bound conformation of WALP-16 is significantly lower in energy than other conformations, and that the insertion of WALP-16 into the bilayer without regular secondary structure is enthalpically unfavorable by 5-10 kcal/mol/residue. The observed insertion/folding pathway disagrees with the dominant conceptual model, which is that a surface-bound helix is an obligatory intermediate for the insertion of alpha-helical peptides into lipid bilayers. In our simulations, the observed insertion/folding pathway is favored because of a large (>100 kcal/mol) increase in system entropy that occurs when the unstructured WALP-16 peptide enters the lipid bilayer interior. The insertion/folding pathway that is lowest in free energy depends sensitively on the near cancellation of large enthalpic and entropic terms. This suggests the possibility that intrinsic membrane peptides may have a diversity of insertion/folding behaviors depending on the exact system of peptide and lipid under consideration.

Simulation of the folding equilibrium of alpha-helical peptides: a comparison of the generalized Born approximation with explicit solvent.

We compare simulations using the generalized Born/surface area (GB/SA) implicit solvent model with simulations using explicit solvent (transferable intermolecular potential 3 point, TIP3P) to test the GB/SA algorithm. We use the replica exchange molecular dynamics method to sample the conformational phase space of two alpha-helical peptides, A21 and the Fs, by using two different classical potentials and both water models. We find that when using GB/SA: (i) A21 is predicted to be more helical than the Fs peptide at all temperatures; (ii) the native structure of the Fs peptide is predicted to be a helical bundle instead of a single helix; and (iii) the persistence length and most probable end-to-end distance are too large in the unfolded state when compared against the explicit solvent simulations. We find that the potential of mean force in the phi(psi) plane is markedly different in the two solvents, making the two simulated peptides respond differently when the backbone torsions are perturbed. A fit of the temperature melting curves obtained in these simulations to a Lifson-Roig model finds that the GB/SA model has an unphysically large nucleation parameter, whereas the explicit solvent model produces values similar to experiment.

Peptide folding simulations.

Developments in the design of small peptides that mimic proteins in complexity, recent advances in nanosecond time-resolved spectroscopy methods to study peptides and the development of modern, highly parallel simulation algorithms have come together to give us a detailed picture of peptide folding dynamics. Two newly implemented simulation techniques, parallel replica dynamics and replica exchange molecular dynamics, can now describe directly from simulations the kinetics and thermodynamics of peptide formation, respectively. Given these developments, the simulation community now has the tools to verify and validate simulation protocols and models (forcefields).

Specific and nonspecific collapse in protein folding funnels.

Experiments with fast folding proteins are beginning to address the relationship between collapse and folding. We investigate how different scenarios for folding can arise depending on whether the folding and collapse transitions are concurrent or whether a nonspecific collapse precedes folding. Many earlier studies have focused on the limit in which collapse is fast compared to the folding time; in this work we focus on the opposite limit where, at the folding temperature, collapse and folding occur simultaneously. Real proteins exist in both of these limits. The folding mechanism varies substantially in these two regimes. In the regime of concurrent folding and collapse, nonspecific collapse now occurs at a temperature below the folding temperature (but slightly above the glass transition temperature).