A systematic molecular dynamics simulation study of temperature dependent bilayer structural properties

Although lipid force fields (FFs) used in molecular dynamics (MD) simulations have proved to be accurate, there has not been a systematic study on their accuracy over a range of temperatures. Motivated by the X-ray and neutron scattering measurements of common phosphatidylcholine (PC) bilayers (Ku?erka et al. BBA. 1808: 2761, 2011), the CHARMM36 (C36) FF accuracy is tested in this work with MD simulations of six common PC lipid bilayers over a wide range of temperatures. The calculated scattering form factors and deuterium order parameters from the C36 MD simulations agree well with the X-ray, neutron, and NMR experimental data. There is excellent agreement between MD simulations and experimental estimates for the surface area per lipid, bilayer thickness (D_B), hydrophobic thickness (D_C), and lipid volume (V_L). The only minor discrepancy between simulation and experiment is a measure of (D_B − D_HH) / 2 where D_HH is the distance between the maxima in the electron density profile along the bilayer normal. Additional MD simulations with pure water and heptane over a range of temperatures provide explanations of possible reasons causing the minor deviation. Overall, the C36 FF is accurate for use with liquid crystalline PC bilayers of varying chain types and over biologically relevant temperatures.     

Osmolyte effects on protein stability and solubility: a balancing act between backbone and side-chains

In adaptation biology the discovery of intracellular osmolyte molecules that in some cases reach molar levels, raises questions of how they influence protein thermodynamics. We've addressed such questions using the premise that from atomic coordinates, the transfer free energy of a native protein (ΔG_tr, N) can be predicted by summing measured water-to-osmolyte transfer free energies of the protein's solvent exposed side chain and backbone component parts. ΔG_tr, D is predicted using a self avoiding random coil model for the protein, and ΔG_tr, D − ΔG_tr, N, predicts the m-value, a quantity that measures the osmolyte effect on the N ? D transition. Using literature and newly measured m-values we show 1:1 correspondence between predicted and measured m-values covering a range of 12 kcal/mol/M in protein stability for 46 proteins and 9 different osmolytes. Osmolytes present a range of side chain and backbone effects on N and D solubility and protein stability key to their biological roles.     

Macromolecular composition of bacteria

Equations are presented that describe the macromolecular composition in exponential bacterial cultures as functions of five parameters: doubling time of the culture (τ), protein per origin of replication (P₀), chromosome replication time (C-period), peptide chain elongation rate (c_p), and the time between termination of replication and cell division (D-period). Implicit in the value for some of these parameters is a specific macromolecular control system: the control of the growth rate (τ), the timing of initiation of rounds of chromosome replication (P₀), and the regulation of cell division (D). The utility of these relations is illustrated by using updated measurements of the macromolecular composition of E. coli B/r to calculate values for the fundamental parameters and to predict the composition of a mutant which has a defect in the control of DNA replication. Furthermore, the meaning of several often-cited physiological parameters (RNA/protein, RNA/cell and RNA/genome) is examined. The relations presented here show that these parameters and their variation with growth rate are not directly relevant to arguments about control of ribosome synthesis or culture growth.     

Heat Resistance and Mechanism of Heat Inactivation in Thermophilic Campylobacters

The heat resistance of Campylobacter jejuni strains AR6 and L51 and the heat resistance of Campylobacter coli strains DR4 and L6 were measured over the temperature range from 50 to 60°C by two methods. Isothermal measurements yielded D₅₅ values in the range from 4.6 to 6.6 min and z values in the range from 5.5 to 6.3°C. Dynamic measurements using differential scanning calorimetry (DSC) during heating at a rate of 10°C/min yielded D₅₅ values of 2.5 min and 3.4 min and z values of 6.3°C and 6.5°C for AR6 and DR4, respectively. Both dynamic and isothermal methods yielded mean D₅₅ values that were substantially greater than those reported previously (0.75 to 0.95 min). DSC analysis of each strain during heating at a rate of 10°C/min yielded a complex series of overlapping endothermic peaks, which were assigned to cell wall lipids, ribosomes, and DNA. Measurement of the decline in the numbers of CFU in calorimetric samples as they were heated showed that the maximum rate of cell death occurred at 56 to 57°C, which is close to the value predicted mathematically from the isothermal measurements of D and z (61°C). Both estimates were very close to the peak m₁ values, 60 to 62°C, which were tentatively identified with unfolding of the 30S ribosome subunit, showing that cell death in C. jejuni and C. coli coincided with unfolding of the most thermally labile regions of the ribosome. Other measurements indicated that several essential proteins, including the α and β subunits of RNA polymerase, might also unfold at the same time and contribute to cell death.     

Tetra(β-phenothiazinyl) zinc phthalocyanine: An easily prepared D4-A system for efficient photoinduced electron transfer

Four identical electron donor (D) moieties, phenothiazines (PTZs), were covalently attached onto the same acceptor (A), zinc phthalocyanine (ZnPc), to form ZnPc(β-PTZ)₄, i.e. D₄-A. The symmetrical D₄-A was synthesized by the condensation method to examine intra-molecular photoinduced electron transfer (PET). The common electron donor-spacer-acceptor (D-A) photosynthetic models, which involve the asymmetrical synthesis of a mono-substituted porphyrin or its analogs, suffer from a low yield and arduous isolation, since D-A is only one of several products (D_n-A or A_n-D, n = 0, 2-4). The D₄-A preparation, however, can be carried out without the problem. The steady state and time-resolved fluorescence of the D₄-A were measured and compared with that of ZnPc(β-R)₄ (R = H, OPh). The result showed that the excited singlet state of phthalocyanine moiety in the D₄-A molecule was efficiently quenched by phenothiazine units owing to intra-molecular PET. The rate constant of PET (k_et) was calculated and the value is much higher than the rate constant of fluorescence emission, intersystem crossing and internal conversion of ZnPc moiety. The laser flash photolysis study revealed the presence of a long-lived charge-separated state due to PET. The results suggest that a D₄-A system can be a more efficient artificial photosynthetic model than D-A towards the practical commercial use.     

Analysis of the primary structure of collagen for the origins of molecular packing

The amino acid sequence in the triplet region of the α1 chain of collagen was analyzed for complementary relationships that would explain the stagger of multiples of 670 Å between the rod-like molecules in the fibril. The analysis was done by moving the sequence of 1011 amino acids past itself and scoring for complementarity between opposing amino acids allowing a range of ±2 to 3 residues. It was found that interactions between amino acids of opposite charge and between large hydrophobic amino acids in the overlapping region between two chains are maximal when the chains are staggered by 0D, 1D, 2D, 3D and 4D, where D = 234 ± 1 residues. The residue repeat derived from this value is 2.86 ± 0.02 Å. The existence of a D separation between interacting residues was shown to be reflected in the actual distribution of large hydrophobic amino acids. Surprisingly, the distribution approximates the pattern ($\text{2D}\text{11}$)₅($\text{D}\text{11}$) repeated over 4.4D intervals. The regularity may arise from structural constraints imposed by super-coiling. The distribution of charged residues is less regular and does not show a well-defined periodicity. However, positively-charged residues tend to be near negatively-charged residues, allowing intramolecular charge neutralization as well as strong intermolecular charge interactions at 0D.     

Influence of lysophospholipid hydrolysis by the catalytic domain of neuropathy target esterase on the fluidity of bilayer lipid membranes

Neuropathy target esterase (NTE) is an integral membrane protein localized in the endoplasmic reticulum in neurons. Irreversible inhibition of NTE by certain organophosphorus compounds produces a paralysis known as organophosphorus compound-induced delayed neuropathy. In vitro, NTE has phospholipase/lysophospholipase activity that hydrolyses exogenously added single-chain lysophospholipids in preference to dual-chain phospholipids, and NTE mutations have been associated with motor neuron disease. NTE's physiological role is not well understood, although recent studies suggest that it may control the cytotoxic accumulation of lysophospholipids in membranes. We used the NTE catalytic domain (NEST) to hydrolyze palmitoyl-2-hydroxy-sn-glycero-3-phosphocholine (p-lysoPC) to palmitic acid in bilayer membranes comprising 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and the fluorophore 1-oleoyl-2-[12-[(7-nitro-2-1,3-benzoxadiazol-4-yl)amino]dodecanoyl]-sn-glycero-3-phosphocholine (NBD-PC). Translational diffusion coefficients (D_L) in supported bilayer membranes were measured by fluorescence recovery after pattern photobleaching (FRAPP). The average D_L for DOPC/p-lysoPC membranes without NEST was 2.44 µm²s^-1 ± 0.09; the D_L for DOPC/p-lysoPC membranes containing NEST and diisopropylphosphorofluoridate, an inhibitor, was nearly identical at 2.45 ± 0.08. By contrast, the D_L for membranes comprising NEST, DOPC, and p-lysoPC was 2.28 ± 0.07, significantly different from the system with inhibited NEST, due to NEST hydrolysis. Likewise, a system without NEST containing the amount of palmitic acid that would have been produced by NEST hydrolysis of p-lysoPC was identical at 2.26 ± 0.06. These results indicate that NTE's catalytic activity can alter membrane fluidity.     

Regular measurement--a new method for biophysical experiment

A system of quantized relations between the value of the quantity being measured and the width of its experimental scattering was experimentally found in the results of measurements of rates of various processes. For determining D, the square of the ratio of the root-mean-square deviation to the mean value of the quantity being measured, particularly long series of stereotypic measurements under stable conditions, so-called regular measurements, are carried out. Regular changes in biochemical, chemical, and physical quantities show that the D value is related by a simple rational expression to the universal dimensionless constant D0 whose numerical value was measured with required accuracy. The simplicity of the ratios of D and D0 may result from the fact that, during regular measurements, the quantum behavior of the system macrodevice-object can be revealed.     

Time-resolved small-angle X-ray scattering study of the folding dynamics of barnase

Structural changes of barnase during folding were investigated using time-resolved small-angle X-ray scattering (SAXS). The folding of barnase involves a burst-phase intermediate, sometimes designated as the denatured state under physiological conditions, D_phys, and a second hidden intermediate. Equilibrium SAXS measurements showed that the radius of gyration (R_g) of the guanidine unfolded state (U) is 26.9 ± 0.7 Å, which remains largely constant over a wide denaturant concentration range. Time-resolved SAXS measurements showed that the R_g value extrapolated from kinetic R_g data to time zero, R_g,0, is 24.3 ± 0.1 Å, which is smaller than that of U but which is expanded from that of folding intermediates of other proteins with similar chain lengths (19 Å). After the burst-phase change, a single-exponential reduction in R_g² was observed, which corresponds to the formation of the native state for the major component containing the native trans proline isomer. We estimated R_g of the minor component of D_phys containing the non-native cis proline isomer (D_phys,cis) to be 25.7 ± 0.6 Å. Moreover, R_g of the major component of D_phys containing the native proline isomer (D_phys,tra) was estimated as 23.9 ± 0.2 Å based on R_g,0. Consequently, both components of the burst-phase intermediate of barnase (D_phys,tra and D_phys,cis) are still largely expanded. It was inferred that D_phys possesses the N-terminal helix and the center of the β-sheet formed independently and that the formation of the remainder of the protein occurs in the slower phase.     

Hydrodynamic properties and structure of fd virus

A length of 8950 ± 200 Å and a diameter of 90 ± 10 Å have been obtained for fd virus from a simultaneous solution of the Broersma equations relating the length and diameter of a rod-like particle to its rotational, D_R, and translational, D_T, diffusion coefficients. Measurements of D_R were by transient electric birefringence, and of D_T by low-angle intensity fluctuation spectroscopy. A mass of (16.4 ± 0.6) × 10⁶ daltons was calculated from the Svedberg equation using our measured values of D_T, the sedimentation coefficient and the density increment. These results, together with the molecular weight of fd DNA, give a total number of major coat protein subunits of 2710 ± 110 and a ratio of nucleotides to protein subunits which is definitely non-integral, 2.30 ± 0.11. These measurements help delineate significant structural differences between fd and other filamentous viruses. Also included in this paper is an Appendix (by L. A. Day & S. A. Berkowitz) concerning the number of nucleotides, 6370 ± 140, and the density and refractive index increments of fd DNA.     

Impact of hapten presentation on antibody binding at lipid membrane interfaces

We report the effects of ligand presentation on the binding of aqueous proteins to solid supported lipid bilayers. Specifically, we show that the equilibrium dissociation constant can be strongly affected by ligand lipophilicity and linker length/structure. The apparent equilibrium dissociation constants (K_D) were compared for two model systems, biotin/anti-biotin and 2,4-dinitrophenyl (DNP)/anti-DNP, in bulk solution and at model membrane surfaces. The binding constants in solution were obtained from fluorescence anisotropy measurements. The surface binding constants were determined by microfluidic techniques in conjunction with total internal reflection fluorescence microscopy. The results showed that the bulk solution equilibrium dissociation constants for anti-biotin and anti-DNP were almost identical, K_D(bulk) = 1.7 ± 0.2 nM vs. 2.9 ± 0.1 nM. By contrast, the dissociation constant for anti-biotin antibody was three orders of magnitude tighter than for anti-DNP at a lipid membrane interface, K_D = 3.6 ± 1.1 nM vs. 2.0 ± 0.2 μM. We postulate that the pronounced difference in surface binding constants for these two similar antibodies is due to differences in the ligands’ relative lipophilicity, i.e., the more hydrophobic DNP molecules had a stronger interaction with the lipid bilayers, rendering them less available to incoming anti-DNP antibodies compared with the biotin/anti-biotin system. However, when membrane-bound biotin ligands were well screened by a poly(ethylene glycol) (PEG) polymer brush, the K_D value for the anti-biotin antibody could also be weakened by three orders of magnitude, 2.4 ± 1.1 μM. On the other hand, the dissociation constant for anti-DNP antibodies at a lipid interface could be significantly enhanced when DNP haptens were tethered to the end of very long hydrophilic PEG lipopolymers (K_D = 21 ± 10 nM) rather than presented on short lipid-conjugated tethers. These results demonstrate that ligand presentation strongly influences protein interactions with membrane-bound ligands.     

Diffusion of Exchangeable Water in Cortical Bone Studied by Nuclear Magnetic Resonance

The rate-limiting step in the delivery of nutrients to osteocytes and the removal of cellular waste products is likely diffusion. The transport of osteoid water across the mineralized matrix of bone was studied by proton nuclear magnetic resonance spectroscopy and imaging by measuring the diffusion fluxes of tissue water in cortical bone specimens from the midshaft of rabbit tibiae immersed in deuterium oxide. From the diffusion coefficient (D_a = (7.8 ± 1.5) × 10⁻⁷ cm²/s) measured at 40°C (close to physiological temperature), it can be inferred that diffusive transport of small molecules from the bone vascular system to the osteocytes occurs within minutes. The activation energy for water diffusion, calculated from D_a measured at four different temperatures, suggests that the interactions between water molecules and matrix pores present significant energy barriers to diffusion. The spatially resolved profile of D_a perpendicular to the cortical surface of the tibia, obtained using a finite difference model, indicates that diffusion rates are higher close to the endosteal and periosteal surfaces, decreasing toward the center of the cortex. Finally, the data reveal a water component (∼30%) diffusing four orders of magnitude more slowly, which is ascribed to water tightly bound to the organic matrix and mineral phase.     

关帝山天然次生针叶林林隙径高比

林隙径高比(D_EG/H)是指林隙直径与林隙高度的比值。它是林隙的一个主要特征因子,是研究森林动态及评价森林采伐强度的一个重要指标。以关帝山三种天然次生针叶林(华北落叶松、云杉、油松林)林隙作为研究对象,分析了3种林分林隙径高比结构,结果为:云杉林林隙径高比D_EG/H以0.6-1.6之间分布最多,占81.82%,油松林林隙径高比主要分布在0.8-1.6之间,占70.72%。华北落叶松林林隙径高比主要分布在0.4-1之间,占97.06%;通过林隙大小与林隙下幼树数量及林隙敏感度与幼树密度之间的散点分布趋势对林隙大小和林隙敏感度两个特征因子进行比较分析,结果为:林隙大小与林隙下幼树数量之间的散点分布无规律,很难反映各自林隙大小与幼树数量之间的具体关系。而D_EG/H与幼树密度之间的散点分布很有规律,能较好的反映幼树密度与林隙径高比之间的关系;利用线性模型、对数模型以及二阶多项分布模型分别对幼树密度和D_EG/H进行回归分析,并利用各自模型的相关系数、参数P值对它们进行比较,结果为:3种模型都可以用来拟合3种林分的幼树密度和林隙敏感度,其中对数模型拟合效果最好。     

On the problem of comparing protein structures: Development and applications of a new method for the assessment of structural similarities of polypeptide conformations

The development of prediction schemes and the search for evolutionary relationships amongst proteins require reliable methods for the comparison of polypeptide structures. It is shown that methods which attempt to describe structural similarities by a single value generally do not yield reliable estimates of the relatedness of two conformations. A new method is reported, called the D_k procedure, which yields a spectrum of deviations between two structures. Each particular D_k value is a measure of the similarity of the diagonals of the distance matrices of the compared conformations, k being the distance of the diagonals relative to the main diagonal.The method has the following features. (1) D_k is independent of chain length; (2) the method yields the relatedness of two conformations in terms of different structural levels; (3) D_k is a high-speed algorithm; (4) the D_k deviations of random structures from any particular conformation are predictable.The following applications are reported. (1) The success of both secondary and tertiary structure predictions are measured in terms of a reliable quality index. (2) The route of a conformation during simulation studies is followed on different structural levels, which exhibit the characteristics of the simulation. (3) The significance of hypotheses on protein folding subject to prediction schemes can be established. (4) A priori information (fixing pieces of secondary structure derived from X-ray investigations during prediction) is extractable from the predicted structures. (5) The evolutionary relatedness of two nucleotide binding proteins is established.The simplicity and speed of the D_k procedure allow its implementation even on minicomputers.     

Chemometric Methods to Quantify 1D and 2D NMR Spectral Differences Among Similar Protein Therapeutics

NMR spectroscopy is an emerging analytical tool for measuring complex drug product qualities, e.g., protein higher order structure (HOS) or heparin chemical composition. Most drug NMR spectra have been visually analyzed; however, NMR spectra are inherently quantitative and multivariate and thus suitable for chemometric analysis. Therefore, quantitative measurements derived from chemometric comparisons between spectra could be a key step in establishing acceptance criteria for a new generic drug or a new batch after manufacture change. To measure the capability of chemometric methods to differentiate comparator NMR spectra, we calculated inter-spectra difference metrics on 1D/2D spectra of two insulin drugs, Humulin R® and Novolin R®, from different manufacturers. Both insulin drugs have an identical drug substance but differ in formulation. Chemometric methods (i.e., principal component analysis (PCA), 3-way Tucker3 or graph invariant (GI)) were performed to calculate Mahalanobis distance (D _M) between the two brands (inter-brand) and distance ratio (D _R) among the different lots (intra-brand). The PCA on 1D inter-brand spectral comparison yielded a D _M value of 213. In comparing 2D spectra, the Tucker3 analysis yielded the highest differentiability value (D _M = 305) in the comparisons made followed by PCA (D _M = 255) then the GI method (D _M = 40). In conclusion, drug quality comparisons among different lots might benefit from PCA on 1D spectra for rapidly comparing many samples, while higher resolution but more time-consuming 2D-NMR-data-based comparisons using Tucker3 analysis or PCA provide a greater level of assurance for drug structural similarity evaluation between drug brands.     

EmrE dimerization depends on membrane environment

The small multi-drug resistant (SMR) transporter EmrE functions as a homodimer. Although the small size of EmrE would seem to make it an ideal model system, it can also make it challenging to work with. As a result, a great deal of controversy has surrounded even such basic questions as the oligomeric state. Here we show that the purified protein is a homodimer in isotropic bicelles with a monomer–dimer equilibrium constant (K_MD^2D) of 0.002–0.009 mol% for both the substrate-free and substrate-bound states. Thus, the dimer is stabilized in bicelles relative to detergent micelles where the K_MD^2D is only 0.8–0.95 mol% (Butler et al. 2004). In dilauroylphosphatidylcholine (DLPC) liposomes K_MD^2D is 0.0005–0.0008 mol% based on Förster resonance energy transfer (FRET) measurements, slightly tighter than bicelles. These results emphasize the importance of the lipid membrane in influencing dimer affinity.     

Differential voltage-sensitivity of D2-like dopamine receptors

Agonist potency at some neurotransmitter receptors has been shown to be regulated by transmembrane voltage, a mechanism which has been suggested to play a crucial role in the regulation of neurotransmitter release by autoreceptors and in synaptic plasticity. We have recently described the voltage-sensitivity of the dopamine D_2L receptor and we now extend our studies to include the other members of the D₂-like receptor subfamily; the D_2S, D₃, and D₄ dopamine receptors. Electrophysiological recordings were performed on Xenopus oocytes coexpressing human dopamine D_2S, D₃, or D₄ receptors with G protein-coupled potassium (GIRK) channels. Comparison of concentration-response relationships at −80 mV and at 0 mV for dopamine-mediated GIRK activation revealed significant rightward shifts for both D_2S and D₄ upon depolarization. In contrast, the concentration-response relationships for D₃-mediated GIRK activation were not appreciably different at the two voltages. Our findings provide new insight into the functional differences of these closely related receptors.     

Room-Temperature Distance Measurements of Immobilized Spin-Labeled Protein by DEER/PELDOR

Nitroxide spin labels are used for double electron-electron resonance (DEER) measurements of distances between sites in biomolecules. Rotation of gem-dimethyls in commonly used nitroxides causes spin echo dephasing times (T_m) to be too short to perform DEER measurements at temperatures between ∼80 and 295 K, even in immobilized samples. A spirocyclohexyl spin label has been prepared that has longer T_m between 80 and 295 K in immobilized samples than conventional labels. Two of the spirocyclohexyl labels were attached to sites on T4 lysozyme introduced by site-directed spin labeling. Interspin distances up to ∼4 nm were measured by DEER at temperatures up to 160 K in water/glycerol glasses. In a glassy trehalose matrix the T_m for the doubly labeled T4 lysozyme was long enough to measure an interspin distance of 3.2 nm at 295 K, which could not be measured for the same protein labeled with the conventional 1-oxyl-2,2,5,5-tetramethyl-3-pyrroline-3-(methyl)methanethio-sulfonate label.     

Determination of wave speed and wave separation in the arteries using diameter and velocity

The determination of arterial wave speed and the separation of the forward and backward waves have been established using simultaneous measurements of pressure (P) and velocity (U). In this work, we present a novel algorithm for the determination of local wave speed and the separation of waves using the simultaneous measurements of diameter (D) and U. The theoretical basis of this work is the solution of the 1D equations of flow in elastic tubes. A relationship between D and U is derived, from which, local wave speed can be determined; C=±0.5(dU_±/d ln D_±). When only unidirectional waves are present, this relationship describes a linear relationship between ln D and U. Therefore, constructing a ln DU-loop should result in a straight line in the early part of the cycle when it is most probable that waves are running in the forward direction. Using this knowledge of wave speed, it is also possible to derive a set of equations to separate the forward and backward waves from the measured D and U waveforms. Once the forward and backward waveforms of D and U are established, we can calculate the energy carried by the forward and backward waves, in a similar way to that of wave intensity analysis. In this paper, we test the new algorithm in vitro and present results from data measured in the carotid artery of human and the ascending aorta of canine. We conclude that the new technique can be reproduced in vitro, and in different vessels of different species, in vivo. The new algorithm is easy to use to determine wave speed and separate D and U waveforms into their forward and backward directions. Using this technique has the merits of utilising noninvasive measurements, which would be useful in the clinical setting.