Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale

The rapidly expanding body of available genomic and protein structural data provides a rich resource for understanding protein dynamics with biomolecular simulation. While computational infrastructure has grown rapidly, simulations on an omics scale are not yet widespread, primarily because software infrastructure to enable simulations at this scale has not kept pace. It should now be possible to study protein dynamics across entire (super)families, exploiting both available structural biology data and conformational similarities across homologous proteins. Here, we present a new tool for enabling high-throughput simulation in the genomics era. Ensembler takes any set of sequences—from a single sequence to an entire superfamily—and shepherds them through various stages of modeling and refinement to produce simulation-ready structures. This includes comparative modeling to all relevant PDB structures (which may span multiple conformational states of interest), reconstruction of missing loops, addition of missing atoms, culling of nearly identical structures, assignment of appropriate protonation states, solvation in explicit solvent, and refinement and filtering with molecular simulation to ensure stable simulation. The output of this pipeline is an ensemble of structures ready for subsequent molecular simulations using computer clusters, supercomputers, or distributed computing projects like Folding@home. Ensembler thus automates much of the time-consuming process of preparing protein models suitable for simulation, while allowing scalability up to entire superfamilies. A particular advantage of this approach can be found in the construction of kinetic models of conformational dynamics—such as Markov state models (MSMs)—which benefit from a diverse array of initial configurations that span the accessible conformational states to aid sampling. We demonstrate the power of this approach by constructing models for all catalytic domains in the human tyrosine kinase family, using all available kinase catalytic domain structures from any organism as structural templates. Ensembler is free and open source software licensed under the GNU General Public License (GPL) v2. It is compatible with Linux and OS X. The latest release can be installed via the conda package manager, and the latest source can be downloaded from https://github.com/choderalab/ensembler.     

Quartz Crystal Microbalance with Dissipation Monitoring: Enabling Real-Time Characterization of Biological Materials and Their Interactions

In recent years, there has been a rapid growth in the number of scientific reports in which the quartz crystal microbalance (QCM) technique has played a key role in elucidating various aspects of biological materials and their interactions. This article illustrates some key advances in the development of a special variation of this technique called quartz crystal microbalance with dissipation monitoring (QCM-D). The main feature and advantage of QCM-D, compared with the conventional QCM, is that it in addition to measuring changes in resonant frequency (Δf), a simultaneous parameter related to the energy loss or dissipation (ΔD) of the system is also measured. Δf essentially measures changes in the mass attached to the sensor surface, while ΔD measures properties related to the viscoelastic properties of the adlayer. Thus, QCM-D measures two totally independent properties of the adlayer. The focus of this review is an overview of the QCM-D technology and highlights of recent applications. Specifically, recent applications dealing with DNA, proteins, lipids, and cells will be detailed. This is not intended as a comprehensive review of all possible applications of the QCM-D technology, but rather a glimpse into a few highlighted application areas in the biomolecular field that were published in 2007.     

The Human–Animal Interaction Scale: Development and Evaluation

The purpose of this study was to develop the Human–Animal Interaction Scale (HAIS) and evaluate its reliability and validity. The HAIS is a 24-item self-report instrument designed to describe and quantify behaviors performed by humans and nonhuman animals during an episode of interaction (e.g., engaging with a pet, participating in an animal-assisted intervention). Participants were 295 adult volunteers who completed the HAIS in one of several different contexts, including both laboratory and applied settings. The scale was tested across several different species, including companion animals (i.e., dogs and cats), small caged animals (i.e., rats, rabbit, hedgehog), and horses. Analyses indicate good reliability, with a Cronbach’s alpha of 0.82 overall and alphas of 0.72 and higher across the different species and settings. Test-retest analyses indicate ratings remain consistent up to one week following an interaction. Evidence of construct validity was gathered by comparing HAIS ratings with other well-established measures of related constructs, as well as comparing participant reports with researcher observations. Potential uses in basic and applied research are discussed.     

Interaction sequences between chimpanzees and human visitors at the Zoo

Data were collected on the behavior and physical characteristics of 259 human visitors and 24 chimpanzees at Chester Zoo. The successive responses of humans and chimpanzees to each other's behavior were recorded, the resulting long sequence being referred to as an interaction sequence. There was no particular set of characteristics that distinguished interactors from noninteractors in either humans or chimpanzees, although there was some evidence that chimpanzees were particularly likely to respond to men carrying objects. Chimpanzee responses were random with respect to the previous human behavior, but human responses were significantly associated with the preceding chimpanzee behavior. In particular, chimpanzee sounds were likely to be followed by human sounds, and begging was likely to be followed by the offer of food. Interaction sequences varied in length, but 9% of chimpanzee-initiated sequences went as far as a ninth interaction. Sequences resulted in the chimpanzees being given food in 25% of human-initiated, but only 8% of chimpanzee-initiated sequences. The results are consistent with the interpretation that humans and chimpanzees are motivated to interact with one another and that the chimpanzees do this primarily to obtain food. © 1995 Wiley-Liss, Inc.     

Interaction between polylysine monolayer and DNA at the air-water interface

The interaction of a polylysine amphiphile, which consists of a poly-L- or -D-lysine (1L or 1D) segment and two long alkyl chains at the C-terminus, with polynucleotides was studied with respect to the highly organized structure of polylysine assemblies on water. The results of surface pressure-area isotherm measurement showed that both of 1L and 1D formed stable monolayers on water in a neutral pH region. The secondary structure of polylysine segment for the surface monolayer was examined by means of circular dichroism and Fourier transform infrared spectroscopies. The helical structure was retained even at neutral pH, at which polylysine has been known to form a complete random coiled conformation in bulk solution. Protonated, positively charged and coiled 1L monolayer could interact electrostatically with guest polyanions including DNA in the subphase, and at the same time the conformation of the polylysine segment was converted from a random coil to an alpha-helix. Deprotonated, helical monolayers did not interact with single stranded polyadenylic acid, but with double stranded DNA. Double stranded DNA was found to interact more strongly with right-handed 1L monolayer than left-handed 1D monolayer. An obvious difference in the melting temperatures for these complexes was observed and discussed on the basis of difference in the interaction mode.     

Real-Time Measurements of the Interaction between Single Cells of Listeria monocytogenes and Nisin on a Solid Surface

A method to obtain real-time measurements of the interactions between nisin and single cells of Listeria monocytogenes on a solid surface was developed. This method was based on fluorescence ratio-imaging microscopy and measurements of changes in the intracellular pH (pH_i) of carboxyfluorescein succinimidyl ester-stained cells during exposure to nisin. Immobilized cells were placed in a chamber mounted on a microscope and attached to a high-precision peristaltic pump which allowed rapid changes in the nisin concentration. In the absence of nisin, the pH_i of L. monocytogenes was almost constant (approximately pH 8.0) and independent of the external pH in the pH range from 5.0 to 9.0. In the presence of nisin, dissipation of the pH gradient (ΔpH) was observed, and this dissipation was both time and nisin concentration dependent. The dissipation of ΔpH resulted in cell death, as determined by the number of CFU. In the model system which we used the immobilized cells were significantly more resistant to nisin than the planktonic cells. The kinetics of ΔpH dissipation for single cells revealed a variable lag phase depending on the nisin concentration, which was followed by a very rapid decrease in pH_i within 1 to 2 min. The differences in nisin sensitivity between single cells in a L. monocytogenes population were insignificant for cells grown to the stationary phase in a liquid laboratory substrate, but differences were observed for cells grown on an agar medium under similar conditions, which resulted in some cells having increased resistance to nisin.     

Characterization of the Interaction between the Chlamydial Adhesin OmcB and the Human Host Cell

In a previous study, we reported that the OmcB protein from Chlamydia pneumoniae mediates adhesion of the infectious elementary body to human HEp-2 cells by interacting with heparin/heparan sulfate-like glycosaminoglycans (GAGs) via basic amino acids located in the first of a pair of XBBXBX heparin-binding motifs (K. Moelleken and J. H. Hegemann, Mol. Microbiol. 67:403–419, 2008). In the present study, we show that the basic amino acid at position 57 (arginine) in the first XBBXBX motif, the basic amino acid at position 61 (arginine) in the second motif, and another amino acid (lysine 69) C terminal to it play key roles in the interaction. In addition, we show that discrimination between heparin-dependent and -independent adhesion by C. trachomatis OmcBs is entirely dependent on three variable amino acids in the so-called variable domain C terminal to the conserved XBBXBX motif. Here, the predicted conformational change in the secondary structure induced by the proline at position 66 seems to be crucial for heparin recognition. Finally, we performed neutralization experiments using different anti-heparan sulfate antibodies to gain insight into the nature of the GAGs recognized by OmcB. The results suggest that C. trachomatis serovar L2 OmcB interacts with 6-O-sulfated domains of heparan sulfate, while C. pneumoniae OmcB apparently interacts with domains of heparan sulfate harboring a diverse subset of O-sulfations.     

Tuberization in Potato at High Temperatures: Interaction between Temperature and Irradiance

Potato plants (Solanum tuberosum L., cv. Sebago) responded similarlyto high temperatures and low irradiance by diverting dry matterto the shoots rather than the tubers, and changes were notedin a range of morphological characteristics. It is proposedthat the effect of both high temperature and low irradianceis brought about by the increased production of a growth substance,possibly gibberellin, which inhibits tuber formation, and thattuber yield is determined by the balance between temperatureand irradiance. Solanum tuberosum L., potato, tuberization, temperature, irradiance, gibberellin     

Rat peptidylglycine alpha-amidating enzyme: the relation between activities at neutral and alkaline pH Values

A substantially high level of alpha-amidating activity at an alkaline pH (8-9.5), often seen as another pH optimum peak in addition to the neutral one, has been observed in various rat tissues. We have also found that crude enzymes from rat brain, pituitary, and small intestine showed a pH profile with two pH optima at neutral pH (6.5-7) and alkaline pH (8.5-9) when D-Tyr-Val-Gly was used as substrate. With a combination of ion-exchange and gel filtration chromatographies, we obtained two fractions, S-1 and S-2, from rat brain; S-1 contained an alpha-amidating enzyme of an apparent molecular weight of 36,000 (36K enzyme) exhibiting a single pH optimum at 8.5. On the other hand, S-2 apparently showed almost no or only marginal activity at either pH 7 or 8.5, but when S-2 was combined with S-1, a neutral pH optimum at 7 could be elicited. The factor in S-2 that was responsible for this combined action was a protein of an apparent molecular weight of 41,000 (41K protein). Both proteins were found to be colocalized in the same subcellular organelle, probably in the secretory granule. It seems likely, then, that the pH profiles characterized by two optimal peaks seen in crude rat enzymes can be attributed to the presence at an appropriate ratio of the 41K protein and 36K enzyme.     

芦丁与人血清白蛋白相互作用的紫外可见光谱特性研究

本文通过测定芦丁与HSA相互作用前后的紫外可见吸收光谱、圆二色性及人血清白蛋白(HSA)的荧光特性,研究了芦丁与HSA结合作用。结果表明,芦丁在紫外区有三个特征的吸收峰(264.0、285.5及354.5nm)、在330～300 nm及300～230 nm处显示圆二色性,HSA引起芦丁紫外可见吸收光谱波峰红移;芦丁与HSA相互作用后,不引起HSA二级结构的改变,但对其三级结构有影响,同时对HSA荧光激发及发生光谱最大峰位及幅度有影响。     

Walking to the Beat of Their Own Drum: How Children and Adults Meet Timing Constraints

Walking requires adapting to meet task constraints. Between 5- and 7-years old, children’s walking approximates adult walking without constraints. To examine how children and adults adapt to meet timing constraints, 57 5- to 7-year olds and 20 adults walked to slow and fast audio metronome paces. Both children and adults modified their walking. However, at the slow pace, children had more trouble matching the metronome compared to adults. The youngest children’s walking patterns deviated most from the slow metronome pace, and practice improved their performance. Five-year olds were the only group that did not display carryover effects to the metronome paces. Findings are discussed in relation to what contributes to the development of adaptation in children.     

Molecular Analysis of the Interaction between Human PTPN21 and the Oncoprotein E7 from Human Papillomavirus Genotype 18

Human papillomaviruses (HPVs) cause cellular hyperproliferation-associated abnormalities including cervical cancer. The HPV genome encodes two major viral oncoproteins, E6 and E7, which recruit various host proteins by direct interaction for proteasomal degradation. Recently, we reported the structure of HPV18 E7 conserved region 3 (CR3) bound to the protein tyrosine phosphatase (PTP) domain of PTPN14, a well-defined tumor suppressor, and found that this intermolecular interaction plays a key role in E7-driven transformation and tumorigenesis. In this study, we carried out a molecular analysis of the interaction between CR3 of HPV18 E7 and the PTP domain of PTPN21, a PTP protein that shares high sequence homology with PTPN14 but is putatively oncogenic rather than tumor-suppressive. Through the combined use of biochemical tools, we verified that HPV18 E7 and PTPN21 form a 2:2 complex, with a dissociation constant of 5 nM and a nearly identical binding manner with the HPV18 E7 and PTPN14 complex. Nevertheless, despite the structural similarities, the biological consequences of the E7 interaction were found to differ between the two PTP proteins. Unlike PTPN14, PTPN21 did not appear to be subjected to proteasomal degradation in HPV18-positive HeLa cervical cancer cells. Moreover, knockdown of PTPN21 led to retardation of the migration/invasion of HeLa cells and HPV18 E7-expressing HaCaT keratinocytes, which reflects its protumor activity. In conclusion, the associations of the viral oncoprotein E7 with PTPN14 and PTPN21 are similar at the molecular level but play different physiological roles.     

Compensatory Interactions between Sir3p and the Nucleosomal LRS Surface Imply Their Direct Interaction

The previously identified LRS (Loss of rDNA Silencing) domain of the nucleosome is critically important for silencing at both ribosomal DNA and telomeres. To understand the function of the LRS surface in silencing, we performed an EMS mutagenesis screen to identify suppressors of the H3 A75V LRS allele. We identified dominant and recessive mutations in histones H3, H4, and dominant mutations in the BAH (Bromo Adjacent Homology) domain of SIR3. We further characterized a surface of Sir3p critical for silencing via the LRS surface. We found that all alleles of the SIR3 BAH domain were able to 1) generally suppress the loss of telomeric silencing of LRS alleles, but 2) could not suppress SIN (Swi/Snf Independent) alleles or 3) could not suppress the telomeric silencing defect of H4 tail alleles. Moreover, we noticed a complementary trend in the electrostatic changes resulting from most of the histone mutations that gain or lose silencing and the suppressor alleles isolated in SIR3, and the genes for histones H3 and H4. Mutations in H3 and H4 genes that lose silencing tend to make the LRS surface more electronegative, whereas mutations that increase silencing make it less electronegative. Conversely, suppressors of LRS alleles in either SIR3, histone H3, or H4 also tend to make their respective surfaces less electronegative. Our results provide genetic evidence for recent data suggesting that the Sir3p BAH domain directly binds the LRS domain. Based on these findings, we propose an electrostatic model for how an extensive surface on the Sir3p BAH domain may regulate docking onto the LRS surface.     

Structural and Mechanistic Insights into the Interaction between Pyk2 and Paxillin LD Motifs

Proline-rich tyrosine kinase 2 (Pyk2) is a member of the focal adhesion kinase (FAK) subfamily of cytoplasmic tyrosine kinases. The C-terminal Pyk2-focal adhesion targeting (FAT) domain binds to paxillin, an adhesion molecule. Paxillin has five leucine-aspartate (LD) motifs (LD1–LD5). Here, we show that the second LD motif of paxillin, LD2, interacts with Pyk2-FAT, similar to the known Pyk2-FAT/LD4 interaction. Both LD motifs can target two ligand binding sites on Pyk2-FAT. Interestingly, they also share similar binding affinity for Pyk2-FAT with preferential association to one site relative to the other. Nevertheless, the LD2-LD4 region of paxillin (paxillin^133 -290) binds to Pyk2-FAT as a 1:1 complex. However, our data suggest that the Pyk2-FAT and paxillin complex is dynamic and it appears to be a mixture of two distinct conformations of paxillin that almost equally compete for Pyk2-FAT binding. These studies provide insight into the underlying selectivity of paxillin for Pyk2 and FAK that may influence the differing behavior of these two closely related kinases in focal adhesion sites.