Internal Packing Research Articles

MP:PD—a data base of internal packing densities, internal packing defects and internal waters of helical membrane proteins

The membrane protein packing database (MP:PD) (http://proteinformatics.charite.de/mppd) is a database of helical membrane proteins featuring internal atomic packing densities, cavities and waters. Membrane proteins are not tightly packed but contain a considerable number of internal cavities that differ in volume, polarity and solvent accessibility as well as in their filling with internal water. Internal cavities are supposed to be regions of high physical compressibility. By serving as mobile hydrogen bonding donors or acceptors, internal waters likely facilitate transition between different functional states. Despite these distinct functional roles, internal cavities of helical membrane proteins are not well characterized, mainly because most internal waters are not resolved by crystal structure analysis. Here we combined various computational biophysical techniques to characterize internal cavities, reassign positions of internal waters and calculate internal packing densities of all available helical membrane protein structures and stored them in MP:PD. The database can be searched using keywords and entries can be downloaded. Each entry can be visualized in Provi, a Jmol-based protein viewer that provides an integrated display of low energy waters alongside membrane planes, internal packing density, hydrophobic cavities and hydrogen bonds.

Toxic Shock Syndrome following Septoplasty: Report of 2 Cases and Literature Review

Objectives: Toxic shock syndrome (TSS) is a rare but potentially life-threatening multisystem disease. Reported incidence after nasal surgery is 16.5 per 100,000 operations. We report 2 such cases from Northern Ireland occurred over last 8 years (2006 and 2012). Diagnostic criteria, pathogenesis, and management of TSS are discussed. Methods: Case 1: A 19-year-old man developed sudden severe facial swelling, fever, diffuse erythroderma, tachycardia, and hypotension 16 hours after routine septoplasty and cautery to inferior turbinates. He had sialastic internal nasal splints and calcium alginate packing. Initially anaphylaxis to latex or diclofenac was suspected but disproved by lab investigations. He had surgical tracheotomy to protect airway from progressive facial cellulitis. Nasal swab confirmed grown staphylococcus aureus (TSST-1 producing-strain), and he recovered slowly with antibiotics. Case 2: A 24 year- old man developed a mild form of TSS 36 hours post-surgery after routine septopasty and Merocel packing, with nausea, hypotension, tachycardia, fever, and erythroderma. TSS was promptly suspected. The patient moved to intensive care for supportive care of refractory hypotension, and he made a slow recovery with antibiotics. Nasal swab had grown staphylococcus aureus. (TSST-1 strain). Results: TSS cases following nasal surgery have been associated with nasal packing, mucosal barrier violation, and prior colonization of toxic-shock-syndrome-toxin-1 (TSST-1) strain as well as low antitoxin antibody levels. Hence TSS requires nasal carriage of a toxigenic strain of staphylococcus aureus by a susceptible patient. Topical or systemic antibiotics did not have a demonstrable protective effect. Conclusions: Early recognition and prompt intervention minimize the morbidity and mortality associated with this disease.

Structural basis of stable PP2A latency by α4‐protein

Phosphoprotein α4 is essential for cell survival and is known as an inhibitor of protein phosphatase 2A (PP2A). α4 binds to PP2A catalytic subunit (PP2Ac) and stabilizes it in an inactive, latent form. Strikingly, we show that α4 binds preferentially to the partially folded PP2Ac. The crystal structure of α4 bound to a folding sub‐domain of PP2Ac (PP2AFD) reveals that α4 binding entails a distorted PP2A active site and displacement of an internal packing near the phosphatase active site. Measurement of the H‐D exchange of the α4‐bound PP2Ac versus active enzyme reveals conformational changes in PP2Ac associated with α4 binding that correlates with the crystal structure. Our structural observations imply that binding of α4 to the inner surface of PP2Ac may serve dual function: 1) establish PP2A latency; 2) stabilize PP2Ac by preventing aggregation of the partially folded or newly synthesized PP2Ac and protecting PP2Ac from proteasomal degradation by shielding a PP2A polyubiquitination site. In addition, disruption of PP2A‐α4 interaction in vivo is sufficient to cause cell death and complete loss of PP2Ac in cells. Our data reveal molecular details of α4‐PP2A interaction and offer structural mechanism of α4 function and stable PP2A latency.

식초절임 무의 HACCP 시스템 적용을 위한 미생물학적 위해 분석

본 연구는 식초절임 무의 HACCP (Hazard Analysis Critical Control Point)시스템 구축을 위하여 생물학적 위해요소분석을 위한 목적으로 2012년 2월 1일~6월 31일까지 약 150일 동안 수행하였다. 일반적인 식초절임 무 제조업체의 제조공정을 참고로 하여 공정도를 작성하였으며, 식초절임 무의 원료 농산물(무), 용수, 첨가물과 포장재료에 입고, 보관, 정선, 세척, 표피제거, 절단, 선별, 충진, 내포장, 금속검출, 외포장, 보관 및 출하공정에 대하여 작성하였다. 원료 무의 세척 전, 세척 후의 Coliform group, Staphylococcus aureus, Salmonella spp., Bacillus cereus, Listeria Monocytogenes, E. coli O157:H7, Clostridium perfringens, Yeast 와 Mold를 측정한 결과 Bacillus cereus는 세척 전 <TEX>$5.00{\times}10$</TEX> CFU/g이었으나, 세척 후 검출되지 않았으며, Yeast 와 Mold 는 세척 전 <TEX>$3.80{\times}10^2$</TEX> CFU/g, 세척 후 10 CFU/g로 감소되었으며 나머지 병원성균은 검출되지 않았다. 조미액의 pH(2~5)별 미생물의 변화를 시험한 결과 모든 균이 검출되지 않은 pH 3~4를 조미액의 pH로 결정하였다. 작업장별 공중낙하균 (일반세균수, 대장균, 진균수) 시험결과 내포장실, 조미액가공실, 세척실, 보관실의 미생물수는 10 CFU/Plate, 2 CFU/Plate, 60 CFU/Plate 그리고 20 CFU/Plate 가 검출되었다. 종사자 손바닥 시험결과 일반세균수 346 <TEX>$CFU/Cm^2$</TEX>, 대장균군 23 <TEX>$CFU/Cm^2$</TEX>로 높게 나타나 개인위생관리에 대한 교육 및 훈련이 요구 되었다. 제조설비 및 기구의 표면오염도를 검사한 결과 모든 시료에서 대장균군은 검출되지 않았고, 일반세균은 PP Packing machin과 Siuping machine (PE Bulk)에서 가장 많은 <TEX>$4.2{\times}10^3CFU/Cm^2$</TEX>, <TEX>$2.6{\times}10^3CFU/Cm^2$</TEX> 검출되었다. 위의 위해분석 결과 병원성미생물을 예방, 감소 또는 제거할 수 있는 조미액 가공 공정이 CCP-B (Biological)로 관리되어야 하고, 한계기준은 pH 3~4로 결정하였다. 따라서 전통한과생산에의 HACCP 모델 적용을 위한 미생물학적 위해도 평가에서와 같이 조미액 가공 공정의 관리기준 및 이탈시 조치방법, 검증방법, 교육 훈련과 기록관리 등 철저한 HACCP 관리계획이 필요할 것으로 생각된다. This study has been performed for 150 days from February 1 - June 31, 2012 aiming at analyzing biologically hazardous factors in order to develop HACCP system for the vinegared pickle radishes. A process chart was prepared as shown on Fig. 1 by referring to manufacturing process of manufacturer of general vinegared pickle radishes regarding process of raw agricultural products of vinegared pickle radishes, used water, warehousing of additives and packing material, storage, careful selection, washing, peeling off, cutting, sorting out, stuffing (filling), internal packing, metal detection, external packing, storage and consignment (delivery). As a result of measuring Coliform group, Staphylococcus aureus, Salmonella spp., Bacillus cereus, Listeria Monocytogenes, E. coli O157:H7, Clostridium perfringens, Yeast and Mold before and after washing raw radishes, Bacillus cereus was <TEX>$5.00{\times}10$</TEX> CFU/g before washing but it was not detected after washing and Yeast and Mold was <TEX>$3.80{\times}10^2$</TEX> CFU/g before washing but it was reduced to 10 CFU/g after washing and other pathogenic bacteria was not detected. As a result of testing microorganism variation depending on pH (2-5) of seasoning fluid (condiment), pH 3-4 was determined as pH of seasoning fluid as all the bacteria was not detected in pH3-4. As a result of testing air-borne bacteria (number of general bacteria, colon bacillus, fungus) depending on each workplace, number of microorganism of internal packing room, seasoning fluid processing room, washing room and storage room was detected to be 10 CFU/Plate, 2 CFU/Plate, 60 CFU/Plate and 20 CFU/Plate, respectively. As a result of testing palm condition of workers, as number of general bacteria and colon bacillus was represented to be high as 346 <TEX>$CFU/Cm^2$</TEX> and 23 <TEX>$CFU/Cm^2$</TEX>, respectively, an education and training for individual sanitation control was considered to be required. As a result of inspecting surface pollution level of manufacturing facility and devices, colon bacillus was not detected in all the specimen but general bacteria was most dominantly detected in PP Packing machine and Siuping machine (PE Bulk) as <TEX>$4.2{\times}10^3CFU/Cm^2$</TEX>, <TEX>$2.6{\times}10^3CFU/Cm^2$</TEX>, respectively. As a result of analyzing above hazardous factors, processing process of seasoning fluid where pathogenic bacteria may be prevented, reduced or removed is required to be controlled by CCP-B (Biological) and threshold level (critical control point) was set at pH 3-4. Therefore, it is considered that thorough HACCP control plan including control criteria (point) of seasoning fluid processing process, countermeasures in case of its deviation, its verification method, education/training and record control would be required.

Continuum Models for the Plastic Deformation of Octet-Truss Lattice Materials Under Multiaxial Loading

The continuum models that take plastic material behavior into consideration are derived to analyze periodic octet-truss lattice materials under multiaxial loading. The main focus of this study is to investigate the basic topology of unit cell structures having the cubic symmetry and to formulate the analytical models for predicting pressure load-dependent stress surfaces accurately. The discrete lattice materials are converted into equivalent model continua that are obtained by physically homogenizing the property of the unit cell structures. The effective continuum models contain information on the mechanical characteristics of internal truss members with respect to axial stiffness, internal stress variable, structural packing, and material density at the microscale level. With the hardening material model introduced in the homogenization process, the plastic flow acting on the microscopic truss members gives rise to extend the elastic domain of the analytical stress function derived from homogenize constitutive equations at the macroscale level. Analytical stress predictions show excellent agreements with the results obtained from finite element (FE) analyses.

Nanoscale structure of protamine/DNA complexes for gene delivery

Understanding the internal packing of gene carriers is a key-factor to realize both gene protection during transport and de-complexation at the delivery site. Here, we investigate the structure of complexes formed by DNA fragments and protamine, applied in gene delivery. We found that complexes are charge- and size-tunable aggregates, depending on the protamine/DNA ratio, hundred nanometers in size. Their compactness and fractal structure depend on the length of the DNA fragments. Accordingly, on the local scale, the sites of protamine/DNA complexation assume different morphologies, seemingly displaying clumping ability for the DNA network only for shorter DNA fragments.

Utility of an optically-based, micromechanical system for printing collagen fibers

Collagen's success as the principal structural element in load-bearing, connective tissue has motivated the development of numerous engineering approaches designed to recapitulate native fibril morphology and strength. It has been shown recently that collagen fibers can be drawn from monomeric solution through a fiber forming buffer (FFB), followed by numerous additional treatments in a complex serial process. However, internal fibril alignment, packing and resultant mechanical behavior of the fibers have not been optimized and remain inferior to native tissue. Further, no system has been developed which permits simultaneous application of molecular crowding, measurement of applied load, and direct observation of polymerization dynamics during fiber printing. The ability to perform well-controlled investigations early in the process of fiber formation, which vary single input parameters (i.e. collagen concentration, crowding agent concentration, draw rate, flow rate, temperature, pH, etc.) should substantially improve fiber morphology and strength. We have thus designed, built, and tested a versatile, in situ, optically-based, micromechanical assay and fiber printing system which permits the correlation of parameter changes with mechanical properties of fibers immediately after deposition into an FFB. We demonstrate the sensitivity of the assay by detecting changes in the fiber mechanics in response to draw rate, collagen type, small changes in the molecular crowding agent concentration and to variations in pH. In addition we found the ability to observe fiber polymerization dynamics leads to intriguing new insights into collagen assembly behavior.

Assessing the Contribution of Cavity Density to Protein Partial Molar Expansivity by High-Pressure NMR

Staphylococcal nuclease (SNase) protein is a model protein folding system. We recently reported that the magnitude of internal void volumes primarily determines proteins sensitivity to pressure (1) and that the tridimensional position of cavities can modulate the folding free-energy landscape (2). Here we characterize the effect of temperature on pressure denaturation of these previously studied cavity containing variants of SNase (L125A and I92A) to address the determinants of thermal expansivity using high-pressure NMR. The experiments show that thermal expansivity is sensitive to changes in the degree of internal packing. We corroborate these observations by measuring the coefficient of thermal expansion using pressure perturbation calorimetry. We also analyze the effect of temperature on the activation volume using pressure-jump kinetics NMR. We find that the transition state ensemble presents structurally heterogeneous expansion with significant differences among the mutants tested. We take advantage of the single residue resolution analysis to map the differences of expansivity on the tridimensional structure of proteins tested. We propose that the network of interactions in the protein interior is responsible for the degree of thermal expansion. Assessing this unexplored thermodynamic parameter will provide unique insight into protein behavior in the pressure-Temperature plane.

Supramolecular polymerization in water harnessing both hydrophobic effects and hydrogen bond formation

The formation of supramolecular polymers in water through rational design of a benzene-1,3,5-tricarboxamide (BTA) motif is presented. Intermolecular hydrogen bonding and hydrophobic effects cooperate in the self-assembly into long fibrillar aggregates. Minimal changes in molecular structure significantly affect the internal packing of the aggregates.

Meso-thienyl and furyl rotor effects in BF2-chelated dipyrrin dyes: solution spectroscopic studies and X-ray structural packing analysis of isomer and congener effects

Well-defined discrete fluorescent molecular systems with very subtle steric/electronic differences are interesting when considering solid-state packing and solution substituent effects. Herein, we report the synthesis and characterization of four 4,4-difluoro-1,3,5,7-tetramethyl-8-(C4H3 X)-4-bora-3a,4a-diaza-s-indacene complexes (X = O, S). Various NMR spectroscopic experiments were used to assign all relevant atoms (CD2Cl2): 19F, 11B, 1H, 13C, 13C–H undecoupled, 1H–1H COSY, 1H–1H NOESY, 1H–13C HSQC, and 1H–13C HMBC NMR spectroscopy. UV-Vis and fluorescence studies were undertaken for all compounds. Chemical shift differences were found between isomers and congeners; for congeners, aromatic δ differences were attributed to electron-poor character. Also, compounds 1–4 were studied crystallographically. In the solid state, internal dihedral planes and intermolecular packing patterns can be compared.

Very rare case of rectal carcinosarcoma

Dear Sir, Carcinosarcoma is a rare type of malignant neoplasm, which was first described by Virchow in 1864. It is composed of two types of neoplastic cells, epithelial, and mesenchymal ones. This neoplasm has a poor prognosis and may develop in many organs, including the uterus and ovaries of older women, the head and neck region, and the lungs and kidneys. Within the gastrointestinal tract, carcinosarcoma is most commonly found in the esophagus [1] and only rarely in the large intestine. Among case reports before 2011, 16 fulfilled the criteria for carcinosarcoma of the large intestine, and of these, only 5 involved the rectum. We report a case of carcinosarcoma of the rectum with necrosis of the intestinal wall. An 83-year-old male was admitted to the surgical ward with signs of massive lower gastrointestinal tract bleeding. The patient had congestive heart failure, diabetes, and chronic respiratory failure secondary to venous thromboembolism. On digital rectal examination, a stenotic, bleeding tumor of the rectum, infiltrating the perianal tissues on the right side could be felt. The distal margin of the tumor was palpable at the level of anorectum, while its superior margin was unreachable. Anal endosonography revealed a tumor (30 mm × 53 mm × 40 mm in size) occupying the right half of the anal canal, infiltrating the sphincter muscles (internal and external), with areas of necrosis (Fig. 1). Fig. 1 a The endosonographic study shows a hyperechoic tumor, measuring 30 × 53 mm in a transversal plane, taking up the right half of the anal canal lumen, infiltrating the anal sphincters, b With anechoic areas of necrosis Due to the deterioration of the patient’s overall condition and continued signs of active bleeding from the tumor, the patient qualified for emergency surgery (ASA IV). Intraoperatively, on rectal examination, a stenotic tumor with an ulceration at the right side of the rectal wall was confirmed. The necrotic tissue was partially removed, the rectum was rinsed with normal saline, then, the site of bleeding was coagulated, and internal packing of the rectum was carried out. An exploratory laparotomy was performed through an infraumbilical midline incision. A loop sigmoidostomy was created due to necrosis of the rectal wall and perirectal tissue. The remaining abdominal organs did not reveal any abnormalities on palpation (e.g., distant metastases). There were no complications in the early postoperative period. However, due to the patient’s poor overall condition, he was not a candidate for oncological treatment. The patient was discharged home on postoperative day 14 and advised to return for the histopathology results. He died 5 weeks after the surgery, due to cardiorespiratory failure. The histopathology examination of the specimen revealed carcinosarcoma of the rectum which was confirmed by immunohistochemical staining which was positive for cytokeratin, vimentin, and smooth muscle antigen (Fig. 2). This mixed neoplasm was formed from epithelial elements of a well-differentiated adenocarcinoma as well as from mesenchymal neoplastic elements, showing differentiation toward muscle tissue. Fig. 2 a Staining using anti-cytokeratin antibodies used to identify cells of epithelial origin; b Staining using anti-vimentin antibodies to identify cells of mesenchymal-origin; c Staining using anti-SMA (smooth muscle antigen) antibodies Carcinosarcoma of the colon is a rare neoplasm composed of both carcinomatous and sarcomatous elements. It has also been called as sarcomatoid carcinoma, carcinoma with mesenchymal stroma, carcinoma with sarcomatous change, spindle cell carcinoma, and pleomorphic anaplastic carcinoma [2]. The prognosis of this carcinoma is poor because it invades deep into the bowel wall, has widespread metastases, and is resistant to multi-agent chemotherapy. Up to now, all the described cases of rectal carcinosarcoma included lymph node metastases at the time of diagnosis [3–5]. Our patient did not have any distant metastases noted at explorative laparotomy. However, the local spread of the neoplasm led to necrosis of a fragment of the rectal wall and secondary bleeding, a complication which had not been described previously. The only published case with necrosis of the intestinal wall involved the carcinosarcoma of the ascending colon [6]. Survival in the reported cases of rectal carcinosarcoma was never more than 6 months. Our patient died within a mere 5 weeks, which should be attributed to the advanced local state of the cancer at the time of diagnosis and the patient’s poor general condition which prevented further treatment. The case presented in this article is, to the best of our knowledge, the first involving bleeding into the gastrointestinal tract secondary to perforation of the rectal wall as a complication associated with this neoplasm. Therefore, the rare diagnosis of carcinosarcoma should be considered in patients with gastrointestinal bleeding.

Small-Angle Neutron-Scattering Studies of Mixed Micellar Structures Made of Dimeric Surfactants Having Imidazolium and Ammonium Headgroups

Planar imidazolium cation based gemini surfactants [16-Im-n-Im-16], 2Br(-) (where n = 2, 3, 4, 5, 6, 8, 10, and 12), exhibit different morphologies and internal packing arrangements by adopting different supramolecular assemblies in aqueous media depending on their number of spacer methylene units (CH(2))(n). Detailed measurements of the small-angle neutron-scattering (SANS) cross sections from different imidazolium-based surfactant micelles in aqueous media (D(2)O) are reported. The SANS data, containing the information of aggregation behavior of such surfactants in the molecular level, have been analyzed on the basis of the Hayter and Penfold model for the macro ion solution to compute the interparticle structure factor S(Q) taking into account the screened Coulomb interactions between the dimeric surfactant micelles. The characteristic changes in the SANS spectra of the dimeric surfactant with n = 4 due to variation of temperature have also been investigated. These data are then compared with the SANS characterization data of the corresponding gemini micelles containing tetrahedral ammonium ion based polar headgroups. The critical micellar concentration of each surfactant micelle (cmc) has been determined using pyrene as an extrinsic fluorescence probe. The variation of cmc as a function of spacer chain length has been explained in terms of conformational variation and progressive looping of the spacer into the micellar interior upon increasing the n values. Small-angle neutron-scattering (SANS) cross sections from different mixed micelles composed of surfactants with ammonium headgroups, 16-A(0), [16-Am-n-Am-16], 2Br(-) (where n = 4), 16-I(0), and [16-Im-n-Im-16], 2Br(-) (where n = 4), in aqueous media (D(2)O) have also been analyzed. The aggregate composition matches with that predicted from the ideal mixing model.

Investigation of mixing characteristics in a packed-bed external loop airlift bioreactor using tomography images

The present research work introduces a recirculated airlift bioreactor (biocontactor), which combines advantages of packed bed and external loop airlift bioreactors. This bioreactor is characterized by an internal gas redistributor placed between two beds of packing in the riser while working fluid recirculates through an external downcomer. The main objective of this research work was to characterize the mixing hydrodynamics of this reactor through the non-intrusive flow visualization technique of electrical resistance tomography (ERT). The tomography images were employed to examine the effects of packing, gas redistributor, sparger configuration, gas flow rate, and liquid height on the mixing time and superficial liquid velocity. Results showed that the mixing time in the bioreactor was decreased with an increase in the superficial gas velocity in the riser. It was found that at a constant riser superficial gas velocity, the mixing time was increased and the superficial liquid velocity decreased when a cross shaped sparger was replaced by a circular sparger, which had the same diameter, and the same number and size of holes. Results also showed that mixing time increased and the superficial liquid velocity decreased by reducing the liquid height in the bioreactor, in addition to installing the internal gas redistributor and packing in the riser. The presence of the internal gas redistributor and packing reduced the cross-sectional area available for flow and increased resistance in the liquid flow path. Results, which were obtained from this study, can be utilized to improve mixing in external loop airlift bioreactors for wider range of applications.

Enhanced performance of organic photovoltaic devices by photo-crosslinkable buffer layer

The performance of organic photovoltaic devices was enhanced by insertion of the photo-crosslinkable buffer layer. This buffer layer was formed by a photo curable precursor with bithiophene and pentadienyl moieties. The fill factor of the device with this buffer layer exceeded 0.7 in the organic photovoltaic cell. The characteristic of the photo-crosslinkable property enabled this buffer layer to be inserted between the hole extraction layer and the active layer, which formed an ohmic contact with both layers. The insertion of the buffer layer induced a 20% enhancement in conversion efficiency by small increases in the short-circuit current and the open-circuit voltage, and a huge increase in the fill factor. This photo-crosslinkable buffer layer acted as a leakage current reducing layer as measured by the reduced dark current. The high crystallinity and smooth surface of this buffer layer resulted in improved surface morphology and internal packing, thus enhanced the fill factor. Open image in new window

Structures of amyloid fibrils formed by the prion protein derived peptides PrP(244–249) and PrP(245–250)

While the formation of amyloid fibrils from diverse peptide and protein sequences is well established, the molecular determinants of structure and assembly are not well understood. In particular, the relationship between amino acid sequence and the type of internal steric zipper packing adopted in amyloid fibrils has not been established. Here we report the structures of two cytotoxic amyloid peptides derived from the mammalian prion protein, PrP(244-249) and PrP(245-250), determined using solid state NMR. While the amino acid composition of these two hexapeptides is very similar (ISFLIF and SFLIFL), the intermolecular interactions that give rise to the intersheet packing within the fibrils differ significantly. PrP(245-250) adopts a class 1 steric zipper, with parallel sheets stacked in an antiparallel face to face arrangement, stabilized by N- to C-terminal salt bridges. PrP(244-249), by contrast, forms two different intersheet interfaces within amyloid fibrils, with parallel opposing sheets in either a face to face (class 3) or face to back (class 2) arrangement. The fibrils formed by this peptide are primarily stabilized by close packing of the hydrophobic side chains, with contributions from side-chain to backbone hydrogen bonding (class 2 only). Thus, the structures presented here provide new insight into the relationship between amino acid sequence and the types of interactions stabilizing amyloid fibrils.

The Shadow Map: A General Contact Definition for Capturing the Dynamics of Biomolecular Folding and Function

Structure-based models (SBMs) are simplified models of the biomolecular dynamics that arise from funneled energy landscapes. We recently introduced an all-atom SBM that explicitly represents the atomic geometry of a biomolecule. While this initial study showed the robustness of the all-atom SBM Hamiltonian to changes in many of the energetic parameters, an important aspect, which has not been explored previously, is the definition of native interactions. In this study, we propose a general definition for generating atomically grained contact maps called "Shadow". The Shadow algorithm initially considers all atoms within a cutoff distance and then, controlled by a screening parameter, discards the occluded contacts. We show that this choice of contact map is not only well behaved for protein folding, since it produces consistently cooperative folding behavior in SBMs but also desirable for exploring the dynamics of macromolecular assemblies since, it distributes energy similarly between RNAs and proteins despite their disparate internal packing. All-atom structure-based models employing Shadow contact maps provide a general framework for exploring the geometrical features of biomolecules, especially the connections between folding and function.

Patterned Monolayer Self-Assembly Programmed by Side Chain Shape: Four-Component Gratings

A molecular recognition strategy based on alkadiyne side chain shape is used to self-assemble a four-component, 1D-patterned monolayer at the solution-HOPG interface. The designed monolayer unit cell contains six molecules and spans 23 nm × 1 nm. The unit cell's internal structure and packing are driven by complementary shapes and lengths of six different alkadiyne side chains. A solution of the four compounds on HOPG self-assembles monolayers (i) comprised, almost entirely, of the intended unit cell, (ii) exhibiting patterned domains spanning 10(4) nm(2), and (iii) which are sufficiently robust that patterned domains survive solvent rinsing and drying. The patterned monolayer affords 1D-feature spacings ranging from 3.3 to 23 nm. The results demonstrate the remarkable selectivity afforded by molecular recognition based on alkadiyne side chain shape and the ability to program highly complex 1D-patterns in self-assembled monolayers.

Population dynamics and production of the seagrass Zostera noltii in colonizing versus established meadows

AbstractThe dynamics of the seagrass Zostera noltii in established and colonizing meadows were assessed in Ria Formosa lagoon, Southern Portugal. Shoot weight, above:belowground biomass ratio, flowering shoot density, meadow production, and biomass–density relationships were investigated. Results indicate that the species population dynamics differ clearly in different development stages of the meadows. The overall mean of flowering shoot density was five times higher in the colonizing (83 flowering shoots m−2) than in the established meadow (16 flowering shoots m−2), revealing a greater contribution of sexual reproduction during the species colonization process. The temporal variation of the biomass–density relationship in the colonizing meadow showed a cyclic seasonal trajectory, a wider range of data, and a simultaneous peak of biomass and density, suggesting no space limitations constraining the internal packing of shoots during the growing season. In the established meadow, density peaked before biomass in agreement to the dominant role of the clonal architecture of seagrasses in the configuration of closed meadows, suggesting the occurrence of self‐thinning and/or regulation of ramet formation. Slope of the biomass–density relationships was similar in the established and colonizing meadows, generally suggesting similar nutritional conditions, regardless of their muddy and sandy sediments. Plants of the colonizing meadow invest mainly on the belowground fraction (above:belowground biomass ratio &lt;1), as meadow expansion is mainly controlled by the elongation of horizontal rhizomes. The annual total production (1163 g C m−2 year−1) and the biomass turnover (34.8 year−1) were also higher in this meadow, corroborating the high investment of the species during the meadow expansion. The faster biomass turnover of the colonizing meadow implies a more limited capacity to accumulate biomass, indicating a greater exportation of organic carbon and nutrients to the coastal area. The different biomass turnover rates suggest different trophic and structural roles of Z. noltii communities in established and colonizing meadows.

Structural Basis for Catalytic Activation of a Serine Recombinase

Sin resolvase is a site-specific serine recombinase that is normally controlled by a complex regulatory mechanism. A single mutation, Q115R, allows the enzyme to bypass the entire regulatory apparatus, such that no accessory proteins or DNA sites are required. Here, we present a 1.86 Å crystal structure of the Sin Q115R catalytic domain, in a tetrameric arrangement stabilized by an interaction between Arg115 residues on neighboring subunits. The subunits have undergone significant conformational changes from the inactive dimeric state previously reported. The structure provides a new high-resolution view of a serine recombinase active site that is apparently fully assembled, suggesting roles for the conserved active site residues. The structure also suggests how the dimer-tetramer transition is coupled to assembly of the active site. The tetramer is captured in a different rotational substate than that seen in previous hyperactive serine recombinase structures, and unbroken crossover site DNA can be readily modeled into its active sites.

Enhancing β3‐Peptide Bundle Stability by Design

We reported recently that certain β(3) -peptides self-assemble in aqueous solution into discrete bundles of unique structure and defined stoichiometry. The first β-peptide bundle reported was the octameric Zwit-1F, whose fold is characterized by a well-packed, leucine-rich core and a salt-bridge-rich surface. Close inspection of the Zwit-1F structure revealed four nonideal interhelical salt-bridge interactions whose heavy atom-heavy atom distances were longer than found in natural proteins of known structure. Here we demonstrate that the thermodynamic stability of a β-peptide bundle can be enhanced by optimizing the length of these four interhelical salt bridges. Combined with previous work on the role of internal packing residues, these results provide another critical step in the "bottom-up" formation of β-peptide assemblies with defined sizes, reproducible structures, and sophisticated function.