scholarly journals Decoding the Structure of Non-Proteinogenic Amino Acids: The Rotational Spectrum of Jet-Cooled Laser-Ablated Thioproline

Molecules ◽  
2021 ◽  
Vol 26 (24) ◽  
pp. 7585
Author(s):  
Juan Carlos López ◽  
Alberto Macario ◽  
Andrés Verde ◽  
Alfonso Pérez-Encabo ◽  
Susana Blanco
Keyword(s):  
Interaction Analysis ◽  
Noncovalent Interaction ◽  
Coupling Constants ◽  
Cooh Group ◽  
Stable Form ◽  
Equatorial Position ◽  
Type I ◽  
Rotational Spectrum ◽  
Type Ii ◽  
The Stability

The broadband rotational spectrum of jet-cooled laser-ablated thioproline was recorded. Two conformers of this system were observed and identified with the help of DFT and ab initio computations by comparison of the observed and calculated rotational constants and 14N quadrupole coupling constants as well as the predicted energies compared to the observed relative populations. These conformers showed a mixed bent/twisted arrangement of the five-membered ring similar to that of the related compound thiazolidine with the N–H bond in axial configuration. The most stable form had the COOH group in an equatorial position on the same side of the ring as N-H. The arrangement of the C=O group close to the N-H bond led to a weak interaction between them (classified as type I) characterized by a noncovalent interaction analysis. The second form had a trans-COOH arrangement showing a type II O–H···N hydrogen bond. In thioproline, the stability of conformers of type I and type II was reversed with respect to proline. We show how the conformation of the ring depends on the function associated with the endocyclic N atom when comparing the structures of isolated thioproline with its zwitterion observed in condensed phases and with peptide forms.

scholarly journals Microfilament modification by dihydrocytochalasin B causes retinoic acid-modulated chondrocytes to reexpress the differentiated collagen phenotype without a change in shape.

1988 ◽  
Vol 106 (1) ◽  
pp. 161-170 ◽  
Author(s):  
P D Benya ◽  
P D Brown ◽  
S R Padilla
Keyword(s):  
Retinoic Acid ◽  
Cell Shape ◽  
Articular Chondrocytes ◽  
Type Ii Collagen ◽  
Phenotypic Change ◽  
Type Iii Collagen ◽  
Type I ◽  
Type Ii ◽  
The Stability ◽  
Rabbit Articular Chondrocytes

Primary monolayers of rabbit articular chondrocytes synthesize high levels of type II collagen and proteoglycan. This capacity was used as a marker for the expression of the differentiated phenotype. Such cells were treated with 1 microgram/ml retinoic acid (RA) for 10 d to produce a modulated collagen phenotype devoid of type II and consisting of predominantly type I trimer and type III collagen. After transfer to secondary culture in the presence of RA, the stability of the RA-modulated phenotype was investigated by culture in the absence of RA. Little reexpression of type II collagen synthesis occurred in this period unless cultures were treated with 3 X 10(-6) M dihydrocytochalasin B to modify microfilament structures. Reexpression of the differentiated phenotype began between days 6-8 and was essentially complete by day 14. Substantial reexpression occurred by day 8 without a detectable increase in cell rounding. Colony formation, characteristic of primary chondrocytes, was infrequent even after reexpression was complete. These data suggest that the integrity of microfilament cytoskeletal structures can be a source of regulatory signals that mechanistically appear to be more proximal to phenotypic change than the overt changes in cell shape that accompany reexpression of subculture-modulated chondrocytes in agarose culture.

scholarly journals Influence of coracoglenoid space on scapular neck fracture stability: biomechanical study

2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Junfeng Chen ◽  
Wei Zhang ◽  
Gang Pang ◽  
Qingling Meng ◽  
Youyu Zhu ◽  
...  
Keyword(s):  
Failure Load ◽  
Anatomical Variation ◽  
Biomechanical Study ◽  
Interindividual Variation ◽  
Type I ◽  
Type Ii ◽  
Average Maximum ◽  
Neck Fracture ◽  
The Stability ◽  
Scapular Neck Fractures

Abstract Background The anatomical variation of the coracoglenoid space has the potential to influence the stability of scapular neck fractures. This paper aimed to investigate the mechanical mechanism underlying the influence of different coracoglenoid space types on scapular neck fractures by morphometric analysis and biomechanical experiments. Methods The morphology of 68 dried scapulae (left: 36; right: 32) was studied. Two variables, the length of the coracoglenoid distance (CGD) and the coracoglenoid notch (CGN), were measured. The distribution of CGN/CGD × 100% was used to identify the morphology of the coracoglenoid space. Each specimen was tested for failure under static axial compression loading. The average failure load, stiffness, and energy were calculated. Results Two coracoglenoid space types were identified. The incidence of Type I (‘‘hook’’ shape) was 53%, and that of Type II (‘‘square bracket’’ shape) was 47%. The CGD and CGN were significantly higher for type I than type II (13.81 ± 0.74 mm vs. 11.50 ± 1.03 mm, P < 0.05; 4.74 ± 0.45 mm vs. 2.61 ± 0.45 mm, P < 0.05). The average maximum failure load of the two types was 1270.82 ± 318.85 N and 1529.18 ± 467.29 N, respectively (P = 0.011). The stiffness and energy were significantly higher for type II than type I (896.75 ± 281.14 N/mm vs. 692.91 ± 217.95 N/mm, P = 0.001; 2100.38 ± 649.54 N × mm vs. 1712.71 ± 626.02 N × mm, P = 0.015). Conclusions There was great interindividual variation in the anatomical morphology of the coracoglenoid space. Type I (hook-like) spaces bore lower forces, were less stiff, and bore less energy, which may constitute an anatomical predisposition to scapular neck fractures.

scholarly journals A Predictive Classification of Charcot Arthropathy of Foot and Ankle

2020 ◽  
Vol 5 (4) ◽  
pp. 2473011420S0008
Author(s):  
Mohamed Abdelaziz Elghazy ◽  
Hani M. El-Mowafi ◽  
Ahmed El-Hawary ◽  
Yasser R. Kandil ◽  
Samer Ali ◽  
...  
Keyword(s):  
Complication Rate ◽  
Classification Systems ◽  
Type I ◽  
Type Ii ◽  
Foot And Ankle ◽  
Charcot Arthropathy ◽  
Lateral Column ◽  
Lisfranc Joints ◽  
The Stability

Category: Diabetes; Other Introduction/Purpose: Charcot arthropathy of foot and ankle is a devastating, chronic and progressive destruction of bone and joint integrity affecting one or more joints. It is commonly associated with diabetes mellitus and is characterized by joint subluxations, dislocation, and pathological fractures in patients with peripheral neuropathy and results in a debilitating deformity, possibly leading to ulceration and amputation.Many classification systems exist for charcot arthopathy of foot and ankle. However, there is still lack of consensus regarding best classification. We are proposing a new classification for charcot arthropathy of foot and ankle based on our experience of large cohort of charcot patients. Our classification can guide treatment and prognosis of diabetic charcot arthropathy of foot and ankle, which we are following for the last decade. Methods: Patients with post-acute charcot who presented at our institution from January 2004 to October 2019 were reviewed and were further classified anatomically into Type I and Type II based on plain radiographs. Type I was characterized by charcot affection of one region. Regions were categorized anatomically as a modification of both Brodsky and Schon classifications into: ankle, Lisfranc (tarsometatarsal), naviculocuneiform, forefoot, and hindfoot which includes one of the following: talonavicular joint, calcaneocuboid joint or calcaneus. Type II was characterized by affection of more than one region like peritalar, perinavicular, transverse tarsal or any other combination. Peritalar complex involves at least two joints of the following: ankle, subtalar, and talonavicular. The perinavicular type includes talonavicular and naviculocuniform or tarsometatarsal and naviculocuniform, while the transverse tarsal involves the calcaneocuboid and talonavicu-lar. Both types were further classified into four stages according to the stability, deformity and associated mechanical ulcers. (Table 1) Results: 235 patients (242 feet) were presented with diabetic charcot arthropathy. Mean age was 56 years (range 22-84). Follow- up ranged from 6 months to 10 years, with a mean of 3.3 years.Types IA and IIA were managed conservatively. All patients in Type IIB, IC, IIC, ID, IID and the majority of type IB received fusion surgery to achieve stability and correction of deformity. Stage IB ankle were fixed, while IB lisfranc were observed, and fixed if transformed to IC.Type II D had the highest complication rate in the form of: infection, nonunion, nail protrusion, implant failure, revision including exostectomy after full union and recurrence of ulcer in midfoot 3-4 years after surgery. Five patients ended up with amputation, and all were stage IID. Conclusion: For post-acute charcot, stage A have the best prognosis and can be managed conservatively provided good diabetes control.Type IB can be managed conservatively but when the ankle is affected in type IB, it is better to be elected for surgery. When charcot affects the Lisfranc joints, it is usually stable unless the lateral column is affected.All cases of type IIB, IC and IIC, ID, IID should receive surgery to achieve stability, correction of deformity and prevent complications.Mechanical ulcer (stage D) carries the worst prognosis and highest complication rate. Type IID might predict the risk of amputation [Table: see text]

Numerical Investigations of the Effect of Radial Power Distribution and Inlet Orifice on the Stability Behavior of Parallel Multichannel Type Natural Circulation Boiling Water Reactor

2018 ◽  
Vol 4 (3) ◽  
Author(s):  
Sapna Singh ◽  
Garima Singal ◽  
A. K. Nayak ◽  
Umasankari Kannan
Keyword(s):  
Low Power ◽  
Radial Direction ◽  
Natural Circulation ◽  
Boiling Water ◽  
Boiling Water Reactor ◽  
Type I ◽  
Type Ii ◽  
Water Reactor ◽  
The Core ◽  
The Stability

In a natural circulation boiling water reactor (BWR), the core power varies in both axial and radial directions inside the reactor core. The variation along the axial direction is more or less constant throughout the reactor; however, there exists variation of reactor power in the radial direction. The channels located at the periphery have low power compared to the center of the core and are equipped with orifices at their inlet. This creates nonuniformity in the radial direction in the core. This study has been performed in order to understand the effect of this radial variation of power on the stability characteristics of the reactor. Four channels of a pressure tube type natural circulation BWR have been considered. The reactor has been modeled using RELAP5/MOD3.2. Before using the model, it was first benchmarked with experimental measurements and then the characteristics of both low power and high power oscillations, respectively, known as type-I and type-II instability, have been investigated. It was observed that the type-I instability shows slight destabilizing effect of increase in power variation among different channels. However, in the case of type-II instability, it was found out that the oscillations get damped with an increase in power variation among the channels. A similar effect was found for the presence of orifices at the inlet in different channels. However, the increase in number of orificed channels showed stabilizing effect for both type-I and type-II instabilities.

scholarly journals A molecular dynamics investigation of CDK8/CycC and ligand binding: conformational flexibility and implication in drug discovery

2017 ◽  
Author(s):  
Wei Chen ◽  
Zhiye Tang ◽  
Tim Cholko ◽  
Chia-en A. Chang
Keyword(s):  
Molecular Dynamics ◽  
Drug Discovery ◽  
Ligand Binding ◽  
Md Simulations ◽  
Electrostatic Energy ◽  
Major Protein ◽  
Type I ◽  
Type Ii ◽  
Protein Motions ◽  
The Stability

AbstractThe activities of CDK8 with partner Cyclin C (CycC) are a common feature of many diseases, especially cancers. Here we report the study of dynamic behaviors and energy profiles of 13 CDK8/CycC systems, including the DMG-in and DMG-out conformations as well as 5 type I ligands and 5 type II ligands, with all-atom unbiased molecular dynamics (MD) simulations. We observed numerous regional motions within CDK8, which move in concert to form five major protein motions. The motion of the activation loop doesn’t appear to influence the binding of both types of ligands. Type I ligands remarkably reduce the motion of the C-terminal tail through the strong cation-π interaction between the ligands and ARG356, and type II ligands stabilize the αC helix by forming stable hydrogen bonds with GLU66. The MD calculations also confirmed the importance of CycC to the stability of the CDK8 system as well as the ligand binding. The MMPB/SA results show that van der Waals interaction is the main driving force for the binding of both types of ligands, but electrostatic energy and entropy penalty plays important roles in the binding of type II ligands. The volume analysis results indicate that the induced fitting theory applies in the binding of type I ligands. These results would help to improve the affinities of the existing ligands. Our MD work is complementary to crystal structures and may have implications in the development of new CDK8 inhibitors as well as in the field of drug discovery.

Studies on the Genetic Mutations of Hereditary Fibrinogen Disorder

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 4954-4954
Author(s):  
Rong-Fu Zhou ◽  
Zhou Na ◽  
OuYang Jian
Keyword(s):  
De Novo ◽  
Conflicts Of Interest ◽  
Genetic Mutations ◽  
Heterozygous Mutation ◽  
Homologous Sequence ◽  
Type I ◽  
Type Ii ◽  
Restriction Digestion ◽  
Pcr Products ◽  
The Stability

Abstract Hereditary fibrinogen disorder is a rare kind of bleeding disease, which divided into two types. Type I is a kind of quantity disorder, including afibrinogenemia and hypofibrinogenemia. Type II is a kind of quality disorder, including dysfibrinogenemia. Fibrinogen is a kind of hexameric glycoprotein and consists of two pairs of three chains, which are Aα, Bβ and γchain. FGA、FGB and FGG code for the relevant glycoprotein. The mutations on these genes are responsible for this disorder. In this study, the levels of fibrinogen antigen of 12 cases with low fibrinogen activity were firstly detected. The results showed that one case had low level, and the patient definded as hypofibrinogenemia, and other 11 cases had normal level, thus these patients identified as dysfibrinogenemia. All exons and their flanks of FGA , FGB and FGG were amplified by PCR. THe PCR products were sequenced directly and blasted to normal sequence of corresponding gene to find the mutation. The result showed that among 11 cases with dysfibrinogenemia, five harbored Aα Arg16His heterozygous mutation and one of those also possessed a de novo γAsp185Asn heterozygous mutation ; one Aα Arg16Cys heterozygous mutation; four γArg275Cys heterozygous mutation and one γArg275His heterozygous mutation.The patient with hypofibrinogenemia harbored Aα Cys36Arg heterozygous mutation. Endonuclease restriction digestion was performed to exclude genetic polymorphism for the γAsp185Asn mutation. In molecular modeling, the hydrogen bonds were changed in the mutational variant of γ185Asn. Besides, a new site of glycosylation might appear after the mutation, which might lead to destroy the stability of molecular structure. The alignment of homologous sequence between different species suggested that γAsp185 was a highly conservative site. In a word, the above mutations might be the causes of dysfibrinogenemia or hypofibrinogenemia for these patients. Disclosures No relevant conflicts of interest to declare.

scholarly journals Structural Variations in the Complete Series of Lanthanoid Complexes of a Calix[4]arene Trisamide

2020 ◽  
Vol 73 (6) ◽  
pp. 424 ◽  
Author(s):  
Gareth L. Nealon ◽  
Matthew J. McIldowie ◽  
Brian W. Skelton ◽  
Mauro Mocerino ◽  
Massimiliano Massi ◽  
...  
Keyword(s):  
Solvent Molecule ◽  
Type I ◽  
Type Ii ◽  
Structural Variations ◽  
Type Iii ◽  
Structural Types ◽  
Complete Series ◽  
Transition Points ◽  
The Stability ◽  
Vacant Space

Lanthanoid picrate (pic) complexes of 5,11,17,23-tetra-tert-butyl-25-hydroxy-26,27,28-tris(diethylcarbamoylmethoxy)calix[4]arene (LH) have been synthesised and structurally characterised, to complete this series for all lanthanoids (other than promethium). From cerium to lutetium, three structural types are observed: Type I, [Ln(L)(O,O′-pic)](pic), Ln=Ce–Dy; Type II, [Ln(L)(O-pic)](pic), Ln=Tb, Ho; Type III, [Ln(L)(HOEt)](pic)2, Ln=Er–Lu. With lanthanum, three different ten-coordinate complexes were characterised; [Ln(L)(O,O′-pic)(HOEt)](pic), [Ln(L)(O,O′-pic)(OH2)](pic), and [Ln(L)(O,O′-pic)(HOMe)](pic). The crystallisation of Type I and II observed for terbium shows that the stability of the different structures are sensitively poised at the transition points. Nevertheless, the structures show that the vacant space in the coordination sphere left by the trisamide L tends to reduce across the series as expected. It is occupied by a bidentate picrate anion and unidentate solvent molecule with lanthanum, a bidentate picrate anion for cerium to dysprosium (Type I), a unidentate picrate anion for terbium and holmium (Type II), and finally a unidentate solvent molecule from erbium to lutetium (Type III). The coordination number thus reduces from 10 to 8 across the series.

scholarly journals Optimal Design of RF Energy-Harvesting Network: Throughput and Delay Perspective

Sensors ◽  
2019 ◽  
Vol 19 (1) ◽  
pp. 145 ◽  
Author(s):  
Yun Han Bae ◽  
Jung Woo Baek
Keyword(s):  
Energy Harvesting ◽  
Packet Delay ◽  
Approximate Model ◽  
System Throughput ◽  
Type I ◽  
Type Ii ◽  
Rf Energy Harvesting ◽  
Closed Form Solutions ◽  
Rf Energy ◽  
The Stability

We consider a wireless network comprising two types of nodes: Type I node and Type II node. The Type I node has unlimited energy supply and the Type II node is powered by radio frequency (RF) energy harvesting where the RF transmissions by the Type I node are the opportunities for the Type II node to replenish its battery. The Type I node has a data queue for storing data packets generated intermittently and the Type II node has a backlogged data queue. Our objective in this paper is to investigate system throughput and packet delay in an RF energy-harvesting network. Specifically, we find the optimal transmission probabilities of the two nodes which minimize the packet delay of the Type I node while maximizing the system throughput subject to the stability condition of the data queue of the Type I node. The whole system of the two interacting nodes can be exactly modeled by a two-dimensional Markov chain. Instead of following such an approach, we resort to another approximate approach so that our optimization problem can be solved more easily and closed-form solutions are available. The accuracy of the approximate model is validated by extensive simulations.

scholarly journals Halogen Bonding: A Halogen-Centered Noncovalent Interaction Yet to Be Understood

Inorganics ◽  
2019 ◽  
Vol 7 (3) ◽  
pp. 40 ◽  
Author(s):  
Pradeep Varadwaj ◽  
Arpita Varadwaj ◽  
Helder Marques
Keyword(s):  
Electron Density ◽  
Weak Interactions ◽  
Early Recognition ◽  
Noncovalent Interactions ◽  
Covalent Bond ◽  
Halogen Bonding ◽  
Noncovalent Interaction ◽  
Type I ◽  
Type Ii ◽  
Halogen Bonds

In addition to the underlying basic concepts and early recognition of halogen bonding, this paper reviews the conflicting views that consistently appear in the area of noncovalent interactions and the ability of covalently bonded halogen atoms in molecules to participate in noncovalent interactions that contribute to packing in the solid-state. It may be relatively straightforward to identify Type-II halogen bonding between atoms using the conceptual framework of σ-hole theory, especially when the interaction is linear and is formed between the axial positive region (σ-hole) on the halogen in one monomer and a negative site on a second interacting monomer. A σ-hole is an electron density deficient region on the halogen atom X opposite to the R–X covalent bond, where R is the remainder part of the molecule. However, it is not trivial to do so when secondary interactions are involved as the directionality of the interaction is significantly affected. We show, by providing some specific examples, that halogen bonds do not always follow the strict Type-II topology, and the occurrence of Type-I and -III halogen-centered contacts in crystals is very difficult to predict. In many instances, Type-I halogen-centered contacts appear simultaneously with Type-II halogen bonds. We employed the Independent Gradient Model, a recently proposed electron density approach for probing strong and weak interactions in molecular domains, to show that this is a very useful tool in unraveling the chemistry of halogen-assisted noncovalent interactions, especially in the weak bonding regime. Wherever possible, we have attempted to connect some of these results with those reported previously. Though useful for studying interactions of reasonable strength, IUPAC’s proposed “less than the sum of the van der Waals radii” criterion should not always be assumed as a necessary and sufficient feature to reveal weakly bound interactions, since in many crystals the attractive interaction happens to occur between the midpoint of a bond, or the junction region, and a positive or negative site.

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