A Physical Organic Approach to Tuning Reagents for Selective and Stable Methionine Bioconjugation

We report a data-driven, physical organic approach to the development of new methionine-selective bioconjugation reagents with tunable adduct stabilities. Statistical modeling of structural features described by intrinsic physical organic parameters was applied to the development of a predictive model and to gain insight into features driving stability of adducts formed from the chemoselective coupling of oxaziridine and methionine thioether partners through Redox Activated Chemical Tagging (ReACT). From these analyses, a correlation between sulfimide stabilities and sulfimide  (C=O) stretching frequencies was revealed. We ex-ploited the rational gains in adduct stability exposed by this analysis to achieve the design and synthesis of a bis-oxaziridine reagent for peptide stapling. Indeed, we observed that a macrocyclic peptide formed by ReACT stapling at methionine exhibited improved uptake into live cells compared to an unstapled congener, highlighting the potential utility of this unique chemical tool for thioether modification. This work provides a template for the broader use of data-driven approaches to bioconjugation chemistry and other chemical biology applications.

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The Structure of Urban Flows

10.20944/preprints202009.0556.v1 ◽

2020 ◽

Author(s):

Pablo Torres ◽

Soledad Le Clainche ◽

Ricardo Vinuesa

Keyword(s):

Thermal Effects ◽

Physical Phenomenon ◽

Pollutant Dispersion ◽

Urban Environments ◽

Data Driven ◽

Thermal Fields ◽

Use Of Data ◽

Sustainability Challenges ◽

The City ◽

Insight Into

Understanding the flow in urban environments is an increasingly relevant problem due to its significant impact on air quality and thermal effects in cities worldwide. In this review we provide an overview of efforts based on experiments and simulations to gain insight into this complex physical phenomenon. We highlight the relevance of coherent structures in urban flows, which are responsible for the pollutant-dispersion and thermal fields in the city. We also suggest a more widespread use of data-driven methods to characterize flow structures as a way to further understand the dynamics of urban flows, with the aim of tackling the important sustainability challenges associated to them.

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Skeletal elements of crinoid echinoderms: High-resolution structural and microanalytical results

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100074768 ◽

1983 ◽

Vol 41 ◽

pp. 194-195

Author(s):

D. F. Blake ◽

L. F. Allard ◽

D. R. Peacor

Keyword(s):

High Resolution ◽

Marine Invertebrates ◽

Sea Urchins ◽

Structural Features ◽

Sea Stars ◽

High Resolution Tem ◽

Relationship Of ◽

The Relationship ◽

Insight Into

Echinodermata is a phylum of marine invertebrates which has been extant since Cambrian time (c.a. 500 m.y. before the present). Modern examples of echinoderms include sea urchins, sea stars, and sea lilies (crinoids). The endoskeletons of echinoderms are composed of plates or ossicles (Fig. 1) which are with few exceptions, porous, single crystals of high-magnesian calcite. Despite their single crystal nature, fracture surfaces do not exhibit the near-perfect {10.4} cleavage characteristic of inorganic calcite. This paradoxical mix of biogenic and inorganic features has prompted much recent work on echinoderm skeletal crystallography. Furthermore, fossil echinoderm hard parts comprise a volumetrically significant portion of some marine limestones sequences. The ultrastructural and microchemical characterization of modern skeletal material should lend insight into: 1). The nature of the biogenic processes involved, for example, the relationship of Mg heterogeneity to morphological and structural features in modern echinoderm material, and 2). The nature of the diagenetic changes undergone by their ancient, fossilized counterparts. In this study, high resolution TEM (HRTEM), high voltage TEM (HVTEM), and STEM microanalysis are used to characterize tha ultrastructural and microchemical composition of skeletal elements of the modern crinoid Neocrinus blakei.

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A Systematic Review on Popularity, Application and Characteristics of Protein Secondary Structure Prediction Tools

Current Drug Discovery Technologies ◽

10.2174/1570163815666180227162157 ◽

2019 ◽

Vol 16 (2) ◽

pp. 159-172 ◽

Cited By ~ 3

Author(s):

Elaheh Kashani-Amin ◽

Ozra Tabatabaei-Malazy ◽

Amirhossein Sakhteman ◽

Bagher Larijani ◽

Azadeh Ebrahim-Habibi

Keyword(s):

Systematic Review ◽

Secondary Structure ◽

Structure Prediction ◽

Web Of Science ◽

Secondary Structure Prediction ◽

Structural Information ◽

Protein Secondary Structure ◽

Structural Features ◽

Prediction Tools ◽

Insight Into

Background: Prediction of proteins’ secondary structure is one of the major steps in the generation of homology models. These models provide structural information which is used to design suitable ligands for potential medicinal targets. However, selecting a proper tool between multiple Secondary Structure Prediction (SSP) options is challenging. The current study is an insight into currently favored methods and tools, within various contexts. Objective: A systematic review was performed for a comprehensive access to recent (2013-2016) studies which used or recommended protein SSP tools. Methods: Three databases, Web of Science, PubMed and Scopus were systematically searched and 99 out of the 209 studies were finally found eligible to extract data. Results: Four categories of applications for 59 retrieved SSP tools were: (I) prediction of structural features of a given sequence, (II) evaluation of a method, (III) providing input for a new SSP method and (IV) integrating an SSP tool as a component for a program. PSIPRED was found to be the most popular tool in all four categories. JPred and tools utilizing PHD (Profile network from HeiDelberg) method occupied second and third places of popularity in categories I and II. JPred was only found in the two first categories, while PHD was present in three fields. Conclusion: This study provides a comprehensive insight into the recent usage of SSP tools which could be helpful for selecting a proper tool.

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The Oxford Handbook of the Brazilian Economy

10.1093/oxfordhb/9780190499983.001.0001 ◽

2018 ◽

Keyword(s):

Direct Investment ◽

Global Economy ◽

Iron Ore ◽

Structural Features ◽

Economic Importance ◽

Closed Economy ◽

Current Characteristics ◽

Insight Into ◽

Contemporary Context ◽

Over Time

Brazil constitutes a globally vital but troubled economy. It accounts for the largest GDP in Latin America and ranks among the world’s largest exporters of critical commodities including iron ore, soya, coffee, and beef. In recent years Brazil’s global economic importance has been magnified by a surge in both outward and inward foreign direct investment. This has served to further internationalize what has been historically a relatively closed economy. The purpose of this Handbook is to offer real insight into the Brazil’s economic development in contemporary context, understanding its most salient characteristics and analyzing its structural features across various dimensions. At a more granular level, this volume accomplishes the following tasks. First, it provides an understanding of the economy’s evolution over time and the connection of its current characteristics to this evolution. Second, it analyzes Brazil’s broader place in the global economy, and considers the ways in which this role has changed, and is likely to change, over coming years. Third, reflecting contemporary concerns, the volume offers an understanding, not only of how one of the world’s key economies has developed and transformed itself, but also of the ways in which this process has yet to be completed. The volume thus analyzes the current challenges facing the Brazilian economy and the kinds of issues that need to be tackled for these to be addressed.

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On the Experimental, Numerical and Data-Driven Methods to Study Urban Flows

Energies ◽

10.3390/en14051310 ◽

2021 ◽

Vol 14 (5) ◽

pp. 1310

Author(s):

Pablo Torres ◽

Soledad Le Clainche ◽

Ricardo Vinuesa

Keyword(s):

Physical Phenomenon ◽

Urban Pollution ◽

Pollutant Dispersion ◽

Urban Environments ◽

Machine Learning Algorithms ◽

Data Driven ◽

Thermal Fields ◽

Use Of Data ◽

Sustainability Challenges ◽

New Research

Understanding the flow in urban environments is an increasingly relevant problem due to its significant impact on air quality and thermal effects in cities worldwide. In this review we provide an overview of efforts based on experiments and simulations to gain insight into this complex physical phenomenon. We highlight the relevance of coherent structures in urban flows, which are responsible for the pollutant-dispersion and thermal fields in the city. We also suggest a more widespread use of data-driven methods to characterize flow structures as a way to further understand the dynamics of urban flows, with the aim of tackling the important sustainability challenges associated with them. Artificial intelligence and urban flows should be combined into a new research line, where classical data-driven tools and machine-learning algorithms can shed light on the physical mechanisms associated with urban pollution.

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Cryo-EM structure of amyloid fibrils formed by the entire low complexity domain of TDP-43

Nature Communications ◽

10.1038/s41467-021-21912-y ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Qiuye Li ◽

W. Michael Babinchak ◽

Witold K. Surewicz

Keyword(s):

Amyloid Fibrils ◽

Low Complexity ◽

Structural Features ◽

Protein Fragments ◽

Hydrophobic Residues ◽

Backbone Conformation ◽

Hydrophobic Amino Acids ◽

Insight Into ◽

Lateral Sclerosis

AbstractAmyotrophic lateral sclerosis and several other neurodegenerative diseases are associated with brain deposits of amyloid-like aggregates formed by the C-terminal fragments of TDP-43 that contain the low complexity domain of the protein. Here, we report the cryo-EM structure of amyloid formed from the entire TDP-43 low complexity domain in vitro at pH 4. This structure reveals single protofilament fibrils containing a large (139-residue), tightly packed core. While the C-terminal part of this core region is largely planar and characterized by a small proportion of hydrophobic amino acids, the N-terminal region contains numerous hydrophobic residues and has a non-planar backbone conformation, resulting in rugged surfaces of fibril ends. The structural features found in these fibrils differ from those previously found for fibrils generated from short protein fragments. The present atomic model for TDP-43 LCD fibrils provides insight into potential structural perturbations caused by phosphorylation and disease-related mutations.

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Insight into the structural features of Zhaotong lignite using multiple techniques

Fuel ◽

10.1016/j.fuel.2015.02.117 ◽

2015 ◽

Vol 153 ◽

pp. 176-182 ◽

Cited By ~ 115

Author(s):

Zhan-Ku Li ◽

Xian-Yong Wei ◽

Hong-Lei Yan ◽

Zhi-Min Zong

Keyword(s):

Structural Features ◽

Insight Into

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Structural basis for distinct inflammasome complex assembly by human NLRP1 and CARD8

Nature Communications ◽

10.1038/s41467-020-20319-5 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Qin Gong ◽

Kim Robinson ◽

Chenrui Xu ◽

Phuong Thao Huynh ◽

Kelvin Han Chung Chong ◽

...

Keyword(s):

Cell Death ◽

Inner Core ◽

Inflammatory Diseases ◽

Structural Features ◽

Structural Basis ◽

Cultured Human Cells ◽

Structural Insight ◽

Sensor Proteins ◽

Insight Into

AbstractNod-like receptor (NLR) proteins activate pyroptotic cell death and IL-1 driven inflammation by assembling and activating the inflammasome complex. Closely related sensor proteins NLRP1 and CARD8 undergo unique auto-proteolysis-dependent activation and are implicated in auto-inflammatory diseases; however, their mechanisms of activation are not understood. Here we report the structural basis of how the activating domains (FIINDUPA-CARD) of NLRP1 and CARD8 self-oligomerize to assemble distinct inflammasome complexes. Recombinant FIINDUPA-CARD of NLRP1 forms a two-layered filament, with an inner core of oligomerized CARD surrounded by an outer ring of FIINDUPA. Biochemically, self-assembled NLRP1-CARD filaments are sufficient to drive ASC speck formation in cultured human cells—a process that is greatly enhanced by NLRP1-FIINDUPA which forms oligomers in vitro. The cryo-EM structures of NLRP1-CARD and CARD8-CARD filaments, solved here at 3.7 Å, uncover unique structural features that enable NLRP1 and CARD8 to discriminate between ASC and pro-caspase-1. In summary, our findings provide structural insight into the mechanisms of activation for human NLRP1 and CARD8 and reveal how highly specific signaling can be achieved by heterotypic CARD interactions within the inflammasome complexes.

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Insight into Inhibitor Binding in the Eukaryotic Proteasome: Computations of the 20S CP

International Journal of Molecular Sciences ◽

10.3390/ijms19123858 ◽

2018 ◽

Vol 19 (12) ◽

pp. 3858

Author(s):

Milan Hodošček ◽

Nadia Elghobashi-Meinhardt

Keyword(s):

Electrostatic Interactions ◽

Active Sites ◽

Sampling Period ◽

Md Simulations ◽

Structural Features ◽

Relaxation Dynamics ◽

Inhibitor Binding ◽

Computational Analyses ◽

Insight Into ◽

Proteolytic Chamber

A combination of molecular dynamics (MD) simulations and computational analyses uncovers structural features that may influence substrate passage and exposure to the active sites within the proteolytic chamber of the 20S proteasome core particle (CP). MD simulations of the CP reveal relaxation dynamics in which the CP slowly contracts over the 54 ns sampling period. MD simulations of the SyringolinA (SylA) inhibitor within the proteolytic B 1 ring chamber of the CP indicate that favorable van der Waals and electrostatic interactions account for the predominant association of the inhibitor with the walls of the proteolytic chamber. The time scale required for the inhibitor to travel from the center of the proteolytic chamber to the chamber wall is on the order of 4 ns, accompanied by an average energetic stabilization of approximately −20 kcal/mol.

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