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

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.

Elucidating the molecular interactions between uremic toxins and the Sudlow II binding site of human serum albumin

2020 ◽  
Author(s):  
Josh Smith ◽  
Jim Pfaendtner
Keyword(s):  
Molecular Dynamics ◽  
Human Serum Albumin ◽  
Serum Albumin ◽  
Human Serum ◽  
Electrostatic Interactions ◽  
Md Simulations ◽  
Uremic Toxins ◽  
Indoxyl Sulfate ◽  
Structural Description ◽  
Insight Into

AbstractProtein bound uremic toxins (PBUTs) are known to bind strongly with the primary drug carrying sites of human serum albumin (HSA), Sudlow site I and Sudlow site II. A detailed energetic and structural description of PBUT interactions with these binding sites would provide useful insight into the design of materials that specifically displace and capture PBUTs. In this work, we used molecular dynamics (MD) simulations to study in atomistic detail 4 PBUTs bound in Sudlow site II. Specifically, we used the experimentally resolved X-ray structure of simulated indoxyl sulfate (IS) bound to Sudlow site II (PBD ID: 2BXH) to generate initial binding poses for p-cresyl sulfate (pCS), indole-3-acetic acid (IAA), and hippuric acid (HA). We calculated the interaction energy between toxin and protein in MD simulations and performed mean shift clustering on the collection of molecular structures from MD to identify the primary binding modes of each toxin. We find that all 4 toxins are primarily stabilized by electrostatic interactions between their anionic moiety and the hydrophilic residues in Sudlow site II. We observed transience in the strongest toxin-protein interaction, a charge-pairing with the positively charged R410 residue. We confirm the finding that the primary binding pose of IS in Sudlow site II is stabilized by a hydrogen bond with the carbonyl oxygen of L430, and find that this is also true for IAA. We provide insight into the chemical functional groups that might be incorporated to improve the specificity of synthetic materials for PBUT capture. This work represents a next step toward the de novo design of solutions to the problem of PBUT management in CKD patients.Significance StatementIn spite of their implication in poor clinical outcomes, surprisingly little information is available about the structure and mechanisms that govern the binding of protein bound uremic toxins to their primary carrier human serum albumin. To date, only the structure of indoxyl sulfate has been determined by experiment. This paper describes a comprehensive characterization of four toxins that are known to bind Sudlow site II using molecular dynamics simulations. Based on the experimental structure of indoxyl sulfate bound to HSA, the binding mode within Sudlow site II of three additional PBUTs was determined. The structures, energetic and mechanistic analysis provide substantial new information for the nephrology community about these toxins as well as new protocols to aid future studies of PBUTs.

scholarly journals Insights into the binding of PARP inhibitors to the catalytic domain of human tankyrase-2

2014 ◽  
Vol 70 (10) ◽  
pp. 2740-2753 ◽  
Author(s):  
Wei Qiu ◽  
Robert Lam ◽  
Oleksandr Voytyuk ◽  
Vladimir Romanov ◽  
Roni Gordon ◽  
...  
Keyword(s):  
Rational Design ◽  
Catalytic Domain ◽  
Parp Inhibitors ◽  
Structural Features ◽  
Binding Modes ◽  
Inhibitor Binding ◽  
New Class ◽  
Double Stranded Dna ◽  
Tankyrase 1 ◽  
Insight Into

The poly(ADP-ribose) polymerase (PARP) family represents a new class of therapeutic targets with diverse potential disease indications. PARP1 and PARP2 inhibitors have been developed for breast and ovarian tumors manifesting double-stranded DNA-repair defects, whereas tankyrase 1 and 2 (TNKS1 and TNKS2, also known as PARP5a and PARP5b, respectively) inhibitors have been developed for tumors with elevated β-catenin activity. As the clinical relevance of PARP inhibitors continues to be actively explored, there is heightened interest in the design of selective inhibitors based on the detailed structural features of how small-molecule inhibitors bind to each of the PARP family members. Here, the high-resolution crystal structures of the human TNKS2 PARP domain in complex with 16 various PARP inhibitors are reported, including the compounds BSI-201, AZD-2281 and ABT-888, which are currently in Phase 2 or 3 clinical trials. These structures provide insight into the inhibitor-binding modes for the tankyrase PARP domain and valuable information to guide the rational design of future tankyrase-specific inhibitors.

scholarly journals Targeting structural features of viral genomes with a nano-sized supramolecular drug

2021 ◽  
Author(s):  
Lazaros Melidis ◽  
Iain B. Styles ◽  
Michael J. Hannon
Keyword(s):  
Experimental Data ◽  
Md Simulations ◽  
Structural Features ◽  
Conformational Flexibility ◽  
Viral Genomes ◽  
Markov State ◽  
Mechanistic Insight ◽  
Tar Rna ◽  
Markov State Modeling ◽  
Insight Into

MD simulations and Markov state modeling explore induced fit binding of metallo-helicates to bulges in dynamic TAR RNA, reproduce experimental data, show how RNA conformational flexibility is reduced, and give mechanistic insight into insertion.

scholarly journals The HD-Domain Metalloprotein Superfamily: An Apparent Common Protein Scaffold with Diverse Chemistries

Catalysts ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 1191
Author(s):  
Michelle Langton ◽  
Sining Sun ◽  
Chie Ueda ◽  
Max Markey ◽  
Jiahua Chen ◽  
...  
Keyword(s):  
Substrate Specificity ◽  
Active Sites ◽  
Functional Divergence ◽  
Structural Features ◽  
Ability To Work ◽  
Biologically Relevant ◽  
Protein Partners ◽  
Additional Protein ◽  
Domain Protein ◽  
Insight Into

The histidine–aspartate (HD)-domain protein superfamily contains metalloproteins that share common structural features but catalyze vastly different reactions ranging from oxygenation to hydrolysis. This chemical diversion is afforded by (i) their ability to coordinate most biologically relevant transition metals in mono-, di-, and trinuclear configurations, (ii) sequence insertions or the addition of supernumerary ligands to their active sites, (iii) auxiliary substrate specificity residues vicinal to the catalytic site, (iv) additional protein domains that allosterically regulate their activities or have catalytic and sensory roles, and (v) their ability to work with protein partners. More than 500 structures of HD-domain proteins are available to date that lay out unique structural features which may be indicative of function. In this respect, we describe the three known classes of HD-domain proteins (hydrolases, oxygenases, and lyases) and identify their apparent traits with the aim to portray differences in the molecular details responsible for their functional divergence and reconcile existing notions that will help assign functions to yet-to-be characterized proteins. The present review collects data that exemplify how nature tinkers with the HD-domain scaffold to afford different chemistries and provides insight into the factors that can selectively modulate catalysis.

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

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.

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

2019 ◽  
Vol 16 (2) ◽  
pp. 159-172 ◽  
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.

The Oxford Handbook of the Brazilian Economy

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.

scholarly journals Intra-Colonial Viral Infections in Western Honey Bees (Apis mellifera)

2021 ◽  
Vol 9 (5) ◽  
pp. 1087
Author(s):  
Loreley Castelli ◽  
María Laura Genchi García ◽  
Anne Dalmon ◽  
Daniela Arredondo ◽  
Karina Antúnez ◽  
...  
Keyword(s):  
Apis Mellifera ◽  
Honey Bee ◽  
Viral Infections ◽  
Sampling Period ◽  
Virus Genome ◽  
The Individual ◽  
Bee Virus ◽  
Insight Into ◽  
Bee Viruses

RNA viruses play a significant role in the current high losses of pollinators. Although many studies have focused on the epidemiology of western honey bee (Apis mellifera) viruses at the colony level, the dynamics of virus infection within colonies remains poorly explored. In this study, the two main variants of the ubiquitous honey bee virus DWV as well as three major honey bee viruses (SBV, ABPV and BQCV) were analyzed from Varroa-destructor-parasitized pupae. More precisely, RT-qPCR was used to quantify and compare virus genome copies across honey bee pupae at the individual and subfamily levels (i.e., patrilines, sharing the same mother queen but with different drones as fathers). Additionally, virus genome copies were compared in cells parasitized by reproducing and non-reproducing mite foundresses to assess the role of this vector. Only DWV was detected in the samples, and the two variants of this virus significantly differed when comparing the sampling period, colonies and patrilines. Moreover, DWV-A and DWV-B exhibited different infection patterns, reflecting contrasting dynamics. Altogether, these results provide new insight into honey bee diseases and stress the need for more studies about the mechanisms of intra-colonial disease variation in social insects.

Structural insights into the repair mechanism of AGT for methyl-induced DNA damage

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Rajendra P. Koirala ◽  
Rudramani Pokhrel ◽  
Prabin Baral ◽  
Purushottam B. Tiwari ◽  
Prem P. Chapagain ◽  
...  
Keyword(s):  
Covalent Bond ◽  
Cancer Therapeutics ◽  
Md Simulations ◽  
Structural Features ◽  
Umbrella Sampling ◽  
Repair Mechanism ◽  
Structural Investigations ◽  
Methylated Dna ◽  
Dna Base ◽  
Dna Alkyltransferase

Abstract Methylation induced DNA base-pairing damage is one of the major causes of cancer. O6-alkylguanine-DNA alkyltransferase (AGT) is considered a demethylation agent of the methylated DNA. Structural investigations with thermodynamic properties of the AGT-DNA complex are still lacking. In this report, we modeled two catalytic states of AGT-DNA interactions and an AGT-DNA covalent complex and explored structural features using molecular dynamics (MD) simulations. We utilized the umbrella sampling method to investigate the changes in the free energy of the interactions in two different AGT-DNA catalytic states, one with methylated GUA in DNA and the other with methylated CYS145 in AGT. These non-covalent complexes represent the pre- and post-repair complexes. Therefore, our study encompasses the process of recognition, complex formation, and separation of the AGT and the damaged (methylated) DNA base. We believe that the use of parameters for the amino acid and nucleotide modifications and for the protein-DNA covalent bond will allow investigations of the DNA repair mechanism as well as the exploration of cancer therapeutics targeting the AGT-DNA complexes at various functional states as well as explorations via stabilization of the complex.

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

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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