Anna D Protopopova

Anna D Protopopova
University of Pennsylvania | UP · Department of Systems Pharmacology and Translational Therapeutics

PhD

About

43
Publications
3,968
Reads
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353
Citations
Additional affiliations
August 2013 - November 2015
Scientific Research Institute of Physical-Chemical Medicine
Position
  • Researcher
March 2013 - June 2013
September 2010 - July 2013
Lomonosov Moscow State University
Position
  • Lead Engineer
Education
June 2002 - February 2008
Lomonosov Moscow State University
Field of study
  • Polymer and Crystal Physics

Publications

Publications (43)
Article
Background: Blood clot contraction, volume shrinkage of the clot, is driven by platelet contraction and accompanied by compaction of the erythrocytes and their gradual shape change from biconcave to polyhedral, with the resulting cells named polyhedrocytes. Objectives: Here, we examined the role of erythrocyte rigidity on clot contraction and eryth...
Article
Full-text available
Objective Soluble fibrin (SF) is a substantial component of plasma fibrinogen (fg), but its composition, functions, and clinical relevance remain unclear. The study aimed to evaluate the molecular composition and procoagulant function(s) of SF. Materials and Methods Cryoprecipitable, SF-rich (FR) and cryosoluble, SF-depleted (FD) fg isolates were p...
Preprint
Full-text available
Transient receptor potential vanilloid 2 (TRPV2) plays a critical role in a variety of physiological and pathophysiological processes, putting TRPV2 on the list of important drug targets. Yet, specific TRPV2 agonists and antagonists are currently unavailable. Their development requires a precise knowledge of how the currently known non-specific sma...
Article
High-resolution atomic force microscopy (AFM) of biomacromolecules is a valuable method for structural studies in biology. Traditionally, the surfaces used for AFM imaging of individual molecules are limited to mica, graphite, and glass. Because these substrates have certain shortcomings, new or modified surfaces that improve the quality of AFM ima...
Article
Introduction Blood coagulation factor XIII (FXIII) is a precursor of the active transglutaminase (FXIIIa) that catalyzes covalent cross-linking within polymeric fibrin to increase mechanical and proteolytic stability of blood clots and thrombi. Structurally, inactive plasma FXIII (pFXIII) with a molecular mass of 326 kDa is a heterotetramer (A2B2)...
Article
Full-text available
We examined the assembly of DNA G-quadruplexes (G4s) into higher-order structures using atomic force microscopy, optical and electrophoretic methods, NMR spectroscopy and molecular modeling. Our results suggest that parallel blunt-ended G4s with single-nucleotide or modified loops may form different types of multimers, ranging from stacks of intram...
Article
Full-text available
Graphical Abstract Highlights d Atomic structures of fibrin oligomers and protofibrils are reconstructed in silico d Structural models show good agreement with high-resolution AFM images d Fibrin protofibrils are double-stranded twisted oligomers that can bend and kink d Hydrodynamic parameters of fibrin oligomers and protofibrils are calculated In...
Article
Fibrinogen denaturation is an important phenomenon in biology and medicine. It has been previously investigated with bulk methods and characterized by parameters, which refer to big protein ensembles. Here we provide a new insight into fibrinogen denaturation with a high-resolution single-molecule atomic force microscopy (AFM). The ultrastructure o...
Article
Full-text available
We studied the ability of oligonucleotides CnT25 (n = 2, 5, 7, 9, 12, 25) to form an intermolecular i-motif using circular dichroism, ultra-violet spectroscopy, nuclear magnetic resonance, high-resolution atomic force microscopy, high-performance liquid chromatography, and molecular dynamics simulations. The arrangement of single-stranded oligonucl...
Article
Full-text available
Modeling tools provide a valuable support for DNA origami design. However, current solutions have limited application for conformational analysis of the designs. In this work we present a tool for a thorough study of DNA origami structure and dynamics. The tool is based on a novel coarse-grained model dedicated to geometry optimization and conforma...
Article
Full-text available
The flexible C-terminal parts of fibrinogen’s Aα chains named the αC regions have been shown to play a role in fibrin self-assembly, although many aspects of their structure and functions remain unknown. To examine the involvement of the αC regions in the early stages of fibrin formation, we used high-resolution atomic force microscopy to image fib...
Article
Full-text available
Fibrin is a filamentous network made in blood to stem bleeding; it forms when fibrinogen is converted into fibrin monomers that self-associate into oligomers and then to polymers. To gather structural insights into fibrin formation and properties, we combined high-resolution atomic force microscopy of fibrin(ogen) oligomers and molecular modeling o...
Conference Paper
G-quadruplex is a prominent example of non-canonical fourstranded DNA structure formed in the G-rich regions of DNA. In this study we are gathering structural information on single G-quadruplexes and trying to determine whether the differences between assembled and dismantled quadruplexes, parallel and antiparallel, quadruplexes composed of two, th...
Conference Paper
We report structural studies of 2-tetrad and 3-tetrad G4s with single-nucleotide loops and their analogs with triethylenglycole (teg) or tetrahydrofuran (tgf, ‘abasic’) derivatives. All these G4s including 5’G2AG2CG2AG2 human ALU-repeat fragment are characterized by parallel topologies and high thermodynamic stabilities. G4s with ‘abasic’ loops are...
Article
Filamentous helical Potato virus X (PVX) can be regarded as one of the well-studied viruses. Nevertheless, some aspects of the PVX assembly remained obscure. Previously, we have shown that the presence of a cap structure at the 5' end of PVX RNA is indispensable for assembly of viral ribonucleoprotein (vRNP) particles varying in length. Here, most...
Article
Background Fibrinogen has been intensively studied with transmission electron microscopy and x-ray diffraction. But until now, a complete 3D structure of the molecule has not yet been available because the two highly flexible αC regions could not be resolved in fibrinogen crystals. This study was aimed at determining whether the αC regions can be v...
Article
The potato virus X (PVX) virion can be reconstituted in vitro from the virus coat protein (CP) and RNA; heterologous RNAs may be used as well. In our recent study, structure and properties of cognate and heterologous viral ribonucleoproteins (vRNPs) were demonstrated to be similar to those of native virions. The assembly was found to be initiated a...
Article
Full-text available
Cajal bodies (CBs) are dynamic subnuclear compartments involved in the biogenesis of ribonucleoproteins. Coilin is a major structural scaffolding protein necessary for CB formation, composition and activity. The predicted secondary structure of Arabidopsis thaliana coilin (Atcoilin) suggests that the protein is composed of three main domains. Analy...
Data
Sequence alignment of the most conserved coilin protein sequences from Arabidopsis thaliana (NM_101173.4; GI:42562030) and Homo sapiens (NP_004636.1; GI:4758024). (A) Alignment of predicted NODs from these two proteins, which have a similarity score of 30%. The positive amino acids whose replacement with Alanines affect RNA-binding, are shown in bo...
Data
Influence of salt concentration on the pattern of the oligomerization of coilin and its isolated domains. DLS measurement of the hydrodynamic radius was used to determine the level aggregation of Atcoilin (A), NOD (B), IDD (C) and CTD (D) after exposure to different NaCl concentrations. Atcoilin and NOD have similar levels of resistance to salt ind...
Data
Full-text available
The putative structural organisation of the Atcoilin molecule. Domains and functionally important regions are indicated. NLS1, NLS2 and 7K (cryptic NoLS) are indicated as black boxes. The alternate charged regions within the central part of the protein are indicated by “+” or “−”, according to their charge. Folded regions are shown as spheres. (PDF...
Data
Comparison of the FoldIndex predicted folded/unfolded regions of coilin proteins from different species. (TIF)
Data
SDS-PAGE of Atcoilin and its isolated domains (NOD, IDD and CTD) expressed and purified from E. coli (Coomassie blue staining). (TIF)
Data
Sequence alignment of Arabidopsis thaliana coilin and several coilin-like proteins from various plant species. The protein sequences were obtained by using Arabidopsis coilin as a query in a Basic protein BLAST search (http://blast.ncbi.nlm.nih.gov/Blast.cgi). Plant proteins with the highest homology ratios (above 39) were selected for the alignmen...
Article
Full-text available
A sensitive turbidimetric method for detecting fibrin association was used to study the kinetics of fibrinogen hydrolysis with thrombin. The data were complemented by high-performance liquid chromatography (HPLC) measurements of the peptide products, fibrinopeptides released during hydrolysis. Atomic force microscopy (AFM) data showed that the fibr...
Article
Full-text available
Potato virus X (PVX) and some other potexviruses can be reconstitutedin vitrofrom viral coat protein (CP) and RNA. PVX CP is capable of forming viral ribonucleoprotein complexes (vRNP) not only with homologous, but also with foreign RNAs. This paper presents the structure and properties of vRNP assembledin vitroupon incubation of PVX CP and RNAs of...
Article
Full-text available
Interactions between fibrinogen molecules proteolytically cleaved with thrombin were investigated using atomic force microscopy (AFM) and dynamic light scattering (DLS). Gradually decreased fibrinogen concentrations were used to study the fibrin network, large separated fibrils, small fibrils in the initial association stages, and protofibrils. In...
Article
Water-soluble cationic polypyridylphenylene dendrimers (wPPPDs) of different generations and various contents of pyridyl and phenylene moieties were synthesized. Interaction of wPPPDs with DNA resulted in the formation of polyelectrolyte complexes stable at physiological pH and ionic strength. Noticeable contribution of hydrophobic interactions pro...

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