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Nobel prize winner Erwin Schrödinger: the physicist, philosopher, and godfather of molecular biology and genetics
T. V. Danylova1*, S. V. Komisarenko2
1National University of Life and Environmental Sciences of Ukraine, Kyiv;
*e-mail: danilova_tv@ukr.net;
2Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, Kyiv;
e-mail: svk@biochem.kiev.ua
Received: 11 March 2020; Accepted: 15 May 2020
The brilliant book “What is Life? The Physical Aspect of the Living Cell” authored by the prominent Nobel Prize-winning Austrian physicist Erwin Schrödinger became a successful attempt to bridge the gap between physics and biology. The philosophical thought of one of the founders of quantum mechanics inspired him to look closer at the enigma of life through the lens of quantum physics. A prominent physicist was focused on the thermodynamics of the living organisms and the nature of heredity. Schrödinger introduced the concept and notion of “negative entropy”, suggested the idea of a genetic code and argued that the genetic material had to have a non-repetitive molecular structure. He considered a molecule as a solid – aperiodic crystal that forms the hereditary substance. Despite the fact that his book provoked different interpretations and his ideas were modified by later scientific development, it was Schrödinger who paved the way for the future research of genes: his book inspired the next generation of scientists to look for a secret life code, which was eventually found. His outstanding writing is still one of the most profound introductions into the subject and raises new questions. Schrödinger’s genius reshapes our view on the nature and essence of life creating a launching pad for the new transdisciplinary paradigm, which can contribute to the development of a unified theory of everything in the spirit of Schrödinger’s philosophy.
The human genome sequencing race ended 20 years ago
M. V. Grigorieva, S. V. Komisarenko
Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, Kyiv;
e-mail: mvgrigorieva@biochem.kiev.ua
Received: 25 June 2020; Accepted: 18 July 2020
The Human Genome Project, one of the most grandiose in contemporary science, was officially launched in 1990. The project aimed at determining the human DNA primary structure and gene localization and functions as well as ensuring free access of researchers to the project’s findings. The HGP was implemented by the International Human Genome Sequencing Consortium, sponsored by the US Department of Energy, and the UK-based private company Celera Genomics. The results of the two teams’ work, including the rough draft of the human genome sequence, were published in Nature and Science in February 2001 within one day of each other, and the final version appeared three years after. The HGP’s revolutionary impact on biology and medicine cannot be overstated.
Men of the molecules
In memoriam of Prof. Russell Doolittle,
Prof. Eduard Lugovskoi and their friendship that outlive both of them
V. O. Chernyshenko
Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, Kyiv;
e-mail: bio.cherv@gmail.com
Received: 02 July 2020; Accepted: 21 July 2020
In memoriam Eduard Lugovskoi and Russell Doolittle we are referring to several episodes of their life and work. Russell Doolittle an American biochemist and his friend and colleague Ukrainian scientist Eduard Lugovskoi, both studied fibrinogen structure and functions and finally united their efforts in the revealing of the new mechanism of intramolecular interactions of fibrin molecule through coiled-coil region. The results of their common work and discussions were included to the article “The fibrin Bβ125-135 site is involved in the lateral association of protofibrils”. Valuable part of the communication dedicated to the poetry of Eduard Lugovskoi that inspired both of scientists in work and life. We are providing some remembrance of their collaboration, their letters sent to each other, fragments of handwriting and common photo of Russell Doolittle and Eduard Lugovskoi.
D-dimer as a potential predictor of thromboembolic and cardiovascular complications in patients with chronic kidney disease
I. S. Mykhaloiko1*, I. O. Dudar2, I. Ja. Mykhaloiko1, O. Ja. Mykhaloiko1
1SHEE “Ivano-Frankivsk National Medical University”, Ivano-Frankivsk, Ukraine;
2SI “Institute of Nephrology AMS of Ukraine”, Kiev, Ukraine;
*e-mail: iralisn@gmail.com
Received: 13 February 2020; Accepted: 30 June 2020
The aim of the study was to evaluate the relationship between D-dimer levels and different biomarkers of renal diseases to identify the relationship between hypercoagulation and chronic kidney disease (CKD). To achieve this aim, we conducted a one-step prospective observational study involving 140 patients with CKD who were hospitalized in Ivano-Frankivsk Regional Clinical Hospital in Ukraine during 2018-2019. Of these patients, 100 patients (71.4%; 95% CI 53.4-76.7) had glomerulonephritis (GN) and 40 patients (28,6%; 95% CI 21.3-36.8) had diabetic nephropathy (DN). All patients underwent standard examination, which included general clinical, biochemical and instrumental research methods. D-dimer was quantitatively determined in blood serum by enzyme-linked immunosorbent assay (ELISA). The 140 patients were divided into two groups according to the level of D-dimers: normal level (<0.5 mg/l) and elevated level (≥0.5 mg/l). Elevated D-dimer levels were associated with an increased age of patients, decreased glomerular filtration rate, decreased blood albumin level, increased daily protein excretion and a tendency to develop thromboembolic complications during 1 year of monitoring. D-dimer is a biological marker that can detect hypercoagulation at an early preclinical stage in patients with CKD and identify patients with an increased cardiovascular risk, thereby promoting the earliest use of antiplatelet agents and anticoagulants and, consequently, it can reduce mortality.
Novel monoclonal antibody to fibrin(ogen) αC-region for detection of the earliest forms of soluble fibrin
N. E. Lugovska1, I. M. Kolesnikova1, Ye. M. Stohnii1, V. O. Chernyshenko1*,
A. V. Rebriev1, O. P. Kostiuchenko1, G .K. Gogolinska1, N. A. Dziubliuk2,
L. D. Varbanets2, T. M. Platonova1, S. V. Komisarenko1
1Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, Kyiv;
2Zabolotny Institute of Microbiology and Virology,National Academy of Sciences of Ukraine, Kyiv;
*e-mail: bio.cherv@gmail.com
Received: 08 May 2020; Accepted: 30 June 2020
Obtaining new monoclonal antibodies (mAbs) towards fibrin(ogen) and its fragments is an important task for studying mechanisms of blood clot formation, searching for novel antithrombotic agents and developing immunodiagnostics. The aim of the present work was to create and characterize a new mAb towards the fibrin(ogen) αС-region. We surmise that having a specific mAb towards this flexible part of the molecule will allow us to study the role of the αС-region in fibrin polymerization and also to develop an approach for detecting the earliest forms of soluble fibrin by sandwich ELISA. Using hybridoma technology we оbtained mAb 1-5A to the αC-region of fibrinogen.. It was characterized using several variations of ELISA and Western blot. Application of specific proteases together with MALDI-TOF analysis allowed us to localize its epitope that is located in fragment 537-595 of the Aα-chain of fibrin(ogen). МAb 1-5A can be used as a detecting tag-antibody in sandwich ELISA for the quantification of the earliest forms of soluble fibrin which are uncleaved by plasmin and preserved C-terminal portions of αC-regions. These earliest forms of soluble fibrin are direct evidence of blood coagulation system activation, thrombin generation and the danger of intravascular thrombus formation. Their determination will provide additional, more accurate information about the state of the blood coagulation system and the risk of blood clotting, which is very important for the timely and correct selection of adequate antithrombotic therapy. MAb 1-5A effectively binds the αC-containing molecules of fibrinogen and fibrin in blood plasma. It also can be used for studying protein-protein and protein-cellular interactions of the αC-regions of fibrin(ogen).
Identification of the binding site for plasminogen kringle 5 in the α-chain of fibrin(ogen) D-fragment
L. G. Kapustianenko*, T. V. Grinenko, A. V. Rebriev,
O. I. Yusova, A. A. Tykhomyrov
Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, Kyiv;
*e-mail: kapustyanenko@biochem.kiev.ua
Received: 17 May 2020; Accepted: 30 June 2020
The interaction of the fifth kringle of Glu-plasminogen with fibrin triggers activation and initiation of fibrinolysis, yet the site on fibrin that binds kringle 5 remains unknown. The aim of our work was to determine an amino acid sequence in the D-fragment of fibrin(ogen) molecule, which is complementary to the lysine-binding site (LBS) in kringle 5. We studied the interaction between kringle 5 of plasminogen with polypeptide chains of the D-fragments of fibrin and cyanogen bromide fragments FCB-2 and t-NDSK and showed that kringle 5 bound specifically to α- and γ-chains of the D-fragment and the α-chain of FCB-2. Tryptic peptides of D-fragment α-chain were obtained, separated by their ability to bind with the immobilized kringle 5, and then all studied peptides were characterized by MALDI-TOF analysis. The critical amino acid residues of the α-chain of D-fragment, which provide its interaction with kringle 5, turned out to be α171Arg and/or α176Lys. The binding site of Glu-plasminogen complementary to the LBS of kringle 5 is located within Аα168Ala−183Lys, a sequence in a weakly structured loop between two supercoils in the α-chain of the D-fragment of the fibrin(ogen) molecule.
The fibrin Bβ125-135 site is involved in the lateral association of protofibrils
E. Lugovskoi1, N. Pydiura2, Y. Makogonenko1*, L. Urvant1,
P. Gritsenko1, I. Kolesnikova1, N. Lugovska1, S. Komisarenko1
1Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, Kyiv;
2Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine Kyiv;
*e-mail: ymakogonenko@gmail.com
Received: 19 May 2020; Accepted: 30 June 2020
Earlier we reported that during the human fibrinogen to fibrin transition a neoantigenic determinant was exposed in the Bβ119-133 fragment, where a hinge locus is situated. The fibrin-specific mAb FnI-3c and its Fab-fragment with epitope in this fragment inhibited the lateral association of protofibrils. We suggested that the epitope coincided with a site involved in this process. In this work we investigated the epitope location more precisely and defined a functional role for its exposure in the hinge locus of the molecule. It was found that mAb FnI-3c bound to human, horse and rabbit fibrins, all of which have Lys in the position corresponding to human BβK130, but not to bovine and rat fibrins, which have other amino acid residues in this position, strongly suggesting that BβK130 provides the integral part of the epitope. This fact, homology data, and structural biological analysis of the amino acid sequences around BβK130 indicate that the site of interest is localized within Bβ125-135. The synthetic peptides Bβ121-138 and Bβ125-135, unlike their scrambled versions, bound to mAb FnI-3c in SPR analysis. Both peptides, but not their scrambled versions, inhibited the lateral association of protofibrils. The FnI-3c epitope is exposed after fibrinopeptide A cleavage and desA fibrin monomer formation. Structural biological analysis of the fibrinogen to fibrin transition showed a distinct increase of flexibility in the hinge locus. We propose that the structural transformation in the fibrin hinge regions leads to the conformation necessary for lateral association of protofibrils.
Structure and function of fibrinogen BβN-domains
L. Medved*, S. Yakovlev
Center for Vascular and Inflammatory Diseases and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA;
*e-mail: Lmedved@som.umaryland.edu
Received: 17 May 2020; Accepted: 30 June 2020
Fibrinogen is a polyfunctional plasma protein involved in various physiological and pathological processes through the interaction of its multiple domains with different ligands and cell receptors. Among fibrinogen domains, two BβN-domains are formed by the N-terminal portions of its two Bβ chains including amino acid residues Bβ1-64. Although their folding status is not well understood and the recombinant disulfide-linked (Bβ1-66)2 fragment corresponding to a pair of these domains was found to be unfolded, some data suggest that these domains may be folded in the parent molecule. In contrast, their major functional properties are well established. Removal of fibrinopeptides B (amino acid residues Bβ1-14) from these domains upon fibrinogen to fibrin conversion results in the exposure of multiple binding sites in fibrin βN-domains (residues β15-64). These sites provide interaction of the βN-domains with different proteins and cells and their participation in various processes including fibrin assembly, fibrin-dependent angiogenesis, and fibrin-dependent leukocyte transmigration and thereby inflammation. The objective of this review is to summarize the current view of the structure and function of these domains in fibrinogen and fibrin and their role in the above-mentioned processes.