Protein Chemistry Research Articles

Chemically Acylated tRNAs are Functional in Zebrafish Embryos.

Genetic code expansion has pushed protein chemistry past the canonical 22 amino acids. The key enzymes that make this possible are engineered aminoacyl tRNA synthetases. However, as the number of genetically encoded amino acids has increased over the years, obvious limits in the type and size of novel side chains that can be accommodated by the synthetase enzyme become apparent. Here, we show that chemically acylating tRNAs allow for robust, site-specific incorporation of unnatural amino acids into proteins in zebrafish embryos, an important model organism for human health and development. We apply this approach to incorporate a unique photocaged histidine analogue for which synthetase engineering efforts have failed. Additionally, we demonstrate optical control over different enzymes in live embryos by installing photocaged histidine into their active sites.

Deep learning methods of predicting RNA torsion angle

Modeling of RNA tertiary structure is one of the basic problems in molecular biophysics, and it is very important in understanding the biological function of RNA and designing new structures. RNA tertiary structure is mainly determined by seven torsions of main-chain and side-chain backbone, the accurate prediction of these torsion angles is the basis of modeling RNA tertiary structure. At present, there are only a few methods of using deep learning to predict RNA torsion angles, and the prediction accuracy needs further improving if it is used to model RNA tertiary structure. In this study, we also develop a deep learning method, 1dRNA, to predict RNA backbone torsions and pseudotorsion angles, including two different deep learning models, the convolution model (DRCNN) that considers the features of adjacent nucleotides and the Hyper-long-short-term memory model (DHLSTM) that considers the features of all the nucleotides. We then empirically show that DRCNN and DHLSTM outperform existing state-of-the-art methods under the same datasets, the prediction accuracy of DRCNN model is improved by 5% to 28% for <i>β</i>, <i>δ</i>, <i>ζ</i>, <i>χ</i>, <i>η</i>, and <i>θ</i> angle, and the prediction accuracy of DHLSTM model is improved by 6% to 15% for <i>β</i>, <i>δ</i>, <i>ζ</i>, <i>χ</i>, <i>η</i>, <i>θ</i> angle. The DRCNN model predicts better results than the DHLSTM model and the existing models in the <i>δ</i>, <i>ζ</i>, <i>χ</i>, <i>η</i>, <i>θ</i> angle, and the DHLSTM model predicts better results than the DRCNN model and the existing model in the <i>β</i> and <i>ε</i> angles, and the existing models predicted better results than the DRCNN model and DHLSTM model in the <i>α</i> and <i>γ</i> angles. The DRCNN model and the existing models predict a richer distribution of angles than the DHLSTM model. In terms of model stability, the DHLSTM model is much more stable than the DRCNN model and the existing models, with fewer outliers. The results also show that the <i>α</i> angle and <i>γ</i> angle are the most difficult to predict, the angles of the ring region is more difficult to predict than the angles of the helix region, the model is also not sensitive to the change of the target sequence length, and the deviation of the model prediction angle from the decoys can also be used to evaluate the RNA tertiary structures quality.

Five questions on how biochemistry can combat climate change

Global warming is caused by human activity, such as the burning of fossil fuels, which produces high levels of greenhouse gasses. As a consequence, climate change impacts all organisms and the greater ecosystem through changing conditions from weather patterns to the temperature, pH and salt concentrations found in waterways and soil. These environmental changes fundamentally alter many parameters of the living world, from the kinetics of chemical reactions and cellular signaling pathways to the accumulation of unforeseen chemicals in the environment, the appearance and dispersal of new diseases, and the availability of traditional foods. Some organisms adapt to extremes, while others cannot. This article asks five questions that prompt us to consider the foundational knowledge that biochemistry can bring to the table as we meet the challenge of climate change. We approach climate change from the molecular point of view, identifying how cells and organisms – from microbes to plants and animals – respond to changing environmental conditions. To embrace the concept of “one health” for all life on the planet, we argue that we must leverage biochemistry, cell biology, molecular biophysics and genetics to fully understand the impact of climate change on the living world and to bring positive change.

Focus on lasers, imaging, microscopy, and nanoscience

Focus on lasers, imaging, microscopy, and nanoscience

On the development of proteomics: a brief history

Although one can trace the roots of proteomics well back into the 20th century, it is basically a discipline of the new millennium. At its outset, it was defined primarily by the technology available to analyze complex mixtures (basically 2D-gel electrophoresis, hybridizations/arrays and mass spectrometry) and what mainly set it aside from protein chemistry, that had flourished since the end of the second world war, was this use of unfractionated starting material as opposed to homogenous samples. Early on, two major new insights were quickly revealed: that the protein complement of cells was overwhelmingly involved in multiple protein–protein interactions and that it was nearly universally involved in a myriad of post-translational modifications. The revelations of the complex networks that result from these two phenomena have created a new understanding of cell biology that has affected our appreciation of such processes as transcription and translation, transmembrane signaling, differentiation, homeostasis and cell death. The development of these methods and strategies that principally characterize the field of proteomics depended heavily on the evolution of those that advanced protein chemistry, particularly during the last half of the twentieth century leading up to the elucidation of the human genome and will be briefly summarized in this article.

Copper trafficking systems in cells: insights into coordination chemistry and toxicity.

Transition metal ions, such as copper, are indispensable components in the biological system. Copper ions which primarily exist in two major oxidation states Cu(I) and Cu(II) play crucial roles in various cellular processes including antioxidant defense, biosynthesis of neurotransmitters, and energy metabolism, owing to their inherent redox activity. The disturbance in copper homeostasis can contribute to the development of copper metabolism disorders, cancer, and neurodegenerative diseases, highlighting the significance of understanding the copper trafficking system in cellular environments. This review aims to offer a comprehensive overview of copper homeostatic machinery, with an emphasis on the coordination chemistry of copper transporters and trafficking proteins. While copper chaperones and the corresponding metalloenzymes are thoroughly discussed, we also explore the potential existence of low-molecular-mass metal complexes within cellular systems. Furthermore, we summarize the toxicity mechanisms originating from copper deficiency or accumulation, which include the dysregulation of oxidative stress, signaling pathways, signal transduction, and amyloidosis. This perspective review delves into the current knowledge regarding the intricate aspects of the copper trafficking system, providing valuable insights into potential treatment strategies from the standpoint of bioinorganic chemistry.

Challenges and perspectives in research and teaching of host pathogen interaction topics: new post-pandemic times to Brazil and other South American countries.

Here is our proposal to improve learning in biomedical sciences for graduate and undergraduate courses with a broad vision integrating disciplines such as molecular cell biology, biochemistry, and biophysics around concepts of pathogen interaction within vertebrate and invertebrate hosts. Our paradigm is based on the possibility offered by the pandemic to have remote activities that give access to students and researchers from different places in Brazil and Latin American countries to discuss science. A multidisciplinary view of host-pathogen interaction allows us to understand better the mechanisms involved in the pathology of diseases, as well as to formulate broad strategies for the diagnosis, treatment, and control of thereof. The approach to integrating heterogeneous groups in science involves the critical analysis of national scientific resource distribution, where only some have the possibilities to conduct competitive scientific research. Solid theoretical training, contact, collaboration with groups of excellence, and training within a multidisciplinary network are our proposals for a permanent platform of scientific strengthening and dissemination for Latin America. Here we will review the concept of host-pathogen interaction, the type of institutions where it is taught and researched, new trends in active teaching methodologies, and the current political context in science.

Impact of neurobiofeedback by beta rhythm of the brain on the functional state of cardiovascular system of athletes with different motor activity

To examine the impact of one procedure of neurobiofeedback by beta rhythm of the brain on the cardiovascular system functional state in the athletes with different character of motor activity. The study included 1020 male athletes aged 18-21 years. Depending on the motor activity, patients were divided into 5 groups: 1st group - cyclic sports athletes (38%); 2nd group - speed-power sports athletes (25%); 3rd group - combat sport athletes (3%); 4th group - team sports athletes (17%) and 5th group - athletes of complex coordination sports (17%). The procedure of neurobiofeedback by beta rhythm of the brain was done in the conditions of active waking at open eyes. Registration of bioelectric activity of the brain and training on beta rhythm were done in the Fz-Cz lead by the international system «10-20» with the arrangement of indifferent electrode on the earlobe of the subjects (PAC «BOSLAB», Institute of Molecular Biology and Biophysics, Novosibirsk, Russia). Heterochronic pattern of changes in the indicators of systemic pressure, cardiac and vascular activity of the athletes' body during a single procedure of neurobiofeedback by beta rhythm of the brain in the preparation period of the training process, depending on the character of athletic activities, was found. In response to the impact, the following indicators have changed significantly: heart rate and index of functional changes in combat sport athletes (3rd group); stroke and cardiac output in all groups. Cardiovascular regulation index and specific peripheral vascular resistance significantly increased in the groups 2-5. Cardiac index significantly decreased in the groups 1, 2, 4 and 5. Qualitative changes in types of blood circulation occurred in all groups: in groups 1, 3 and 5 - from hyperkinetic to eukinetic, in group 2 - from hyperkinetic to hypokinetic, in group 4 - from eukinetic to hypokinetic, contributing to the economization of cardiovascular activity function. The use of neurobiofeedback by the beta rhythm of the brain in the practice of sports medicine requires additional detailed research of the features and development of individual methods depending on the type of athletic activity, features of cardiac activity regulation, etc.

New Insights into Vibrio cholerae Biofilms from Molecular Biophysics to Microbial Ecology.

With the discovery that 48% of cholera infections in rural Bangladesh villages could be prevented by simple filtration of unpurified waters and the detection of Vibrio cholerae aggregates in stools from cholera patients it was realized V. cholerae biofilms had a central function in cholera pathogenesis. We are currently in the seventh cholera pandemic, caused by O1 serotypes of the El Tor biotypes strains, which initiated in 1961. It is estimated that V. cholerae annually causes millions of infections and over 100,000 deaths. Given the continued emergence of cholera in areas that lack access to clean water, such as Haiti after the 2010 earthquake or the ongoing Yemen civil war, increasing our understanding of cholera disease remains a worldwide public health priority. The surveillance and treatment of cholera is also affected as the world is impacted by the COVID-19 pandemic, raising significant concerns in Africa. In addition to the importance of biofilm formation in its life cycle, V. cholerae has become a key model system for understanding bacterial signal transduction networks that regulate biofilm formation and discovering fundamental principles about bacterial surface attachment and biofilm maturation. This chapter will highlight recent insights into V. cholerae biofilms including their structure, ecological role in environmental survival and infection, regulatory systems that control them, and biomechanical insights into the nature of V. cholerae biofilms.

Return from a Distant Country by Alister McGrath

Reviewed by: Return from a Distant Country by Alister McGrath Mark Mattes Return from a Distant Country. By Alister McGrath. Minneapolis: Fortress Press, 2020. 92pp. This slim volume belongs to the Fortress “My Theology” series which, according to the back page, allows thinkers “a platform to reflect on the meaning of God in their lives and the way they have constructed their life of faith.” McGrath is a well-known theologian, intellectual historian, and Christian apologist currently serving in a religion and science chair at Oxford University. As a youth, McGrath was an atheist. He became a Christian after he read thinkers who challenged the notion that knowledge is reducible to the scientifically verifiable (since, after all, that view is not itself scientifically verifiable), such as Karl Popper, as well as experiencing ambiguity through Marxism. Marxism helped McGrath appreciate a “Big Picture” approach to reality but as he started reading theology, he found it less satisfying than Christianity. While earning a doctorate in Molecular Biophysics in 1978, he concurrently read C. S. Lewis. Although Lewis was a popularist, his thinking was rich, grounded in decades of reflection on how faith and wider culture intersect. [End Page 456] After becoming a Christian, McGrath studied with Gordon Rupp and published books in historical theology, offering interpretations of Luther’s theology of the cross, the history of justification by grace alone through faith alone, and the perspectives of first- generation Reformers. Additionally, McGrath contributed to late twentieth-century discussions about the relationship between science and religion and defended faith against Richard Dawkins’ attacks. As a result, he helped Anglican clergy understand and convey the rationality of religious belief (22). The most important factor in McGrath’s appreciation of the Christian faith is precisely its ability to offer a satisfying, comprehensive approach to reality. That said, theology is best seen as discerning mystery throughout the world and not particularly as an exercise in “problem solving” (34). With respect to science, McGrath contends that science deals with how things work while theology deals with what things mean (66). Currently theologians should direct clergy and laity to immerse themselves in the tradition and discover treasures there that address people in their needs today. This volume is valuable because it offers a pithy summary of how a man who is both a theologian and a scientist finds compatibility between the two when so many do not. Mark Mattes Grand View University Des Moines, Iowa Copyright © 2022 Johns Hopkins University Press and Lutheran Quarterly, Inc

Rare missense variant (R251G) on APOE counterbalances the Alzheimer’s disease risk associated with APOE‐ε4

AbstractBackgroundDespite decades of research, the mechanisms linking APOE to Alzheimer’s disease (AD) remain poorly understood. Finding additional risk variants at the APOE locus, beyond the common APOE‐ε2 and APOE‐ε4 alleles, may help elucidate how APOE is involved in the disease.MethodAssociation with case‐control status was tested in a sequenced discovery sample (Stage 1) and followed‐up in several microarray imputed cohorts as well as the UK Biobank whole‐exome sequencing resource using a proxy‐AD phenotype (Stages 2+3) (Table 1). Stage 1 included 37,409 non‐unique participants of European or Admixed‐European ancestry, with 11,868 cases and 11,934 controls passing analysis inclusion criteria. In Stages 2+3, 475,473 participants were considered across 8 cohorts, of which 56,029 cases, 28,484 proxy‐AD cases, and 328,372 healthy‐controls passed inclusion criteria, and were of European ancestry.ResultTwo missense variants were associated with a two to three‐fold decreased AD risk: R251G (odds ratio, 0.44; 95% confidence interval [CI], 0.33‐0.59; P = 4.7×10‐8) and V236E (odds ratio, 0.37; 95% CI, 0.25‐0.56; P = 1.9×10‐6) (Table 2, Figures 1, 2). Additionally, the cumulative incidence of AD in carriers of these variants was found to grow more slowly with age compared to non‐carriers (Table 3).ConclusionWe identified a novel variant associated with AD, R251G, which mitigates the ε4 associated AD risk, and confirmed the protective effect of the V236E variant. The location of the variants confirms that the carboxyl‐terminal portion of apoE plays an important role in AD pathogenesis. The large risk reductions reported here, suggest that protein chemistry and functional assays of these variants have the potential to identify novel pathways for drug development.

Barts and The London School of Medicine and Dentistry

The Institute of Dentistry at Barts and The School of Medicine and Dentistry, Queen Mary University of London, has seen much change since 1857 when surgeon dentist, H. J. Barrett, was appointed to The London to oversee the extraction of teeth. However, the mission remains the same: provision of excellent patient care through our education and research to improve the oral health and general health of our local population, but also with global impact.The Institute of Dentistry is embedded in a fundamentally multidisciplinary environment of the wider university and this is reflected in our research activity. The available complementary skills in cell and molecular biology, microbiology, materials science, chemistry, biophysics, clinical science and population health allows us to undertake basic science research, patient- and population-based research and clinical biometric research.Our Centre for Teaching and Innovation is a catalyst for educational research, including that related to new technologies and the expansion of e-learning, to ultimately inform local practice and the experience of our students.

Development of Naturally Inspired Peptide and Protein Chemistry.

Diverse naturally occurring events relevant to proteins, including processing and post-translational modification, provide significant clues enabling advances in peptide/protein chemistry. Our motivation to synthesize large proteins prompted us to seek scientific bases utilized in synthetic experiments on the intein-mediated protein processing system. This account describes peptide/protein thioester-producing protocols whose design is based on acyl transfer reactions observed in the intein system, and the development of the stimulus-responsive amide cleavage and its application to the modulation of peptide function. Finally, several findings derived from nature-inspired research efforts, including peptide mimetic synthesis and S-protected cysteine chemistry, are described.

Polyvalent guide RNAs for CRISPR antivirals

CRISPR effector Cas13 recognizes and degrades RNA molecules that are complementary to its guide RNA (gRNA) and possesses potential as an antiviral biotechnology because it can degrade viral mRNA and RNA genomes. Because multiplexed targeting is a critical strategy to improve viral suppression, we developed a strategy to design of gRNAs where individual gRNAs have maximized activity at multiple viral targets, simultaneously, by exploiting the molecular biophysics of promiscuous target recognition by Cas13. These "polyvalent" gRNA sequences ("pgRNAs") provide superior antiviral elimination across tissue/organ scales in a higher organism (Nicotiana benthamiana) compared to conventionally-designed gRNAs-reducing detectable viral RNA by >30-fold, despite lacking perfect complementarity with either of their targets and, when multiplexed, reducing viral RNA by >99.5%. Pairs of pgRNA-targetable sequences are abundant in the genomes of RNA viruses, and this work highlights the need for specific approaches to the challenges of targeting viruses in eukaryotes using CRISPR.

Solid-state NMR methods for the characterization of bioconjugations and protein-material interactions

Protein solid-state NMR has evolved dramatically over the last two decades, with the development of new hardware and sample preparation methodologies. This technique is now ripe for complex applications, among which one can count bioconjugation, protein chemistry and functional biomaterials. In this review, we provide our account on this aspect of protein solid-state NMR.

An open call for contributions to a special issue of Biophysical Reviews highlighting the research themes of VII Congress of Russian Biophysicists 2023.

We announce a call for contributions to a Special Issue of Biophysical Reviews associated with the VII Congress of Russian Biophysicists (to be held in Krasnodar, Russia, 17-23 April 2023). The Congress is the main biophysical meeting held within Russia and is organized every four years. The Congress will focus on both the physical principles and mechanisms of biological processes occurring at different levels of structural organization, from molecular to cellular to organism and to population levels. The Special Issue will accept reviews on topics from molecular biophysics, structure and dynamics of biopolymers, biophysics of the cell, energy transformation mechanisms, biophotonics, ecological biophysics, and medical biophysics, following the sections of the Congress. The VII Congress of Russian Biophysicists is supported by International Union of Pure and Applied Biophysics (IUPAB). Here we describe main topics and sections of the coming event, the paper types for the journal issue, and the key deadline dates.

Electrostatics in Computational Biophysics and Its Implications for Disease Effects.

This review outlines the role of electrostatics in computational molecular biophysics and its implication in altering wild-type characteristics of biological macromolecules, and thus the contribution of electrostatics to disease mechanisms. The work is not intended to review existing computational approaches or to propose further developments. Instead, it summarizes the outcomes of relevant studies and provides a generalized classification of major mechanisms that involve electrostatic effects in both wild-type and mutant biological macromolecules. It emphasizes the complex role of electrostatics in molecular biophysics, such that the long range of electrostatic interactions causes them to dominate all other forces at distances larger than several Angstroms, while at the same time, the alteration of short-range wild-type electrostatic pairwise interactions can have pronounced effects as well. Because of this dual nature of electrostatic interactions, being dominant at long-range and being very specific at short-range, their implications for wild-type structure and function are quite pronounced. Therefore, any disruption of the complex electrostatic network of interactions may abolish wild-type functionality and could be the dominant factor contributing to pathogenicity. However, we also outline that due to the plasticity of biological macromolecules, the effect of amino acid mutation may be reduced, and thus a charge deletion or insertion may not necessarily be deleterious.

7th International conference NBP-2021 “Nanobiophysics: fundamental and applied aspects”

7th International conference “NANOBIOPHYSICS: Fundamental and Applied Aspects” (NBP-2021) took place on October 4-8, 2021 at B. Verkin Institute for Low Temperature Physics and Engineering of the National Academy of Sciences of Ukraine (Kharkiv, Ukraine). Previous six conferences, starting from 2009, were organized due to joint efforts of B. Verkin Institute for Low Temperature Physics and Engineering of the NAS of Ukraine and Institute of Physics of the NAS of Ukraine on biennial basis in Kharkiv and Kyiv alternatively. Among 80 registered participants from 16 countries about 40 scientists have presented their lectures and posters offline and other participants were joining the sessions online. 16 keynote lectures and 18 oral presentations were made and 51 posters were discussed offline and online. The goal of the conference was achieved: urgent problems, advances and perspectives of the topical scientific direction of nanobiophysics which embraces achievements of modern molecular biophysics and nanotechnology were discussed. The subjects of physical aspects of biomolecular nanosystems, properties of biomolecules on nanoparticles and nanostructured surfaces, nanobiohybrids formation by 1-D or 2-D nanomaterials with bioobjects, theoretical calculations and computer modeling of nanobiosystems, and applied aspects of nanobiophysics were highlighted at the related sessions. Several additional accompanying events were organized in the framework of the conference, including a Round Table “How biophysics and nanosciences meet modern challenges: the case of COVID-19”, a special session of the Ukrainian Biophysical Society, and SPIE (The International Society of Optics and Photonics) and OSA (The Optical Society) Workshop “Career development opportunities for young scientist and students”. Book of abstract based on NBP-2021 materials was published.

A New Model of Hemoglobin Oxygenation.

The study of hemoglobin oxygenation, starting from the classical works of Hill, has laid the foundation for molecular biophysics. The cooperative nature of oxygen binding to hemoglobin has been variously described in different models. In the Adair model, which better fits the experimental data, the constants of oxygen binding at various stages differ. However, the physical meaning of the parameters in this model remains unclear. In this work, we applied Hill’s approach, extending its interpretation; we obtained a good agreement between the theory and the experiment. The equation in which the Hill coefficient is modulated by the Lorentz distribution for oxygen partial pressure approximates the experimental data better than not only the classical Hill equation, but also the Adair equation.

Identification and quantification of within-burst dynamics in singly labeled single-molecule fluorescence lifetime experiments

Single-molecule spectroscopy has revolutionized molecular biophysics and provided means to probe how structural moieties within biomolecules spatially reorganize at different timescales. There are several single-molecule methodologies that probe local structural dynamics in the vicinity of a single dye-labeled residue, which rely on fluorescence lifetimes as readout. Nevertheless, an analytical framework to quantify dynamics in such single-molecule single dye fluorescence bursts, at timescales of microseconds to milliseconds, has not yet been demonstrated. Here, we suggest an analytical framework for identifying and quantifying within-burst lifetime-based dynamics, such as conformational dynamics recorded in single-molecule photo-isomerization-related fluorescence enhancement. After testing the capabilities of the analysis on simulations, we proceed to exhibit within-burst millisecond local structural dynamics in the unbound α-synuclein monomer. The analytical framework provided in this work paves the way for extracting a full picture of the energy landscape for the coordinate probed by fluorescence lifetime-based single-molecule measurements.