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Abstract
Homochirality is a feature of life, but its origin is still disputed. Recent theories indicate that the origin of homochirality coincided with that of the RNA world, but proteins have not yet been incorporated into the story. Ribosome is considered a living fossil that survived the RNA world and records the oldest interaction between RNA and proteins. Inspired by several ribosome-related findings, we propose a hypothesis as follows: the substrate chirality preference of some primitive peptide synthesis ribozymes can mediate the chirality transmission from RNA to protein. In return, the chiral preference of protective peptide-RNA interaction can bring these ribozymes an evolutionary advantage and facilitate the expansion of enantiomeric excess in peptides. Monte Carlo simulation results show that this system's chemistry model is plausible. This model can be further tested through investigation of the chirality preference for the interactions between d/l-ribose-composed rRNA homologs and l/d-amino acid-composed peptides.
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Affiliation(s)
- Xin-Yi Chu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, P. R. China
| | - Hong-Yu Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, P. R. China
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2
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Li S, Wang J, Xiao Y, Zhang L, Fang J, Yang N, Zhang Z, Nasser MI, Qin H. D-ribose: Potential clinical applications in congestive heart failure and diabetes, and its complications (Review). Exp Ther Med 2021; 21:496. [PMID: 33791005 PMCID: PMC8005739 DOI: 10.3892/etm.2021.9927] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 12/22/2020] [Indexed: 12/12/2022] Open
Abstract
The quality of life of patients with certain diseases may be improved through the development of technologies and advancements in pharmacology, with the aim of prolonging their life. However, congestive heart failure (CHF), as well their complications, continue to be the leading cause of disease-associated death. The mechanisms underlying the development and progression of diabetes and CHF have been uncovered in a stepwise manner and the understanding of these mechanisms has improved the management of these diseases, resulting in reduced mortality and morbidity rates; however, CHF remains the leading cause of death worldwide, particularly in developed countries. In the past decades, research has indicated that several supplements and naturally occurring compounds may be used to treat muscle weakness, for cardiac failure management, rehabilitation following myocardial ischemia-reperfusion and various complications of diabetes. D-ribose is an essential component of the respiratory, skeletal and nervous systems and is a popular compound, as its supplementation may have beneficial effects. In the present review, the physiological roles, toxic reactions and the potential use of D-ribose in the management of clinical diseases are summarized.
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Affiliation(s)
- Shuai Li
- Institute of Cytology and Genetics, Hengyang Medical College, University of South China, Hengyang, Hunan 421000, P.R. China
| | - Juanjing Wang
- School of Pharmaceutical Science, University of South China, Hengyang, Hunan 421000, P.R. China
| | - Yutian Xiao
- Institute of Cytology and Genetics, Hengyang Medical College, University of South China, Hengyang, Hunan 421000, P.R. China
| | - Li Zhang
- Institute of Cytology and Genetics, Hengyang Medical College, University of South China, Hengyang, Hunan 421000, P.R. China
| | - Jinren Fang
- Institute of Cytology and Genetics, Hengyang Medical College, University of South China, Hengyang, Hunan 421000, P.R. China
| | - Nanyang Yang
- Institute of Cytology and Genetics, Hengyang Medical College, University of South China, Hengyang, Hunan 421000, P.R. China.,The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical College, University of South China, Hengyang, Hunan 421000, P.R. China
| | - Zhixia Zhang
- Institute of Cytology and Genetics, Hengyang Medical College, University of South China, Hengyang, Hunan 421000, P.R. China
| | - Moussa Ide Nasser
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510100, P.R. China
| | - Hui Qin
- Institute of Cytology and Genetics, Hengyang Medical College, University of South China, Hengyang, Hunan 421000, P.R. China.,The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical College, University of South China, Hengyang, Hunan 421000, P.R. China
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3
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Abstract
The preponderance of a specific d- or l-chirality in fats, sugars, amino acids, nucleic acids, and so on is ubiquitous in nature, yet the biological origin of such chiral dominance (i.e., with one enantiomer overwhelmingly present) remains an open question. One plausible proposal for the predominance of l-chirality in amino acids could be through evolutionary templating of chiral RNA-folding via chaperone activity. To help evaluate this possibility, single molecule fluorescence experiments have been performed that measure the chiral dependence of chaperone folding dynamics for the simple tetraloop-tetraloop receptor (TL-TLR) tertiary binding motif in the presence of a series of chiral amino acids. Specifically, d- vs l-arginine is found to accelerate the unfolding of this RNA motif in a chirally selective fashion, with temperature-dependent studies of the kinetics performed to extract free energy, enthalpy, and entropy landscapes for the underlying thermodynamics. Furthermore, all-atom molecular dynamics (MD) simulations are pursued to provide additional physical insight into this chiral sensitivity, which reveal enantiomer-specific sampling of nucleic acid surfaces by d- vs l-arginine and support a putative mechanism for chirally specific denaturation of RNA tertiary structure by arginine but not other amino acids.
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Affiliation(s)
- David A Nicholson
- JILA, National Institute of Standards and Technology and University of Colorado Boulder, Boulder, Colorado 80309 United States.,Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Abhigyan Sengupta
- Department of Physics, Technical University of Munich, Garching, Munich, Germany 85748
| | - David J Nesbitt
- JILA, National Institute of Standards and Technology and University of Colorado Boulder, Boulder, Colorado 80309 United States.,Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States.,Department of Physics, University of Colorado Boulder, Boulder, Colorado 80309, United States
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4
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Abstract
Thresholds are widespread in origin of life scenarios, from the emergence of chirality, to the appearance of vesicles, of autocatalysis, all the way up to Darwinian evolution. Here, we analyze the “error threshold,” which poses a condition for sustaining polymer replication, and generalize the threshold approach to other properties of prebiotic systems. Thresholds provide theoretical predictions, prescribe experimental tests, and integrate interdisciplinary knowledge. The coupling between systems and their environment determines how thresholds can be crossed, leading to different categories of prebiotic transitions. Articulating multiple thresholds reveals evolutionary properties in prebiotic scenarios. Overall, thresholds indicate how to assess, revise, and compare origin of life scenarios.
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Affiliation(s)
- Cyrille Jeancolas
- Laboratoire de Biochimie, UMR CNRS-ESPCI 8231 Chimie Biologie Innovation, PSL University, ESPCI Paris, 10 rue Vauquelin, 75005 Paris, France.,Laboratoire d'Anthropologie Sociale, Collège de France, 52 rue du Cardinal Lemoine, 75005 Paris, France
| | - Christophe Malaterre
- Département de Philosophie and Centre de Recherche Interuniversitaire sur la Science et la Technologie (CIRST), Université du Québec à Montréal (UQAM), 455 boulevard René-Lévesque Est, Montréal, QC H3C 3P8, Canada
| | - Philippe Nghe
- Laboratoire de Biochimie, UMR CNRS-ESPCI 8231 Chimie Biologie Innovation, PSL University, ESPCI Paris, 10 rue Vauquelin, 75005 Paris, France
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5
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Baek Y, Emami P, Singh N, Ilott A, Sahin E, Zydney A. Stereospecific interactions between histidine and monoclonal antibodies. Biotechnol Bioeng 2019; 116:2632-2639. [DOI: 10.1002/bit.27109] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/25/2019] [Accepted: 06/30/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Youngbin Baek
- Department of Chemical EngineeringThe Pennsylvania State University State College Pennsylvania
- Department of BiotechnologySungshin Women's University Seoul South Korea
| | - Parinaz Emami
- Department of Chemical EngineeringThe Pennsylvania State University State College Pennsylvania
| | - Nripen Singh
- Global Product Development and SupplyBristol‐Myers Squibb Devens Massachusetts
| | - Andrew Ilott
- Drug Product Science & Technology, Global Product and SupplyBristol‐Myers Squibb New Brunswick New Jersey
| | - Erinc Sahin
- Drug Product Science & Technology, Global Product and SupplyBristol‐Myers Squibb New Brunswick New Jersey
| | - Andrew Zydney
- Department of Chemical EngineeringThe Pennsylvania State University State College Pennsylvania
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6
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Abstract
A significant part of the genetic code likely originated via a chemical interaction, which should be experimentally verifiable. One possible verification relates bound amino acids (or perhaps their activated congeners) and ribonucleotide sequences within cognate RNA binding sites. To introduce this interaction, I first summarize how amino acids function as targets for RNA binding. Then the experimental method for selecting relevant RNA binding sites is characterized. The selection method’s characteristics are related to the investigation of the RNA binding site model treated at the outset. Finally, real binding sites from selection and also from extant natural RNAs (for example, the Sulfobacillus guanidinium riboswitch) are connected to the genetic code, and by extension, to the evolutionary progression that produced the code. During this process, peptides may have been produced directly on an instructive amino acid binding RNA (a DRT; Direct RNA Template). Combination of observed stereochemical selectivity with adaptation and co-evolutionary refinement is logically required, and also potentially sufficient, to create the striking order conserved throughout the present coding table.
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Affiliation(s)
- Michael Yarus
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309-0347, USA.
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7
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Porter EB, Polaski JT, Morck MM, Batey RT. Recurrent RNA motifs as scaffolds for genetically encodable small-molecule biosensors. Nat Chem Biol 2017; 13:295-301. [PMID: 28092358 DOI: 10.1038/nchembio.2278] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 11/21/2016] [Indexed: 12/05/2022]
Abstract
Allosteric RNA devices are increasingly viewed as important tools capable of monitoring enzyme evolution, optimizing engineered metabolic pathways, facilitating gene discovery and regulators of nucleic acid-based therapeutics. A key bottleneck in the development of these platforms is the availability of small molecule binding RNA aptamers that robustly function in the cellular environment. While aptamers can be raised against nearly any desired target by in vitro selection, many cannot be easily integrated into devices or do not reliably function in a cellular context. Here, we describe a new approach using secondary and tertiary structural scaffolds derived from biologically active riboswitches and small ribozymes. Applied to neurotransmitter precursors 5-hydroxytryptophan and 3,4-dihydroxyphenylalanine, this approach yields easily identifiable and characterizable aptamers predisposed for coupling to readout domains to engineer nucleic acid sensory devices that function in vitro and in the cellular context.
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Vemula S, Dedaniya A, Thunuguntla R, Mallu MR, Parupudi P, Ronda SR. Simplified in vitro refolding and purification of recombinant human granulocyte colony stimulating factor using protein folding cation exchange chromatography. J Chromatogr A 2014; 1379:74-82. [PMID: 25576039 DOI: 10.1016/j.chroma.2014.12.057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Revised: 12/09/2014] [Accepted: 12/18/2014] [Indexed: 02/05/2023]
Abstract
Protein folding-strong cation exchange chromatography (PF-SCX) has been employed for efficient refolding with simultaneous purification of recombinant human granulocyte colony stimulating factor (rhG-CSF). To acquire a soluble form of renatured and purified rhG-CSF, various chromatographic conditions, including the mobile phase composition and pH was evaluated. Additionally, the effects of additives such as urea, amino acids, polyols, sugars, oxidizing agents and their amalgamations were also investigated. Under the optimal conditions, rhG-CSF was efficaciously solubilized, refolded and simultaneously purified by SCX in a single step. The experimental results using ribose (2.0M) and arginine (0.6M) combination were found to be satisfactory with mass yield, purity and specific activity of 71%, ≥99% and 2.6×10(8)IU/mg respectively. Through this investigation, we concluded that the SCX refolding method was more efficient than conventional methods which has immense potential for the large-scale production of purified rhG-CSF.
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Affiliation(s)
- Sandeep Vemula
- K L E F University, Centre for Bioprocess Technology, Department of Biotechnology, Guntur 522 502, Andhra Pradesh, India
| | - Akshay Dedaniya
- K L E F University, Centre for Bioprocess Technology, Department of Biotechnology, Guntur 522 502, Andhra Pradesh, India
| | - Rahul Thunuguntla
- K L E F University, Centre for Bioprocess Technology, Department of Biotechnology, Guntur 522 502, Andhra Pradesh, India
| | - Maheswara Reddy Mallu
- K L E F University, Centre for Bioprocess Technology, Department of Biotechnology, Guntur 522 502, Andhra Pradesh, India
| | - Pavani Parupudi
- Andhra University, College of Engineering, Visakhapatnam 530 003, Andhra Pradesh, India
| | - Srinivasa Reddy Ronda
- K L E F University, Centre for Bioprocess Technology, Department of Biotechnology, Guntur 522 502, Andhra Pradesh, India.
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9
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Contino A, Maccarrone G, Zimbone M, Musumeci P, Giuffrida A, Calcagno L. The pivotal role of copper(II) in the enantiorecognition of tryptophan and histidine by gold nanoparticles. Anal Bioanal Chem 2014; 406:481-91. [PMID: 24232750 DOI: 10.1007/s00216-013-7466-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 10/23/2013] [Accepted: 10/25/2013] [Indexed: 12/18/2022]
Abstract
Stereoselective amino acid analysis has increasingly moved into the scope of interest of the scientific community. In this work, we report a study on the chiral recognition of D,L-Trp and D,L-His using L -Cys-capped gold nanoparticles (AuNPs) and copper(II) ion. In the L -Cys-capped AuNPs, the thiol group of the amino acid interacts with AuNPs through the formation of Au–S bond, whereas the α-amino and α-carboxyl groups of the surface-confined cysteine can coordinate the copper(II) ion, which in turn, binds the L- or D-amino acid present in solution forming diastereoisomeric complexes. The resulting systems have been characterized by UV–Vis spectra and dynamic light scattering measurements, obtaining different results for L- and D-Trp, as well as for L- and D-His. The knowledge of the solution equilibria of the investigated systems allowed us to accurately calculate in advance the concentrations of the species presentin solution and to optimize the system performances, highlighting the pivotal role of copper(II) ion in the enantiodiscrimination processes.
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Lojková L, Vranová V, Rejšek K, Formánek P. Natural Occurrence of Enantiomers of Organic Compounds Versus Phytoremediations: Should Research on Phytoremediations Be Revisited? A Mini-review. Chirality 2013; 26:1-20. [DOI: 10.1002/chir.22255] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 06/19/2013] [Accepted: 08/28/2013] [Indexed: 11/05/2022]
Affiliation(s)
- Lea Lojková
- Mendel University in Brno; Faculty of Agriculture, Department of Chemistry and Biochemistry; Brno Czech Republic
| | - Valerie Vranová
- Mendel University in Brno; Faculty of Forestry and Wood Technology, Department of Geology and Soil Science, Brno; Czech Republic
| | - Klement Rejšek
- Mendel University in Brno; Faculty of Forestry and Wood Technology, Department of Geology and Soil Science, Brno; Czech Republic
| | - Pavel Formánek
- Mendel University in Brno; Faculty of Forestry and Wood Technology, Department of Geology and Soil Science, Brno; Czech Republic
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11
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Abstract
In early papers, the intent was to find a simple protein-RNA/DNA recognition code. Many people expected a one-to-one correspondence between amino acids and nucleic bases, similar to the code that specifies how one DNA base pairs with another. Despite the lack of such a code, which was evident in the first crystal structures, researchers were indeed unwilling to give up on the idea. Despite the intense interest, a simple one-to-one correspondence has not materialised. The work presented here revisits this theme, and reports a general trend in which four elementary amino acids - G, A, V, and D - have a specific selectivity for four basic nucleotides - g, c, u, and a. During the evolution, as amino acid alphabets increased, new amino acids substituted G, A, V, D amino acids in way to keep hydropathic similarity and the selectivity to minimise errors in established RNA-protein interactions, 1-letter code was created. Additionally, the first nucleotide in codons is used for a 2-letter code. Protein-RNA recognition, visualised by these two code principles, uses a rotation of sensing and anti-sensing sequences in architecture of recognising peptides.
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Affiliation(s)
- Jozef Nahalka
- Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Dúbravská cesta 9, SK-84538 Bratislava, Slovak Republic; Institute of Chemistry, Centre of Excellence for White-Green Biotechnology, Slovak Academy of Sciences, Trieda Andreja Hlinku 2, SK-94976 Nitra, Slovak Republic.
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12
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Turk-Macleod RM, Puthenvedu D, Majerfeld I, Yarus M. The plausibility of RNA-templated peptides: simultaneous RNA affinity for adjacent peptide side chains. J Mol Evol 2012; 74:217-25. [PMID: 22538927 PMCID: PMC3346935 DOI: 10.1007/s00239-012-9501-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Accepted: 04/05/2012] [Indexed: 01/11/2023]
Abstract
According to the RNA world hypothesis, coded peptide synthesis (translation) must have been first catalyzed by RNAs. Here, we show that small RNA sequences can simultaneously bind the dissimilar amino acids His and Phe in peptide linkage. We used in vitro counterselection/selection to isolate a pool of RNAs that bind the dipeptide NH2-His-Phe-COOH with KD ranging from 36 to 480 μM. These sites contact both side chains, usually including the protonated imidazole of His, but bind-free l-His and l-Phe with much lower, sometimes undetectable, affinities. The most frequent His–Phe sites do not usually contain previously isolated sites for individual amino acids, and are only ≈35 % larger than previously known separate His and Phe sites. Nonetheless, His–Phe sites appear enriched in His anticodons, as previous l-His sites also were. Accordingly, these data add to existing experimental evidence for a stereochemical genetic code. In these peptide sites, bound amino acids approach each other to a proximity that allows a covalent peptide linkage. Isolation of several RNAs embracing two amino acids with a linking peptide bond supports the idea that a direct-RNA-template could encode primordial peptides, though crucial experiments remain.
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Affiliation(s)
- Rebecca M Turk-Macleod
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309-0347, USA
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