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Artikel ; Online: Sometimes pulses just have to be perfect - An example based on the measurement of amide proton transverse relaxation rates in proteins.

Rangadurai, Atul Kaushik / Toyama, Yuki / Kay, Lewis E

Journal of magnetic resonance (San Diego, Calif. : 1997)

2023 Band 349, Seite(n) 107412

Abstract: The measurement of spin relaxation rates provides a unique avenue for quantifying dynamic processes in biomolecules. In order to simplify analysis of the measurements so that a few key intuitive parameters can be extracted, it is often the case that ... ...

Abstract	The measurement of spin relaxation rates provides a unique avenue for quantifying dynamic processes in biomolecules. In order to simplify analysis of the measurements so that a few key intuitive parameters can be extracted, it is often the case that experiments are designed to eliminate interference effects between different classes of spin relaxation. One example emerges in the measurement of amide proton (
Mesh-Begriff(e)	Protons ; Amides ; Nuclear Magnetic Resonance, Biomolecular ; Proteins
Chemische Substanzen	Protons ; Amides ; Proteins
Sprache	Englisch
Erscheinungsdatum	2023-03-02
Erscheinungsland	United States
Dokumenttyp	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1469665-4
ISSN	1096-0856 ; 1557-8968 ; 1090-7807 ; 0022-2364
ISSN (online)	1096-0856 ; 1557-8968
ISSN	1090-7807 ; 0022-2364
DOI	10.1016/j.jmr.2023.107412
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: NMR measurements of transient low-populated tautomeric and anionic Watson-Crick-like G·T/U in RNA:DNA hybrids: implications for the fidelity of transcription and CRISPR/Cas9 gene editing.

Szekely, Or / Rangadurai, Atul Kaushik / Gu, Stephanie / Manghrani, Akanksha / Guseva, Serafima / Al-Hashimi, Hashim M

Nucleic acids research

2024 Band 52, Heft 5, Seite(n) 2672–2685

Abstract: Many biochemical processes use the Watson-Crick geometry to distinguish correct from incorrect base pairing. However, on rare occasions, mismatches such as G·T/U can transiently adopt Watson-Crick-like conformations through tautomerization or ionization ... ...

Abstract	Many biochemical processes use the Watson-Crick geometry to distinguish correct from incorrect base pairing. However, on rare occasions, mismatches such as G·T/U can transiently adopt Watson-Crick-like conformations through tautomerization or ionization of the bases, giving rise to replicative and translational errors. The propensities to form Watson-Crick-like mismatches in RNA:DNA hybrids remain unknown, making it unclear whether they can also contribute to errors during processes such as transcription and CRISPR/Cas editing. Here, using NMR R1ρ experiments, we show that dG·rU and dT·rG mismatches in two RNA:DNA hybrids transiently form tautomeric (Genol·T/U $ \mathbin{\lower.3ex\hbox{$\buildrel\textstyle\rightarrow\over {\smash{\leftarrow}\vphantom{_{\vbox to.5ex{\vss}}}}$}}$ G·Tenol/Uenol) and anionic (G·T-/U-) Watson-Crick-like conformations. The tautomerization dynamics were like those measured in A-RNA and B-DNA duplexes. However, anionic dG·rU- formed with a ten-fold higher propensity relative to dT-·rG and dG·dT- and this could be attributed to the lower pKa (ΔpKa ∼0.4-0.9) of U versus T. Our findings suggest plausible roles for Watson-Crick-like G·T/U mismatches in transcriptional errors and CRISPR/Cas9 off-target gene editing, uncover a crucial difference between the chemical dynamics of G·U versus G·T, and indicate that anionic Watson-Crick-like G·U- could play a significant role evading Watson-Crick fidelity checkpoints in RNA:DNA hybrids and RNA duplexes.
Mesh-Begriff(e)	Base Pairing ; CRISPR-Cas Systems ; DNA/genetics ; DNA/chemistry ; Gene Editing ; Nucleic Acid Conformation ; RNA/chemistry ; Nucleic Acid Hybridization
Chemische Substanzen	DNA (9007-49-2) ; RNA (63231-63-0)
Sprache	Englisch
Erscheinungsdatum	2024-01-28
Erscheinungsland	England
Dokumenttyp	Journal Article
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkae027
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel: Measurement of 1Hα transverse relaxation rates in proteins: application to solvent PREs

Toyama, Yuki / Rangadurai, Atul Kaushik / Kay, Lewis E.

Journal of biomolecular NMR. 2022 Aug., v. 76, no. 4

2022

Abstract: It has recently been demonstrated that accurate near surface electrostatic potentials can be calculated for proteins from solvent paramagnetic relaxation enhancements (PREs) of amide protons measured using spin labels of similar structures but different ... ...

Abstract	It has recently been demonstrated that accurate near surface electrostatic potentials can be calculated for proteins from solvent paramagnetic relaxation enhancements (PREs) of amide protons measured using spin labels of similar structures but different charges (Yu et al. in Proc Natl Acad Sci 118(25):e2104020118, 2021). Here we develop methodology for extending such measurements to intrinsically disordered proteins at neutral pH where amide spectra are of very poor quality. Under these conditions it is shown that accurate PRE values can be measured using the haCONHA experiment that has been modified for recording ¹Hᵅ transverse relaxation rates. The optimal pulse scheme includes a spin-lock relaxation element for suppression of homonuclear scalar coupled evolution for all ¹Hᵅ protons, except those derived from Ser and Thr residues, and minimizes the radiation damping field from water magnetization that would otherwise increase measured relaxation rates. The robustness of the experiment is verified by developing a second approach using a band selective adiabatic decoupling scheme for suppression of scalar coupling modulations during ¹Hᵅ relaxation and showing that the measured PRE values from the two methods are in excellent agreement. The near surface electrostatic potential of a 103-residue construct comprising the C-terminal intrinsically disordered region of the RNA-binding protein CAPRIN1 is obtained at pH 5.5 using both ¹Hᴺ and ¹Hᵅ-based relaxation rates, and at pH 7.4 where only ¹Hᵅ rates can be quantified, with very good agreement between potentials obtained under all experimental conditions.
Schlagwörter	RNA-binding proteins ; evolution ; pH ; solvents
Sprache	Englisch
Erscheinungsverlauf	2022-08
Umfang	p. 137-152.
Erscheinungsort	Springer Netherlands
Dokumenttyp	Artikel
ZDB-ID	1081696-3
ISSN	0925-2738
ISSN	0925-2738
DOI	10.1007/s10858-022-00401-4
Datenquelle	NAL Katalog (AGRICOLA)

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Artikel ; Online: Measurement of

Toyama, Yuki / Rangadurai, Atul Kaushik / Kay, Lewis E

Journal of biomolecular NMR

2022 Band 76, Heft 4, Seite(n) 137–152

Abstract	It has recently been demonstrated that accurate near surface electrostatic potentials can be calculated for proteins from solvent paramagnetic relaxation enhancements (PREs) of amide protons measured using spin labels of similar structures but different charges (Yu et al. in Proc Natl Acad Sci 118(25):e2104020118, 2021). Here we develop methodology for extending such measurements to intrinsically disordered proteins at neutral pH where amide spectra are of very poor quality. Under these conditions it is shown that accurate PRE values can be measured using the haCONHA experiment that has been modified for recording
Mesh-Begriff(e)	Amides/chemistry ; Intrinsically Disordered Proteins/chemistry ; Nuclear Magnetic Resonance, Biomolecular/methods ; Protons ; Solvents
Chemische Substanzen	Amides ; Intrinsically Disordered Proteins ; Protons ; Solvents
Sprache	Englisch
Erscheinungsdatum	2022-08-26
Erscheinungsland	Netherlands
Dokumenttyp	Journal Article
ZDB-ID	1081696-3
ISSN	1573-5001 ; 0925-2738
ISSN (online)	1573-5001
ISSN	0925-2738
DOI	10.1007/s10858-022-00401-4
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel: NMR measurements of transient low-populated tautomeric and anionic Watson-Crick-like G·T/U in RNA:DNA hybrids: Implications for the fidelity of transcription and CRISPR/Cas9 gene editing.

Szekely, Or / Rangadurai, Atul Kaushik / Gu, Stephanie / Manghrani, Akanksha / Guseva, Serafima / Al-Hashimi, Hashim M

bioRxiv : the preprint server for biology

2023

Abstract: Many biochemical processes use the Watson-Crick geometry to distinguish correct from incorrect base pairing. However, on rare occasions, mismatches such as G•T/U can transiently adopt Watson-Crick-like conformations through tautomerization or ionization ... ...

Abstract	Many biochemical processes use the Watson-Crick geometry to distinguish correct from incorrect base pairing. However, on rare occasions, mismatches such as G•T/U can transiently adopt Watson-Crick-like conformations through tautomerization or ionization of the bases, giving rise to replicative and translational errors. The propensities to form Watson-Crick-like mismatches in RNA:DNA hybrids remain unknown, making it unclear whether they can also contribute to errors during processes such as transcription and CRISPR/Cas editing. Here, using NMR
Sprache	Englisch
Erscheinungsdatum	2023-08-24
Erscheinungsland	United States
Dokumenttyp	Preprint
DOI	10.1101/2023.08.24.554670
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Awareness, medication adherence, and diet pattern among hypertensive patients attending teaching institution in western Rajasthan, India

Deepti Mathur / Surender Deora / Atul Kaushik / Pankaj Bhardwaj / Kuldeep Singh

Journal of Family Medicine and Primary Care, Vol 9, Iss 5, Pp 2342-

2020 Band 2349

Abstract: Background and Objectives: Hypertension is an important disease of public health concern. Awareness and medication adherence with diet modification have an important effect on the control of blood pressure and its associated morbidity and mortality. ... ...

Abstract	Background and Objectives: Hypertension is an important disease of public health concern. Awareness and medication adherence with diet modification have an important effect on the control of blood pressure and its associated morbidity and mortality. Therefore, this study was conducted to assess the awareness of hypertension, medication adherence, and dietary pattern in hypertensive population of western Rajasthan. Materials and Methods: The study was hospital based cross-sectional. Blood pressure measurements were taken in a sitting position in right arm after a 5-min rest using nonmercury sphygmomanometer and required cuff size. A prevalidated and pretested questionnaire for the assessment of awareness of hypertension was used. Results: Out of the total 384 patients, the majority of the patients were males (62.5%). There was a statistically significant difference found in awareness of hypertension among rural and urban patients. Nonadherence to antihypertensive medications was seen more in males (60.0%) as compared to females (40.0%). The most common reason for nonadherence was found to be forgetfulness (27.6%) followed by poor knowledge about the hypertension and ignorance of long-term treatment (22.9%). Out of the total hypertensive patient studied, 54.9% were taking normal salt intake and 45.1% of the subjects were found to be taking excess intake of salt. Interpretation and Conclusions: In the present study, good awareness about hypertension was found with urban patients. Among all the variables, education and employment status showed a positive and significant association with awareness. The most common reason of poor adherence was found to be forgetfulness behavior followed by poor knowledge and lack of awareness about hypertension.
Schlagwörter	adherence ; awareness ; diet pattern ; hypertension ; rajasthan ; Medicine ; R
Thema/Rubrik (Code)	610
Sprache	Englisch
Erscheinungsdatum	2020-01-01T00:00:00Z
Verlag	Wolters Kluwer Medknow Publications
Dokumenttyp	Artikel ; Online
Datenquelle	BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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Artikel ; Online: Surface electrostatics dictate RNA-binding protein CAPRIN1 condensate concentration and hydrodynamic properties.

Toyama, Yuki / Rangadurai, Atul Kaushik / Forman-Kay, Julie D / Kay, Lewis E

The Journal of biological chemistry

2022 Band 299, Heft 1, Seite(n) 102776

Abstract: Biomolecular condensates concentrate proteins, nucleic acids, and small molecules and play an essential role in many biological processes. Their formation is tuned by a balance between energetically favorable and unfavorable contacts, with charge-charge ... ...

Abstract	Biomolecular condensates concentrate proteins, nucleic acids, and small molecules and play an essential role in many biological processes. Their formation is tuned by a balance between energetically favorable and unfavorable contacts, with charge-charge interactions playing a central role in some systems. The positively charged intrinsically disordered carboxy-terminal region of the RNA-binding protein CAPRIN1 is one such example, phase separating upon addition of negatively charged ATP or high concentrations of sodium chloride (NaCl). Using solution NMR spectroscopy, we measured residue-specific near-surface electrostatic potentials (ϕ
Mesh-Begriff(e)	Adenosine Triphosphate ; Hydrodynamics ; Intrinsically Disordered Proteins/chemistry ; RNA-Binding Proteins/chemistry ; Sodium Chloride/metabolism ; Static Electricity
Chemische Substanzen	Adenosine Triphosphate (8L70Q75FXE) ; Intrinsically Disordered Proteins ; RNA-Binding Proteins ; Sodium Chloride (451W47IQ8X)
Sprache	Englisch
Erscheinungsdatum	2022-12-07
Erscheinungsland	United States
Dokumenttyp	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2022.102776
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Mapping the per-residue surface electrostatic potential of CAPRIN1 along its phase-separation trajectory.

Toyama, Yuki / Rangadurai, Atul Kaushik / Forman-Kay, Julie D / Kay, Lewis E

Proceedings of the National Academy of Sciences of the United States of America

2022 Band 119, Heft 36, Seite(n) e2210492119

Abstract: Electrostatic interactions and charge balance are important for the formation of biomolecular condensates involving proteins and nucleic acids. However, a detailed, atomistic picture of the charge distribution around proteins during the phase-separation ... ...

Abstract	Electrostatic interactions and charge balance are important for the formation of biomolecular condensates involving proteins and nucleic acids. However, a detailed, atomistic picture of the charge distribution around proteins during the phase-separation process is lacking. Here, we use solution NMR spectroscopy to measure residue-specific near-surface electrostatic potentials (
Mesh-Begriff(e)	Adenosine Triphosphate/metabolism ; Biochemical Phenomena ; Intrinsically Disordered Proteins/chemistry ; Intrinsically Disordered Proteins/metabolism ; Nuclear Magnetic Resonance, Biomolecular ; Phase Transition ; RNA-Binding Proteins/chemistry ; RNA-Binding Proteins/metabolism ; Static Electricity ; Surface Properties
Chemische Substanzen	Intrinsically Disordered Proteins ; RNA-Binding Proteins ; Adenosine Triphosphate (8L70Q75FXE)
Sprache	Englisch
Erscheinungsdatum	2022-08-30
Erscheinungsland	United States
Dokumenttyp	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2210492119
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Assessment of inpatient antibiotic use in Halibet National Referral Hospital using WHO indicators

Nebyu Daniel Amaha / Yohana Haile Berhe / Atul Kaushik

BMC Research Notes, Vol 11, Iss 1, Pp 1-

a retrospective study

2018 Band 5

Abstract: Abstract Objective Inappropriate use of antibiotics in primary care and hospital settings is a major contributing factor to the spread of antibiotic resistance. Many microorganisms were tested in Eritrea and have proven resistant to ampicillin. The aim ... ...

Abstract	Abstract Objective Inappropriate use of antibiotics in primary care and hospital settings is a major contributing factor to the spread of antibiotic resistance. Many microorganisms were tested in Eritrea and have proven resistant to ampicillin. The aim of this study was to investigate the prescription pattern, hospital indicator and patient care indicator of antibiotics among hospitalized patients in Halibet National Referral Hospital, Asmara, Eritrea. Results The data on prescription patterns showed 79% of hospitalizations had at least one antibiotic prescribed and on average 1.29 antibiotics were prescribed per hospitalization; prescribing using generic name was at 97%; all (100%) of the antibiotics were prescribed from the Eritrean National List of Medicines. On average an antibiotic was prescribed for 6.36 days (SD = 6.06). Ampicillin was the most commonly prescribed antibiotic (42.1%) and parenteral was the most common route prescribed (81.4%). The data on hospital indicators showed key antibiotics were out of stock on average for 78.18 days; 87.5% of key antibiotics were available on the day of the study. The data on patient care indicator showed patients taking antibiotics stayed in the hospital for 9.97 days (± 7.33 days).
Schlagwörter	Antibiotic ; Rational drug use ; WHO indicators ; Inpatient study ; Prescription ; Medicine ; R ; Biology (General) ; QH301-705.5 ; Science (General) ; Q1-390
Thema/Rubrik (Code)	360
Sprache	Englisch
Erscheinungsdatum	2018-12-01T00:00:00Z
Verlag	BMC
Dokumenttyp	Artikel ; Online
Datenquelle	BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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Artikel ; Online: Chest pain and exercise induced left bundle branch block – A clinical dilemma

Surender Deora / Jai Bharat Sharma / Rahul Choudhary / Atul Kaushik

Journal of Family Medicine and Primary Care, Vol 8, Iss 10, Pp 3434-

2019 Band 3436

Abstract: Exercise-induced left bundle branch block is a rare electrocardiographic phenomenon. We present two patients with angina pectoris who developed left bundle branch block on ECG during treadmill test. The first patient had non-obstructive coronary arteries ...

Abstract	Exercise-induced left bundle branch block is a rare electrocardiographic phenomenon. We present two patients with angina pectoris who developed left bundle branch block on ECG during treadmill test. The first patient had non-obstructive coronary arteries with slow flow and is a rarely reported entity. The second patient had typical chest pain with single vessel Coronary Artery Disease. Left bundle branch block occurred in stage I of Treadmill Testing and persisted for approximately 4 hours and then reverted spontaneously. These two interesting cases of this rare phenomenon are presented here with review of relevant literature.
Schlagwörter	angina pectoris ; coronary artery disease ; exercise induced ; left bundle branch block ; Medicine ; R
Sprache	Englisch
Erscheinungsdatum	2019-01-01T00:00:00Z
Verlag	Wolters Kluwer Medknow Publications
Dokumenttyp	Artikel ; Online
Datenquelle	BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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