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Article ; Online: Editorial

Ghazala Muteeb / Md Tabish Rehman / Bibhusita Pani / Rizwan Hasan Khan

Frontiers in Molecular Biosciences, Vol

Novel drug-designing approaches to combat antimicrobial resistance

2024 Volume 10

Keywords	immunoinformatics ; antimicrobial resistance ; in-silico ; African catfish antimicrobial peptides (ACAPs) ; structure-activity relationship (SAR) ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2024-01-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Exploration of ligand-induced protein conformational alteration, aggregate formation, and its inhibition: A biophysical insight

Nusrat, Saima / Rizwan Hasan Khan

Preparative biochemistry & biotechnology. 2018 Jan. 2, v. 48, no. 1

2018

Abstract: The association of protein aggregates with plentiful human diseases has fascinated studies regarding the biophysical characterization of protein misfolding and ultimately their aggregate formation mechanism. Protein–ligand interaction, their mechanism, ... ...

Abstract	The association of protein aggregates with plentiful human diseases has fascinated studies regarding the biophysical characterization of protein misfolding and ultimately their aggregate formation mechanism. Protein–ligand interaction, their mechanism, conformational changes by ligands, and protein aggregate formation have been studied upon exploiting experimental techniques and computational methodologies. Such studies for the exploration of ligand-induced conformational changes in protein, misfolding and aggregation, has confirmed drastic progresses in the study of aggregate formation pathways. This review comprises of an inclusive description of contemporary experimental techniques as well as theoretical improvements in the interpretation of the conformational properties of protein. We have also discussed various factors responsible for the microenvironment change around protein that sequentially causes amyloidoses. Biophysical techniques and cell-based assays to gain comprehensive understandings of protein–ligand interaction, protein folding, and aggregation pathways have also been described. The promising therapeutic methods used to inhibit the protein fibrillogenesis have also been discussed.
Keywords	human diseases ; ligands ; protein aggregates ; protein folding ; therapeutics
Language	English
Dates of publication	2018-0102
Size	p. 43-56.
Publishing place	Taylor & Francis
Document type	Article
ZDB-ID	1322522-4
ISSN	1532-2297 ; 1082-6068
ISSN (online)	1532-2297
ISSN	1082-6068
DOI	10.1080/10826068.2017.1387561
Database	NAL-Catalogue (AGRICOLA)

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Article: Mechanistic insight into interaction of Sodium Dodecyl Sulphate to asialylated form of glycoprotein: A mimic of membrane protein-lipid system

Zaidi, Nida / Rizwan Hasan Khan

International journal of biological macromolecules. 2017 Oct., v. 103

2017

Abstract: The SDS-glycoprotein system is mimic of membrane protein-lipid system. Fate of glycoprotein, conformation and the interactive forces involved in membrane milieu are expected to be decided by the net charge on glycoprotein that may change during acidic ... ...

Abstract	The SDS-glycoprotein system is mimic of membrane protein-lipid system. Fate of glycoprotein, conformation and the interactive forces involved in membrane milieu are expected to be decided by the net charge on glycoprotein that may change during acidic environment in a range of pathological states, including cancer, stroke, and ischemia. Asialofetuin (ASF; asialylated form of glycoprotein) and SDS interaction is studied when glycoprotein bears varying range of net charge (i.e. at different pHâs) by steady state and time-resolved spectroscopic, calorimetric and microscopic approaches. SDS interacts differently with ASF when protein is in cationic (at pH 2, 3 and 4) and in anionic states (pH 7.4). ASF undergo aggregation at pH 2, 3 and 4 whereas have enhancement in Î±-helical structure at pH 7.4 at sub-micellar concentrations of SDS. At pH 2, 3 and 4, the positively charged ASF interacts electrostatically with negatively charged head groups of SDS, leaving its hydrophobic tail free to interact with other protein-SDS complex and consequently lead to amyloid formation. However, at pH 7.4, the ASF interacts hydrophobically with SDS and an increase in Î±-helical content occurs that constrains the environment of Trp51 and consequently decreases movement of Trp conformers.
Keywords	amyloid ; calorimetry ; glycoproteins ; ischemia ; neoplasms ; pH ; sodium dodecyl sulfate ; spectroscopy ; stroke
Language	English
Dates of publication	2017-10
Size	p. 65-73.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2017.05.026
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: An insight into structural plasticity and conformational transitions of transcriptional co-activator Sus1.

Akhilendra Pratap Bharati / Mohd Kashif / Sumit Kumar Chaturvedi / Rizwan Hasan Khan / Abrar Ahmad

PLoS ONE, Vol 15, Iss 3, p e

2020 Volume 0229216

Abstract: RNA biogenesis and mRNA transport are an intricate process for every eukaryotic cell. SAGA, a transcriptional coactivator and TREX-2 are the two major complexes participate in this process. Sus1 is a transcription export factor and part of both the SAGA ... ...

Abstract	RNA biogenesis and mRNA transport are an intricate process for every eukaryotic cell. SAGA, a transcriptional coactivator and TREX-2 are the two major complexes participate in this process. Sus1 is a transcription export factor and part of both the SAGA and the TREX-2 complex. The competitive exchange of Sus1 molecule between SAGA and TREX-2 complex modulates their function which is credited to structural plasticity of Sus1. Here, we portray the biophysical characterization of Sus1 from S. cerevisiae. The recombinant Sus1 is a α-helical structure which is stable at various pH conditions. We reported the α-helix to β-sheet transition at the low pH as well as at high pH. Sus1 showed 50% reduction in the fluorescence intensity at pH-2 as compared to native protein. The fluorescence studies demonstrated the unfolding of tertiary structure of the protein with variation in pH as compared to neutral pH. The same results were obtained in the ANS binding and acrylamide quenching studies. Similarly, the secondary structure of the Sus1 was found to be stable till 55% alcohol concentration while tertiary structure was stable up to 20% alcohol concentration. Further increase in the alcohol concentration destabilizes the secondary as well as tertiary structure. The 300 mM concentration of ammonium sulfate also stabilizes the secondary structure of the protein. The structural characterization of this protein is expected to unfold the process of the transportation of the mRNA with cooperation of different proteins.
Keywords	Medicine ; R ; Science ; Q
Subject code	612 ; 500
Language	English
Publishing date	2020-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Taxon-specific zeta-crystallin of camel eye lens

Ajamaluddin Malik / Javed Masood Khan / Malik Hisamuddin / Abdullah S. Alhomida / Anwar Ahmed / Hamza Odeibat / Rizwan Hasan Khan / Rafat Ali / Mohammad Tarique

Journal of King Saud University: Science, Vol 34, Iss 4, Pp 101973- (2022)

A comparative in silico studies

2022

Abstract: The eye lens is a specialized organ of the visual system, which is transparent due to its complex geometry and unique protein composition. Nature has designed it to focus light on the retina throughout the life span. Several factors (post-translational ... ...

Abstract	The eye lens is a specialized organ of the visual system, which is transparent due to its complex geometry and unique protein composition. Nature has designed it to focus light on the retina throughout the life span. Several factors (post-translational modifications, thermal and solar radiations) causes aggregation of the lens proteins and result in early-onset of cataract. A cataract is one of the major causes of blindness worldwide. It's interesting how camel eyes maintain lens transparency in a harsh desert climate? The camel eye lenses contain a novel protein zeta (ζ)-crystallin in a bulk amount that is also present in two other animals (guinea pig and Japanese frog) but is adopted for milder habitats. The camel lens ζ-crystallin is a poorly characterized protein. This study has investigated the physicochemical and structural properties of camel, guinea pig, and Japanese frog’s ζ-crystallin. The docking results showed a strong affinity between NADPH and ζ-crystallin. RMSD, RMSF, radius of gyration, and SASA analysis in the ligand-free and bound states showed distinct prope6rties in these ζ-crystallins. Moreover, the hydrophobicity of camel and Japanese frog ζ-crystallin is lower than ζ-crystallin of other mammalian sources. The unique physicochemical and structural properties of taxon-specific ζ-crystallin are likely to maintain lens transparency.
Keywords	Zeta-crystallin ; Structure modeling ; Eye lens proteins ; Camel ; Protein solubility ; Science (General) ; Q1-390
Language	English
Publishing date	2022-06-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Acid pH promotes bispecific antibody formation by the redox procedure

Gupta, Jyoti / Mehboob Hoque / Md Fahim Ahmad / Rizwan Hasan Khan / M. Saleemuddin

International journal of biological macromolecules. 2019 Mar. 15, v. 125

2019

Abstract: Bispecific antibodies (BsAbs), are potential theranostics. Chemical procedures of preparation of BsAbs, in which two monospecific antibodies are split into half molecules and heterodimerized, continue to attract attention in view of their simplicity. ... ...

Abstract	Bispecific antibodies (BsAbs), are potential theranostics. Chemical procedures of preparation of BsAbs, in which two monospecific antibodies are split into half molecules and heterodimerized, continue to attract attention in view of their simplicity. Poor dissociation of antibodies with reduced inter-heavy chain disulfides into half molecules under neutral conditions however restricts the BsAbs formation. In this study, we report that the heterodimerization of antibodies can be improved leading to over 6-fold increase in the yield of BsAbs, by carrying out the redox procedure at pH 4.0. In view of improvement in heterodimerization, BsAbs could be conveniently prepared starting from partially purified ion-exchange fraction of the antiserum and purified by twin affinity chromatography on antigen supports. The UV, CD, intrinsic and extrinsic fluorescence spectral analysis of BsAbs prepared by the modified redox procedure were comparable with the native IgG, which suggest the absence of significant acid-pH-induced damage. ThT binding studies and native size exclusion chromatography ruled out amyloid fibril formation.
Keywords	affinity chromatography ; amyloid ; antibodies ; antibody formation ; antigens ; antiserum ; dimerization ; dissociation ; fluorescence ; gel chromatography ; immunoglobulin G ; ion exchange ; pH ; precision medicine ; spectral analysis ; sulfides
Language	English
Dates of publication	2019-0315
Size	p. 469-477.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2018.12.063
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Biophysical Insight into the Interaction of Human Lysozyme with Anticancer Drug Anastrozole

Fahad M. Almutairi / Mohammad Rehan Ajmal / Adel Ibrahim Al Alawy / Rizwan Hasan Khan / Ali Saber Abdelhameed

The Scientific World Journal, Vol

A Multitechnique Approach

2020 Volume 2020

Abstract: In the present study, we employ fluorescence spectroscopy, dynamic light scattering, and molecular docking methods. Binding of anticancer drug anastrozole with human lysozyme (HL) is studied. Binding of anastrozole to HL is moderate but spontaneous. ... ...

Abstract	In the present study, we employ fluorescence spectroscopy, dynamic light scattering, and molecular docking methods. Binding of anticancer drug anastrozole with human lysozyme (HL) is studied. Binding of anastrozole to HL is moderate but spontaneous. There is anastrozole persuaded hydrodynamic change in HL, leading to molecular compaction. Binding of anastrozole to HL also decreased in vitro lytic activity of HL. Molecular docking results suggest the electrostatic interactions and van der Waals forces played key role in binding interaction of anastrozole near the catalytic site. Binding interaction of anastrozole to proteins other than major transport proteins in blood can significantly affect pharmacokinetics of this molecule. Hence, rationalizing drug dosage is important. This study also points to unrelated effects that small molecules bring in the body that are considerable and need thorough investigation.
Keywords	Technology ; T ; Medicine ; R ; Science ; Q
Language	English
Publishing date	2020-01-01T00:00:00Z
Publisher	Hindawi Limited
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Protein folding, misfolding and aggregation: A tale of constructive to destructive assembly

Khan, Mohsin Vahid / Syed Mohammad Zakariya / Rizwan Hasan Khan

International journal of biological macromolecules. 2018 June, v. 112

2018

Abstract: The newly synthesized unfolded polypeptide attains its functional and unique three-dimensional conformation through the process of protein folding for which several models have been proposed. The protein misfolding diseases include Alzheimer's, Parkinson' ...

Abstract	The newly synthesized unfolded polypeptide attains its functional and unique three-dimensional conformation through the process of protein folding for which several models have been proposed. The protein misfolding diseases include Alzheimer's, Parkinson's and Cataract which are result of formation of amyloid or amorphous aggregates, respectively. The distinction in morphology shows relation with the melting temperature (Tm). The temperatures near or slightly higher than Tm induces amyloids while much higher or low temperature mediate amorphous aggregation. The aggregation is not always deleterious rather it also performs several important cellular functions essential for survival wide range of organisms called as functional amyloids. Protein gets modulated by several modulators which mediate the aggregation, acceleration, delay, transformations, inhibition and disaggregation of protein aggregates. The exclusive properties of inhibition and disaggregation displayed by various molecules can be employed to treat the life threatening disorders.
Keywords	Alzheimer disease ; amyloid ; cataract ; melting point ; models ; polypeptides ; protein aggregates ; protein folding ; temperature
Language	English
Dates of publication	2018-06
Size	p. 217-229.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2018.01.099
Database	NAL-Catalogue (AGRICOLA)

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Article: Carboxylic acids of different nature induces aggregation of hemoglobin

Hasan, Samra / Aabgeena Naeem / Masihuz Zaman / Rizwan Hasan Khan / Seerat Fatma

International journal of biological macromolecules. 2018,

2018

Abstract: Misfolded proteins that escape cellular quality control check lay the foundation for several progressively widespread neurodegenerative diseases, diabetes and others. Here, crotonic and citric acid are employed to study aggregation behaviour of ... ...

Abstract	Misfolded proteins that escape cellular quality control check lay the foundation for several progressively widespread neurodegenerative diseases, diabetes and others. Here, crotonic and citric acid are employed to study aggregation behaviour of hemoglobin (Hb). A systematic investigation on varying concentrations of acids from 0 to 60 mM on Hb gives an idea that transition is taking place in the vicinity of 10–30 mM. Hb showed increased intrinsic Trp fluorescence in the presence of both acids. A red shift of 10 nm in presence of citric acid contrary to a blue shift of 5 nm in presence of crotonic acid is observed. ANS and ThT fluorescence marked aggregation at 50 mM, supported by Congo red and Soret absorbance spectroscopy. CD, RLS and DLS studies also validate the findings. Molecular docking analysis exhibited the binding mode of Hb with acids. Aggregates were dense, beaded structure as visualised under TEM. Crotonic and citric acid at 20 and 30 mM, respectively, induced structural changes in Hb which transmutes to aggregate at higher concentration. These alterations remained almost constant and no significant changes were observed on increasing concentration further. Also, crotonic acid is more noxious, as it instigates conformational alterations at lower concentration than citric acid.
Keywords	absorbance ; aggregation behavior ; citric acid ; diabetes ; fluorescence ; hemoglobin ; molecular models ; neurodegenerative diseases ; quality control ; spectroscopy ; transmission electron microscopy
Language	English
Size	p. .
Publishing place	Elsevier B.V.
Document type	Article
Note	Pre-press version
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2018.07.003
Database	NAL-Catalogue (AGRICOLA)

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Article: Nanoparticle formulations in the diagnosis and therapy of Alzheimer's disease

Gupta, Jyoti / Munazza Tamkeen Fatima / Zeyaul Islam / Rizwan Hasan Khan / Vladimir N. Uversky / Parveen Salahuddin

International journal of biological macromolecules. 2019 June 01, v. 130

2019

Abstract: Alzheimer's disease (AD) is one of the most common age-related diseases that occurs because of the deposition of amyloid fibrils in a form of extracellular plaques containing β-amyloid peptide (Aβ) and tangles are found as intracellular deposit in the ... ...

Abstract	Alzheimer's disease (AD) is one of the most common age-related diseases that occurs because of the deposition of amyloid fibrils in a form of extracellular plaques containing β-amyloid peptide (Aβ) and tangles are found as intracellular deposit in the brain made up of twisted strands of aggregated microtubule binding protein. Scores of small molecule inhibitors have been designed for the treatment of AD. However some of these drugs cannot pass through the brain-blood-barrier (BBB). To overcome this problem, various nanoparticles (NPs) or nanomedicines (NMs) have been synthesized. These nanoparticles exploit the existing physiological mechanisms of passing through the BBB, including receptor- and adsorptive-mediated transcytosis that facilitate the transcellular transport of nanoparticle from the blood to the brain. During the last decades, varieties of nanoparticles that differ in the composition have been developed, and they have the potential application in the diagnostics and therapy of AD. The most common NP formulations that have major impact in the diagnosis and therapy of AD include polymeric NPs (PPs), gold NPs, gadolinium NPs, selenium NPs, protein-based NPs, polysaccharide-based NPs, etc. The goal of this review is to provide discussion of the application of different types of NP formulations in the diagnosis and therapy of AD.
Keywords	Alzheimer disease ; amyloid ; binding proteins ; blood ; brain ; diagnostic techniques ; drugs ; gadolinium ; microtubules ; nanogold ; nanomedicine ; nanoparticles ; peptides ; physiological transport ; polymers ; polysaccharides ; selenium ; therapeutics
Language	English
Dates of publication	2019-0601
Size	p. 515-526.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2019.02.156
Database	NAL-Catalogue (AGRICOLA)

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