Abstract:
:MAP/microtubule affinity-regulating kinase 4 (MARK4) is a member of adenosine monophosphate-activated protein kinases, directly associated with cancer and neurodegenerative diseases. Here, we have cloned, expressed, and purified two variants of MARK4 [the kinase domain (MARK4-F2), and kinase domain along with 59 N-terminal residues (MARK4-F1)] and compared their stability at varying pH range. Structural and functional changes were observed by incubating both forms of MARK4 in buffers of different pH. We measured the secondary structure of MARK4 using circular dichroism and tertiary structure by measuring intrinsic fluorescence and absorbance properties along with the size of proteins by dynamic light scattering. We observed that at extremes of pH (below pH 3.5 and above pH 9.0), MARK4 is quite stable. However, a remarkable aggregate formation was observed at intermediate pH (between pH 3.5 and 9.0). To further validate this result, we have modeled both forms of MARK4 and performed molecular dynamics simulation for 15 ns. The spectroscopic observations are in excellent agreement with the findings of molecular dynamics simulation. We also performed ATPase activity at varying pH and found a significant correlation of structure of MARK4 with its enzyme activity. It is interesting to note that both forms of MARK4 are showing a similar pattern of structure changes with reference to pH.
journal_name
J Biomol Struct Dynjournal_title
Journal of biomolecular structure & dynamicsauthors
Naz F,Singh P,Islam A,Ahmad F,Imtaiyaz Hassan Mdoi
10.1080/07391102.2015.1074942subject
Has Abstractpub_date
2016-06-01 00:00:00pages
1241-51issue
6eissn
0739-1102issn
1538-0254journal_volume
34pub_type
杂志文章abstract::A new model for simulation of protein folding of alpha-helical proteins with known secondary structure is proposed. We are dealing here with the analysis of alpha-helix packings rather than with a detailed atom structure of a whole protein. Starting from a random compact packing of the helices the search is focused on...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1998.10508232
更新日期:1998-08-01 00:00:00
abstract::Epidermal growth factor (EGF) plays important roles in multiple biological processes, such as the regulation of cell growth, proliferation, and differentiation. EGF exerts their pharmacologic effects via receptor-mediated mechanism associated with high affinity to epidermal growth factor receptor (EGFR) on the cell su...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2016.1171799
更新日期:2017-04-01 00:00:00
abstract::The insertion of viral DNA into the host chromosome is an essential step in the replication of HIV-1, and is carried out by an enzyme, HIV-1 integrase (IN). Since the latter has no human cellular counterpart, it is an attractive target for antiviral drug design. Several IN inhibitors having activities in the micromola...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2002.10506820
更新日期:2002-08-01 00:00:00
abstract::Despite the intensive research efforts towards antiviral drug against COVID-19, no potential drug or vaccines has not yet discovered. Initially, the binding site of COVID-19 main protease was predicted which located between regions 2 and 3. Structure-based virtual screening was performed through a hierarchal mode of e...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1791957
更新日期:2020-07-15 00:00:00
abstract::The assembly origin (AO) region of the tobacco mosaic virus RNA melts in an usually narrow (2.5 degrees C) temperature range. In an 0.01 M phosphate buffer the melting temperature of AO was found to be 41.5 degrees C. This value corresponds to the regions with the most stable secondary/tertiary structure of the whole ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1987.10506379
更新日期:1987-08-01 00:00:00
abstract::The flavivirus membrane fusion is triggered by the acid pH of the endosomes after virus endocytosis. The proposed mechanism involves changes in the protonation state of conserved histidine residues of the E protein present in the viral surface that undergoes a series of structural rearrangements that result in the fus...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2013.827132
更新日期:2014-01-01 00:00:00
abstract::The algorithms of the analysis of R-looped DNA molecules from electron micrographs are presented. We propose a two-dimensional R-loop distribution map with abscissa and ordinate axes corresponding to the positions of the left and right ends of the loop respectively. A transcription analysis of the hybrid plasmid pSCV1...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1986.10508495
更新日期:1986-06-01 00:00:00
abstract::In negatively supercoiled DNA molecules some inverted repeat sequences adopt a perturbed conformation which is characterised by the following properties. They are centrally hypersensitive to single-strand-specific nucleases such as S1, and to a much lower extent the flanking regions may also be sensitive. They are als...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章,评审
doi:10.1080/07391102.1983.10507433
更新日期:1983-10-01 00:00:00
abstract::The 1H NMR relaxation effects produced by paramagnetic Cr(III) complexes on nucleoside 5'-mono- and -triphosphates in D2O solution at pH' = 3 were measured. The paramagnetic probes were [Cr(III)(H2O)6]3+, [Cr(III)(H2O)3(HATP)], [Cr(III)(H2O)3(HCTP)] and [Cr(III)(H2O)3(UTP)-, while the matrix nucleotides (0.1 M) were H...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1990.10508529
更新日期:1990-02-01 00:00:00
abstract::In search of suitable therapy for the management of Alzheimer's disease, this study was designed to evaluate metal complexes against its biochemical targets. Zinc metal carboxylates (AAZ1-AAZ6) were evaluated against acetylcholinesterase (AChE) and butyrylcholinesterase (BChE). The antioxidant in combination with anti...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1724569
更新日期:2020-02-13 00:00:00
abstract::Colchicine, a tricyclic alkaloid, has a remarkable range of biological activities. It binds with tubulin and prevents the formation of microtubules. This compound consists of a six membered aromatic ring (A ring), a seven membered troponoid ring (C ring) and another seven membered aliphatic ring (B ring). Using molecu...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1998.10508219
更新日期:1998-04-01 00:00:00
abstract::Tetra-(4-N-methylpyridyl)-porphyrin, (T4MPyP), is a tetracationic porphyrin that binds to G-C sequences of DNA by means of an intercalative mode. In order to extend its selective sequence recognition capacity for bases beyond the intercalation site, and in the major groove, we have undertaken the theoretical design of...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1993.10508730
更新日期:1993-10-01 00:00:00
abstract::Notch is a single-pass transmembrane receptor protein which is composed of a short extracellular region, a single-pass transmembrane domain and a small intracellular region. Notch ligand like Delta, member of the DSL protein family, is also single-pass transmembrane protein. It has been demonstrated that of the 36 EGF...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章,收录出版
doi:10.1080/07391102.2011.10507386
更新日期:2011-10-01 00:00:00
abstract::Proton ENDOR has been observed from frozen solutions (ca. 38K degrees) of copper meso-(4-N-tetra-methylpyridyl)porphyrin (CuTMpyP(4)) complexed with Salmon sperm DNA in water and D2O. Lines from exchangeable protons of the DNA bases have been observed in these ENDOR spectra. Analyses of these ENDOR data show that the ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1992.10507962
更新日期:1992-04-01 00:00:00
abstract::TATA-box binding protein (TBP) in a monomeric form and the complexes it forms with DNA have been elucidated with molecular dynamics simulations. Large TBP domain motions (bend and twist) are detected in the monomer as well as in the DNA complexes; these motions can be important for TBP binding of DNA. TBP interacts wi...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1996.10508872
更新日期:1996-02-01 00:00:00
abstract::Hinge-bending in T4 lysozyme has been inferred from single amino acid mutant crystalline allomorphs by Matthews and coworkers. This raises an important question: are the different conformers in the unit cell artifacts of crystal packing forces, or do they represent different solution state structures? The objective of...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1994.10508751
更新日期:1994-10-01 00:00:00
abstract::The present study employed the spectroscopic techniques, i.e. fluorescence, and circular dichroism (CD) and the molecular docking approach to investigate the mechanism of interaction of a potent anticancer glucosinolate, sinigrin (SIN), with bovine serum albumin (BSA). SIN binding to BSA resulted in the quenching of i...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2015.1110835
更新日期:2016-10-01 00:00:00
abstract::Oligonucleotides containing 1-(beta-D-2'-deoxy-threo-pentofuranosyl)cytosine (dCx) and/or 1-(beta-D-2'-deoxy-threo-pentofuranosyl)thymine (dTx) in place of dC and dT residues in the EcoRII and MvaI recognition site CC(A/T)GG were synthesized in order to investigate specific recognition of the DNA sugar-phosphate backb...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2000.10506574
更新日期:2000-04-01 00:00:00
abstract::Communicated by Ramaswamy H. Sarma. ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 信件
doi:10.1080/07391102.2019.1580220
更新日期:2020-02-01 00:00:00
abstract::The guanine-rich sequence, specifically in DNA, telomeric DNA, is a potential target of anticancer drugs. In this work, a mononuclear Fe(III) complex containing two meloxicam ligands was synthesized as a G-quadruplex stabilizer. The interaction between the Fe(III) complex and G-quadruplex with sequence of 5'-G3(T2AG3)...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2014.1003195
更新日期:2015-01-01 00:00:00
abstract::The x-ray crystallographic structure of the nucleosome core particle has been determined using 8 A resolution diffraction data. The particle has a mean diameter of 106 A and a maximum thickness of 65 A in the superhelical axis direction. The longest chord through the histone core measures 85 A and is in a non-axial di...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章,评审
doi:10.1080/07391102.1989.10507747
更新日期:1989-08-01 00:00:00
abstract::The energetics of the B-Z transition of two different types of cloned alternating purine/pyrimidine DNA sequences have been analysed by a two dimensional electrophoretic technique. Since the transition between right handed and left handed forms of these polymers is detected by alterations of electrophoretic mobilities...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1983.10507467
更新日期:1983-12-01 00:00:00
abstract::A first principles calculation of the correlation function for conformational motion (CM) in proteins is carried out within the framework of a microscopic model of a protein as a heterogeneous system. The fragments of the protein are assumed to be identical hard spheres undergoing the CM within their conformational po...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2000.10506563
更新日期:2000-02-01 00:00:00
abstract::Two recombinant purine nucleoside phosphorylases from thermophilic bacterium Thermus thermophilus HB27 encoded by genes TT_C1070 (TthPNPI) and TT_C0194 (TthPNPII) were purified and characterized. The comparative analysis of their sequences, molecular weight, enzymes specificity and kinetics of the catalyzed reaction w...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1848628
更新日期:2020-11-23 00:00:00
abstract::Tumor suppressor proteins play a crucial role in cell cycle regulation. Retinoblastoma protein (pRB) is one among them which regulates G1-S transition by binding with transcription factors. The activity of pRB is deregulated by cyclin dependent kinases-mediated hyper-phosphorylation and also due to cancer-derived muta...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2012.732345
更新日期:2013-01-01 00:00:00
abstract::About one-third of the existing proteins require metal ions as cofactors for their catalytic activities and structural complexities. While many of them bind only to a specific metal, others bind to multiple (different) metal ions. However, the exact mechanism of their metal preference has not been deduced to clarity. ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2015.1080629
更新日期:2016-07-01 00:00:00
abstract::Continuum finite element material models used for traumatic brain injury lack local injury parameters necessitating nanoscale mechanical injury mechanisms be incorporated. One such mechanism is membrane mechanoporation, which can occur during physical insults and can be devastating to cells, depending on the level of ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2018.1453376
更新日期:2019-03-01 00:00:00
abstract::Beta-N-acetyl-D-glucosaminidase (NAGase, EC.3.2.1.52), which catalyzes the cleavage of N-acetylglucosamine polymers, is a composition of chitinase and cooperates with endo-chitinase and exo-chitinase to disintegrate chitin into N-acetylglucosamine (NAG). In this investigation, A NAGase from green crab (Scylla serrata)...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2009.10507266
更新日期:2009-02-01 00:00:00
abstract::A procedure is described for the complete resolution of concentration profiles of oligonucleotide triplexes as a function of pH and temperature. The pH and temperature ranges at which triplexes are present and the relative concentrations of all the species involved in acid-base and conformational equilibria are succes...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2003.10506922
更新日期:2003-10-01 00:00:00
abstract::Inside a living cell there can be a variety of interactions for any given protein, which serve to regulate denaturation and renaturation processes. Insights into some of them can be obtained by in vitro studies using various denaturing agents. In this study, all-atom MD simulations in explicit solvent and NMR relaxati...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/073911012010525025
更新日期:2012-01-01 00:00:00