16 results match your criteria AIMS biophysics[Journal]

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Single-molecule FRET reveals proofreading complexes in the large fragment of DNA polymerase I.

AIMS Biophys 2018 10;5(2):144-154. Epub 2018 May 10.

Konigsberg Laboratory, Yale University, 333 Cedar Street, New Haven, CT 06520, USA.

There is increasing interest in the use of DNA polymerases (DNA pols) in next-generation sequencing strategies. These methodologies typically rely on members of the A and B family of DNA polymerases that are classified as high-fidelity DNA polymerases. These enzymes possess the ability to selectively incorporate the correct nucleotide opposite a templating base with an error frequency of only 1 in 10 insertion events. Read More

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http://dx.doi.org/10.3934/biophy.2018.2.144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5990039PMC

The effect of different divalent cations on the kinetics and fidelity of DNA polymerase.

AIMS Biophys 2018 25;5(2):125-143. Epub 2018 Apr 25.

Yale University, 333 Cedar St., SHM C-E14, New Haven, CT, 06520, USA.

Although Mg is the metal ion that functions as the cofactor for DNA polymerases (DNA pols) , Mn can also serve in this capacity but it reduces base discrimination. Metal ions aside from Mg or Mn can act as cofactors for some DNA pols but not for others. Here we report on the ability of several divalent metal ions to substitute for Mg or Mn with BST DNA polymerase (BST pol), an A family DNA pol. Read More

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http://dx.doi.org/10.3934/biophy.2018.2.125DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5992921PMC
April 2018
15 Reads

Free-radicals and advanced chemistries involved in cell membrane organization influence oxygen diffusion and pathology treatment.

AIMS Biophys 2017 6;4(2):240-283. Epub 2017 Apr 6.

Biomaterials, SDB 539, 1919 7th Avenue South, University of Alabama at Birmingham, Birmingham, AL 35294, USA.

A breakthrough has been discovered in pathology chemistry related to increasing molecular structure that can interfere with oxygen diffusion through cell membranes. Free radicals can crosslink unsaturated low-viscosity fatty acid oils by chain-growth polymerization into more viscous liquids and even solids. Free radicals are released by mitochondria in response to intermittent hypoxia that can increase membrane molecular organization to reduce fluidity and oxygen diffusion in a possible continuing vicious cycle toward pathological disease. Read More

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http://www.aimspress.com/article/10.3934/biophy.2017.2.240
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http://dx.doi.org/10.3934/biophy.2017.2.240DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5707132PMC
April 2017
2 Reads

Protein crystallization: Eluding the bottleneck of X-ray crystallography.

AIMS Biophys 2017 26;4(4):557-575. Epub 2017 Sep 26.

Department of Microbiology, Immunology, and Biochemistry, Wayne State University School of Medicine, Detroit, MI, USA.

To date, X-ray crystallography remains the gold standard for the determination of macromolecular structure and protein substrate interactions. However, the unpredictability of obtaining a protein crystal remains the limiting factor and continues to be the bottleneck in determining protein structures. A vast amount of research has been conducted in order to circumvent this issue with limited success. Read More

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http://dx.doi.org/10.3934/biophy.2017.4.557DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5645037PMC
September 2017
2 Reads

Mechanisms and applications of the anti-inflammatory effects of photobiomodulation.

AIMS Biophys 2017 19;4(3):337-361. Epub 2017 May 19.

Wellman Center for Photomedicine, Massachusetts General Hospital, BAR414, 40 Blossom Street, Boston, MA 02114, USA.

Photobiomodulation (PBM) also known as low-level level laser therapy is the use of red and near-infrared light to stimulate healing, relieve pain, and reduce inflammation. The primary chromophores have been identified as cytochrome c oxidase in mitochondria, and calcium ion channels (possibly mediated by light absorption by opsins). Secondary effects of photon absorption include increases in ATP, a brief burst of reactive oxygen species, an increase in nitric oxide, and modulation of calcium levels. Read More

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http://dx.doi.org/10.3934/biophy.2017.3.337DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5523874PMC
May 2017
71 Reads

New open conformation of SMYD3 implicates conformational selection and allostery.

AIMS Biophys 2017 20;4(1):1-18. Epub 2016 Dec 20.

Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan, USA.

SMYD3 plays a key role in cancer cell viability, adhesion, migration and invasion. SMYD3 promotes formation of inducible regulatory T cells and is involved in reducing autoimmunity. However, the nearly "closed" substrate-binding site and poor in vitro H3K4 methyltransferase activity have obscured further understanding of this oncogenically related protein. Read More

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http://dx.doi.org/10.3934/biophy.2017.1.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5189988PMC
December 2016
7 Reads

G protein-coupled receptors: the evolution of structural insight.

AIMS Biophys 2017 21;4(3):491-527. Epub 2017 Aug 21.

Department of Chemistry, University of Memphis, 3744 Walker Ave, Memphis, TN 38152, USA.

G protein-coupled receptors (GPCR) comprise a diverse superfamily of over 800 proteins that have gained relevance as biological targets for pharmaceutical drug design. Although these receptors have been investigated for decades, three-dimensional structures of GPCR have only recently become available. In this review, we focus on the technological advancements that have facilitated efforts to gain insights into GPCR structure. Read More

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http://dx.doi.org/10.3934/biophy.2017.3.491DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6018013PMC

SMYD proteins in immunity: dawning of a new era.

AIMS Biophys 2016 17;3(4):450-455. Epub 2016 Oct 17.

Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5079279PMC
http://dx.doi.org/10.3934/biophy.2016.4.450DOI Listing
October 2016
7 Reads

STIM1 activation is regulated by a 14 amino acid sequence adjacent to the CRAC activation domain.

AIMS Biophys 2016;3(1):99-118. Epub 2016 Feb 28.

Department of Chemistry and Chemical Biology Cornell University, Ithaca, NY 14853.

Oligomerization of the Ca sensor, STIM1, in the endoplasmic reticulum (ER) membrane, caused by depletion of ER Ca stores, results in STIM1 coupling to the plasma membrane Ca channel protein, Orai1, to activate Ca influx in a process known as store-operated Ca entry. We use fluorimetry-based fluorescence resonance energy transfer (FRET) to monitor changes in STIM1 oligomerization in COS7 cells transfected with STIM1 constructs containing selected truncations, deletions, and point mutations, and labeled with donor and acceptor fluorescent proteins at either the luminal (N-terminal) or the cytoplasmic (C-terminal) ends. Our results with sequential truncations of STIM1 from the C-terminus support previous evidence that the CRAC activation domain (CAD/SOAR, human sequence 342-448) is an oligomer-promoting segment of STIM1, and they show that truncation just after CAD/SOAR (1-448) causes significantly elevated basal cytoplasmic Ca and spontaneous STIM1 clustering. Read More

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http://dx.doi.org/10.3934/biophy.2016.1.99DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4883682PMC
February 2016

Biophysical characterization and modeling of human Ecdysoneless (ECD) protein supports a scaffolding function.

AIMS Biophys 2016 9;3(1):195-208. Epub 2016 Mar 9.

Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA.

The human homolog of Drosophila ecdysoneless protein (ECD) is a p53 binding protein that stabilizes and enhances p53 functions. Homozygous deletion of mouse is early embryonic lethal and deletion delays G-S cell cycle progression. Importantly, ECD directly interacts with the Rb tumor suppressor and competes with the E2F transcription factor for binding to Rb. Read More

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http://dx.doi.org/10.3934/biophy.2016.1.195DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5421643PMC
March 2016
27 Reads

Morphology and ultrastructure of retrovirus particles.

AIMS Biophys 2015;2(3):343-369. Epub 2015 Aug 18.

Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA ; Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN, USA ; Pharmacology Graduate Program, University of Minnesota, Minneapolis, MN, USA ; Department of Microbiology, University of Minnesota, Minneapolis, MN, USA.

Retrovirus morphogenesis entails assembly of Gag proteins and the viral genome on the host plasma membrane, acquisition of the viral membrane and envelope proteins through budding, and formation of the core through the maturation process. Although in both immature and mature retroviruses, Gag and capsid proteins are organized as paracrystalline structures, the curvatures of these protein arrays are evidently not uniform within one or among all virus particles. The heterogeneity of retroviruses poses significant challenges to studying the protein contacts within the Gag and capsid lattices. Read More

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http://www.aimspress.com/fileOther/PDF/biophysics/201503343.
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http://www.aimspress.com/article/10.3934/biophy.2015.3.343
Publisher Site
http://dx.doi.org/10.3934/biophy.2015.3.343DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4593330PMC
August 2015
15 Reads

Validation of 3D EM Reconstructions: The Phantom in the Noise.

AIMS Biophys 2015;2(1):21-35

National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, 50 South Dr, Bethesda, MD 20892, USA.

Validation is a necessity to trust the structures solved by electron microscopy by single particle techniques. The impressive achievements in single particle reconstruction fuel its expansion beyond a small community of image processing experts. This poses the risk of inappropriate data processing with dubious results. Read More

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http://dx.doi.org/10.3934/biophy.2015.1.21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4440490PMC
January 2015

Protein chainmail variants in dsDNA viruses.

AIMS Biophys 2015 17;2(2):200-218. Epub 2015 Jun 17.

Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90095, USA.

First discovered in bacteriophage HK97, biological chainmail is a highly stable system formed by concatenated protein rings. Each subunit of the ring contains the HK97-like fold, which is characterized by its submarine-like shape with a 5-stranded β sheet in the axial (A) domain, spine helix in the peripheral (P) domain, and an extended (E) loop. HK97 capsid consists of covalently-linked copies of just one HK97-like fold protein and represents the most effective strategy to form highly stable chainmail needed for dsDNA genome encapsidation. Read More

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http://dx.doi.org/10.3934/biophy.2015.2.200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5701804PMC
June 2015
2 Reads

Structure and function of histone acetyltransferase MOF.

AIMS Biophys 2015 19;2(4):555-569. Epub 2015 Oct 19.

Department of Environmental Medicine, NYU School of Medicine, Tuxedo, NY, USA.

MOF was first identified in as an important component of the dosage compensation complex. As a member of MYST family of histone acetyltransferase, MOF specifically deposits the acetyl groups to histone H4 lysine 16. Throughout evolution, MOF and its mammalian ortholog have retained highly conserved substrate specificity and similar enzymatic activities. Read More

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http://dx.doi.org/10.3934/biophy.2015.4.555DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5425159PMC
October 2015
10 Reads

Topological diversity of chromatin fibers: Interplay between nucleosome repeat length, DNA linking number and the level of transcription.

AIMS Biophys 2015 3;2(4):613-629. Epub 2015 Nov 3.

Laboratory of Cell Biology, National Cancer Institute, NIH Bethesda, MD 20892, USA.

The spatial organization of nucleosomes in 30-nm fibers remains unknown in detail. To tackle this problem, we analyzed all stereochemically possible configurations of two-start chromatin fibers with DNA linkers L = 10-70 bp (nucleosome repeat length NRL = 157-217 bp). In our model, the energy of a fiber is a sum of the elastic energy of the linker DNA, steric repulsion, electrostatics, and the H4 tail-acidic patch interaction between two stacked nucleosomes. Read More

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http://www.aimspress.com/article/10.3934/biophy.2015.4.613
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http://dx.doi.org/10.3934/biophy.2015.4.613DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5271602PMC
November 2015
6 Reads

The interplay of long non-coding RNAs and MYC in cancer.

AIMS Biophys 2015;2(4):794-809. Epub 2015 Dec 1.

Department of Biochemistry, University of California, Riverside, CA 92521, USA.

Long non-coding RNAs (lncRNAs) are a class of RNA molecules that are changing how researchers view eukaryotic gene regulation. Once considered to be non-functional products of low-level aberrant transcription from non-coding regions of the genome, lncRNAs are now viewed as important epigenetic regulators and several lncRNAs have now been demonstrated to be critical players in the development and/or maintenance of cancer. Similarly, the emerging variety of interactions between lncRNAs and MYC, a well-known oncogenic transcription factor linked to most types of cancer, have caught the attention of many biomedical researchers. Read More

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http://dx.doi.org/10.3934/biophy.2015.4.794DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4827443PMC
December 2015
2 Reads
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