joshua sakon - Academia.edu (original) (raw)

Papers by joshua sakon

Soft Matter and Biomaterials on the Nanoscale, 2020

Bioresources and Bioprocessing, 2020

This study aims to optimize strong acid hydrolysis-based production of cellulose nanocrystals (CN... more This study aims to optimize strong acid hydrolysis-based production of cellulose nanocrystals (CNCs) and cellulose nanofibers (CNFs) from pre-extracted and fully bleached kraft pulp of loblolly pinewood, the most abundant and commercially significant softwood species in southeastern United States. The effect of four parameters, including acid concentration, temperature, duration and pulp particle size, on the yield and properties of CNCs was investigated using the central composite design (CCD) of response surface methodology (RSM) for process optimization. While CNC yield was significantly affected by acid concentration and hydrolysis temperature and was adequately explained by an empirical model, none of the characteristic properties of CNCs, including crystallinity index, surface charge and particle size, displayed any strong correlation to the process parameters within the experimental ranges tested. At different hydrolysis severities, we not only analyzed the waste streams to d...

Nanoscale, 2016

A multifunctional fluorescent derivative of a beta-lactam antibiotic, ampicillin (termed iAmp) sh... more A multifunctional fluorescent derivative of a beta-lactam antibiotic, ampicillin (termed iAmp) shows high promise as a biocompatible shielding agent and an effective dispersant for improving the in vivo effectiveness of theranostic nanomaterials.

Journal of Biological Chemistry, 2008

HCV NS3 helicase exhibits activity toward DNA and RNA substrates. The DNA helicase activity of NS... more HCV NS3 helicase exhibits activity toward DNA and RNA substrates. The DNA helicase activity of NS3 has been proposed to be optimal when multiple NS3 molecules are bound to the same substrate molecule. NS3 catalyzes little or no measurable DNA unwinding under single cycle conditions in which the concentration of substrate exceeds the concentration of enzyme by 5-fold. However, when NS3 (100 nM) is equimolar with the substrate, a small burst amplitude of ϳ8 nM is observed. The burst amplitude increases as the enzyme concentration increases, consistent with the idea that multiple molecules are needed for optimal unwinding. Protein-protein interactions may facilitate optimal activity, so the oligomeric properties of the enzyme were investigated. Chemical cross-linking indicates that fulllength NS3 forms higher order oligomers much more readily than the NS3 helicase domain. Dynamic light scattering indicates that full-length NS3 exists as an oligomer, whereas NS3 helicase domain exists in a monomeric form in solution. Size exclusion chromatography also indicates that full-length NS3 behaves as an oligomer in solution, whereas the NS3 helicase domain behaves as a monomer. When NS3 was passed through a small pore filter capable of removing protein aggregates, greater than 95% of the protein and the DNA unwinding activity was removed from solution. In contrast, only ϳ10% of NS3 helicase domain and ϳ20% of the associated DNA unwinding activity was removed from solution after passage through the small pore filter. The results indicate that the optimally active form of fulllength NS3 is part of an oligomeric species in vitro.

Biochemistry, 1996

The crystal structure of the catalytic domain of the thermostable endocellulase E1 from Acidother... more The crystal structure of the catalytic domain of the thermostable endocellulase E1 from Acidothermus cellulolyticus in complex with cellotetraose has been solved by multiple isomorphous replacement and refined at 2.4 A resolution to an R-factor of 0.18 (Rfree = 0.24). E1cd is a member of the 4/7 superfamily of hydrolases, and as expected, its structure is an (alpha/beta)8 barrel, which constitutes a prototype for family 5-subfamily 1 cellulases. The cellotetraose molecule binds in a manner consistent with the expected Michaelis complex for the glycosylation half-reaction and reveals that all eight residues conserved in family 5 enzymes are involved in recognition of the glycosyl group attacked during cleavage. Whereas only three residues are conserved in the whole 4/7 superfamily (the Asn/Glu duo and the Glu from which the name is derived), structural comparisons show that all eight residues conserved in family 5 have functional equivalents in the other 4/7 superfamily members, strengthening the case that mechanistic details are conserved throughout the superfamily. On the basis of the structure, a detailed sequence of physical steps of the cleavage mechanism is proposed. A close approach of two key glutamate residues provides an elegant mechanism for the shift in the pKa of the acid/base for the glycosylation and deglycosylation half-reactions. Finally, purely structural based comparisons are used to show that significant differences exist in structural similarity scores resulting from different methods and suggest that caution should be exercised in interpreting such results in terms of implied evolutional relationships.

Applied Biochemistry and Biotechnology, 2002

Understanding the interactions between cellulases and cellulosic substrates is critical to the de... more Understanding the interactions between cellulases and cellulosic substrates is critical to the development of an efficient artificial cellulase system for conversion of biomass to sugars. We directed specific mutations to the interactive surface of the Acidothermus cellulolyticus EI endoglucanase catalytic domain. The cellulose-binding domain is not translated in these mutants. Amino acid mutations were designed either to change the surface charge of the protein or to modify the potential for hydrogen bonding with cellulose. The relationship between cellulase-to-cellulose (Avicel PH101) binding and hydrolysis activity was determined for various groupings of mutations. While a significant increase in hydrolysis activity was not observed, certain clusters of residues did significantly alter substrate binding and some interesting correlations emerged. In the future, these observations may be used to aid the design of endoglucanases with improved performance on pretreated biomass.

Acta Crystallographica Section A Foundations of Crystallography

Journal of Biotechnology, 2016

The production of collagen binding domain fusion proteins is of significant importance because of... more The production of collagen binding domain fusion proteins is of significant importance because of their potential as therapeutic biomaterials. It was previously reported that the expression of collagen-binding domain fusion proteins in Escherichia coli was higher when expressed using lactose as an inducer and chemically defined growth media on a shake flask scale. In an effort to further investigate factors that affect expression levels on a fed-batch scale, alternative induction techniques were tested in conjunction with fed-batch fermentation. In this paper, we discuss ten fed-batch fermentation experiments utilizing either glucose or glycerol feed and using lactose or isopropyl-β-d-thiogalactopyranoside (IPTG) as an induction source. It was found that glycerol-fed fermentations induced with lactose allowed for greater expression of target protein, though lesser cell densities were achieved.

Archives of Biochemistry and Biophysics

is an essential bacterial protein that belongs to the YycF family of response regulators and cons... more is an essential bacterial protein that belongs to the YycF family of response regulators and consists of two domains: an N-terminal receiver domain and a C-terminal effector domain. Streptococcus pneumoniae RR02 (MicA; residues 2±234) has been crystallized using the sitting-drop vapour-diffusion technique. The crystals belong to space group P2 1 , with unit-cell parameters a = 46.46, b = 32.61, c = 63.35 A Ê , = 90.01. X-ray diffraction data have been collected to 1.93 A Ê resolution.