AU Biomaterials Design Lab:Reading/CHEM571Fall2012LitSurvey

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Adenosine Deaminase

Structure, Function (General Info)

N-linked glycosylation of dipeptidyl peptidase IV (CD26): effects on enzyme activity, homodimer formation, and adenosine deaminase binding

• Article talked about the adenosine deaminase binding protein, known as type II transmembrane serine protease dipeptidyl peptidase IV, and studies on DPPIV binding. It was revealed that the N-linked glycosylation on Asn residues in DPPIV interacts with adenosine deaminase. The N-linked glycosylation contribute to binding with the ADA protein but does not contribute to peptidase activity of DPPIV. This article is helpful in terms of understanding how adenosine deaminase binds with other proteins for further stimulation.
• Keyun Wang 16:59, 24 September 2012 (EDT):

Structural basis for the growth factor activity of human adenosine deaminase ADA2

• Aertgerrts et al. investigated the structure of human adenosine deaminase ADA2 through protein models and enzymatic kinetics with wild and mutated protein. Crystalized structures were used for model accuracy. ADA2 revealed to be more complex than ADA1 with only a monomeric single domain. Figures in paper showed structures of human adenosine deaminase and could be used for reference in determining how ADA minds with gold nanoparticles.
• Keyun Wang 18:03, 24 September 2012 (EDT):

Autoimmune dysregulation and purine metabolism in adenosine deaminase deficiency

• Sauer et al. provided an overview of Adenosine deaminase cause for severe combined immunodeficiency (ADA-SCID) and patterns before and after treatments in patients. Immune dysregulation are related to alterations in purine metabolism that is caused by the lack of ADA. Article help explain the importance of adenosine deaminase in cellular signaling and highlighted descreased immune functions when adenosine deaminase is lacking.
• Keyun Wang 18:23, 24 September 2012 (EDT):

Atomic Structure of Adenosine Deaminase Complexed with a Transition-State Analog: Understanding Catalysis and Immunodeficiency Mutations

• ADA was complexed with a transition state analog, which has the effect of inhibiting the enzyme. The structure of the complex was determined with C13 NMR and a previously undiscovered Zinc cofactor was found in the transition state analog. A partial mechanism for the catalysis was proposed.
• Michael F. Nagle 21:15, 10 October 2012 (EDT):

Efficient, Low-Cost Protein Factories: Expression of Human Adenosine Deaminase in Baculovirus-Infected Insect Larvae

• A coding sequence for ADA was recombined into a baculovirus, which was used to infect insect larvae. After 4 days, the ADA was extracted and purified. 8-9mg of homogenous ADA was obtained from 22 larvae. This may be a more efficient method for making ADA than expressing it in E Coli.
  • Michael F. Nagle 21:32, 10 October 2012 (EDT):

Activity Assays

Development of a rapid, microplate-based kinetic assay for measuring adenosine deaminase activity in bodily fluids

• The conversion of adenosine to inosine by adenosine deaminase was spectroscopically analyzed at 265 nm for a period of 15 minutes. The number of assays that could be conducted at one time was increased by carrying out analysis in 96-well microplates. This assay also varies from the standard procedure in that the reaction time was decreased from 60 minutes.
• Melissa Novy 20:19, 21 September 2012 (EDT):

A new strategy based on aptasensor to time-resolved fluorescence assay for adenosine deaminase activity

• Aptamer-based sensor is reported in this article for time-resolved fluorescence assay of adenosine deaminase. The aptasensor works by binding to DNA strands which interacts with adenosine deaminase, receiving a strong signal. This could be potential jumpoff point to design experiments for fluorscence assay for adenosine deaminase activity.
• Keyun Wang 16:51, 24 September 2012 (EDT):

Bovine Serum Albumin

Structure, Function (General Info)

Locating the Binding Sites of Pb(II) Ion with Human and Bovine Serum Albumins

• Ahmed et al. located binding sites of lead, Pb(II) with human serum and bovine serum albumins(BSA) at physiological conditions. Through the use of UV-visible, fluorescence, and X-ray photoelectron spectroscopics, Pb binding sites were found and analyzed. Pb bound is 0.7 per HSA and BSA complex. Article provide protocol in measure concentration of bound BSA under UV-visible and fluorescence spectroscopic, which could be used for reference.
• Keyun Wang 18:28, 24 September 2012 (EDT):

Locations of the Three Primary Binding Sites for Long-Chain Fatty Acids on Bovine Serum Albumin

• C₁₃-enriched oleic acid was bound to BSA so that the locations of binding sites could be identified by C₁₃NMR. In addition to being bound to BSA, the modified oleic acid was bound to three fragments that make the entirety of BSA. When mixed in equimolar quantities, these fragments produced the same spectra as BSA.
• Michael F. Nagle 23:09, 8 October 2012 (EDT):

Interaction with other noble metals

Quenching of the intrinsic fluorescence of bovine serum albumin by chlorpromazine and hemin

• Silva et al. studied the binding of chlorpromazine and hemin to bSA via the use of fluorescence quenching technique. A range from 300 to 450nm has shown to be the emission spectra for each quencher addition to BSA. Primary binding site for hemin to BSA was found in this article between the two tryptophan residue in BSA protein. This could help in understanding how BSA binds to other molecules and help in understanding the structure of BSA itself.
• Keyun Wang 18:44, 24 September 2012 (EDT):

Studies on interaction of colloidal Ag nanoparticles with Bovine Serum Albumin (BSA)

• Tests the biofunctionalization of silver nano-particles and as a result investigates the interaction between AgNPs and BSA at different concentrations as observed by a UV-Vis.
• Discovered that AgNPs coated in BSA were observed under UV-Vis to be quite different than the uncoated particles. The BSA adsorption on the surface prevented the Ag nanoparticles from aggregating in solutions of pH greater than 5 which may prevent the uptake of the NPs in live cells.
  • ""Puja Mody 21:08, 22 September 2012 (EDT)""

Radiation synthesis and characterization of protein stabilized gold nanoparticles

• A. Akhavan, H.R. Kalhor, M.Z. Kassaee, N. Sheikh, M. Hassanlou, Chemical Engineering Journal 2010.
• Au/BSA produced via γ-irradiation
• It is interesting because many of the steps in the procedure is similar to our experiment, however instead of letting the reaction occur in an oven for 4 hours, the HAuCl₄, BSA, and phosphate solution buffer were stirred at room temperature and then purged with N₂ and irradiated for various times. After the irradiation and stirring, the samples were centrifuged and run under UV-vis.

--Dhea Patel 23:07, 25 September 2012 (EDT)

Synthesis and characterization of bovine serum albumin-conjugated copper sulfide nanocomposites

• Copper sulfide nanoparticles were synthesised using BSA and analyzed with UV/Vis. Thioacetamide (TAA) was needed to catalyze the formation of colloids, because if alone, BSA and CuS will form a complex. A catalyst is required to seperate them and unfold the BSA so it can wrap around the CuS, forming colloids.

--Michael F. Nagle 23:32, 8 October 2012 (EDT)

Lysozyme

Structure, Function (General Info)

• information about lysozyme -- "Lysozyme is a globular protein with a molecular weight of approximately 14.7 kDa. Lysozyme has been used as a model protein for this study, since its biophysical properties are well understood and the specific contribution of the sugar to its stability over a range of solution conditions can easily be compared with that of the native protein. Lysozyme is a widely studied protein due to its rich phase behavior(17, 18) including crystallization,(19) liquid–liquid phase separation,(20-22) and the formation of equilibrium clusters(23-25) and gels.(24) The solution behavior of lysozyme is also well understood in terms of its interaction with salt ions.(26-28)" from James and McManus J. Phys. Chem. B, 2012, 116 (34), pp 10182–10188

Stability

Thermal and Solution Stability of Lysozyme in the Presence of Sucrose, Glucose, and Trehalose

• James and McManus J. Phys. Chem. B, 2012, 116 (34), pp 10182–10188
• xxxx
  • Abigail E. Miller 12:53, 5 September 2012 (EDT):

Identification and characterization of a highly thermostable bacteriophage lysozyme

• Article looked at domains of lysozyme and determined the optimal enzymatic conditions for activity for highly thermostable lysoenzyme. The thermostability can be applied for maximum reactivity when conducting assays on lysozyme. Furthermore, Enzymatic activity were quantified through the use of mass spectroscopy. Protocal could be considered for replication.
• Keyun Wang 16:39, 25 September 2012 (EDT)

Surfactant-induced refolding of lysozyme

• A novel technique of unfolding and then refolding lysozyme was investigated and analyzed using spectroscopy, circular dichroism, and activity assay for lysozyme. The lysozyme was first precipitated out of solution by adding a negatively-charged surfactants, then dissolved by adding a positively-charged surfactant. Upon its dissolution, lysozyme was observed to spontaneously refold to its native state.
• The anionic/cationic surfactant pairs studied all produced similar results in that the amount of lysozyme that refolded was observed to be the same in each surfactant pair.
• Melissa Novy 22:15, 24 September 2012 (EDT)

Horseradish Peroxidase

Structure, Function (General Info)

The effect of chemical modification with pyromellitic anhydride on structure, function, and thermal stability of horseradish peroxidase.

• Lysine modification in horseradish peroxidase decreases stability of the protein when the protein is unfolded. Under 60°C, the structure of horseradish peroxidase becomes less compact. This brings insights to performing the reaction between gold nanoparticles with the enzyme under the ideal temperatures.
• Keyun Wang 14:20, 25 September 2012 (EDT):

A novel approach to construct a horseradish peroxidase hydrophilic ionic liquids Au nanoparticles dotted titanate nanotubes biosensor for amperometric sensing of hydrogen peroxide.

• Horseperoxidase catalyze the reduction of H2O2. Biosensor was developed to measure the concentration of horseradish peroxidase in aqueous solution as gelation reagent to immobolize nanocomposite onto electrode surface. Furthermore, UV-vis and FT-IR spectroscopic analysis of HRP among other enzymes were made. This data could be used for reference during HRP assay tests.
• Keyun Wang 15:27, 25 September 2012 (EDT):

Activity Assays

Low concentration of silver nanoparticles not only enhances the activity of horseradish peroxidase but alter the structure also

• Ranges for silver nanoparticles were determined for HRP activity. The results could be used to predict the range of gold nanoparticles through the use of horseradish peroxidase.
• Low concentration of silver and gold nanoparticles increases the activity of horseradish peroxidase and also altering the structure of silver or gold nanoparticles.
• Keyun Wang 14:12, 25 September 2012 (EDT):

Luminol-based enhanced chemiluminescence assay for quantification of peroxidase and hydrogen peroxide in aqueous solutions: Effect of reagent pH and ionic strength

• The horseradish peroxidase assay using luminol and enhanced by p-iodophenol was optimized for determining the presence and concentration of H₂O₂ in solution. The intensity of the chemiluminescence was found to be optimal at pH 8.5. The study outlines a protocol that is less vague than others and also includes calibration curves.
• Melissa Novy 15:18, 25 September 2012 (EDT)

Protein/Peptide Nanoparticle Synthesis

Bovine Serum Albumin

Investigation and modeling effective parameters influencing the size of BSA protein nanoparticles as colloidal carrier

• Mathematical models were used to determine the effects of reaction conditions, including pH, concentration, temperature, and solvent addition rate, on the formation of BSA nanoparticles. The BSA NPs were synthesized by coacervation, then crosslinked with glutaraldehyde. The study indicated that glutaraldehyde did not have an effect on the size of the NPs, stabilized the BSA NPs, and decreased swelling in water.
• Melissa Novy 13:57, 25 September 2012 (EDT)

Highly stable, protein capped gold nanoparticles as effective drug delivery vehicles for amino-glycosidic antibiotics

• Lori Rastogi, Aruna Jyothi Kora, Arunachalam J., Materials Science and Engineering C [Elsevier] (2012)
• Contains UV-vis absorption spectra of Au/BSA loaded with various antibotics.
• AuNPs produced in this paper were stable against pH changes and high salt concentrations and had good antibacterial activity (more than pure antibiotics).

--Dhea Patel 15:39, 25 September 2012 (EDT)

Other

Chitosan Reduced Gold Nanoparticles as Novel Carriers for Transmucosal Delivery of Insulin

• Devika R. Bhumkar, Hrushikesh M. Joshi, Murali Sastry, and Varsha B. Pokharkar, Pharmaceutical Research, 2007
• Uses Biodegradable polymer, chitosan
  • requires high concentrations of chitosan
  • long term NP stability (~6 months)
• Effective for Insulin Delivery

--Dhea Patel 22:00, 24 September 2012 (EDT)
Formation of silk fibroin nanoparticles in water-miscible organic solvent and their characterization

• Silk fibroin nanoparticles were synthesized by first dissolving silk fibers in CaCl₂, then adding water-miscible organic solvents. Analysis of the NPs indicated that they were insoluble in water and that their morphology depended on the types of organic solvents used. The study indicated that acetone produced NPs with the most globular shape.
• Melissa Novy 14:08, 25 September 2012 (EDT)

Bio-functionalized Gold Nanoparticles for Surface-Plasmon- Absorption-Based Protein Detection

• Wan-Joong Kim, Soo-Hee Choi, Young S. Rho, and Dong Jin Yoo, Bull, Korean Chem. Soc. 2011
• Bio-functionalized AuNps specifically interact with protein biotin-streptavidin
• Based on UV-vis data, addition of streptavidin to AuNP + biotin-linked thiol shifts the peak towards blue (from 526nm to 550nm) and the absorbance peak reduces.
• Also considers Cyctochrome C, Myoglobin, and Hemoglobin (This may be useful when applying AuNP to drug delivery).

--Dhea Patel 21:30, 25 September 2012 (EDT)

Interfacing biology with nanoparticles

• Saikat Mandal, Sumant Phadtare, Murali Sastry, Current Applied Physics 5 [Elsevier], 2005
• contains UV-vis of lysine-capped Au at various stages of NP preparation
• contain UV-vis of lysine-capped AuNP at pH 3, 7, and 10 (and explains the results in terms of ionic strength).
• also, on page 123, it has an illustration of the assembly of AuNP to better visualize the big picture of our experiment.

--Dhea Patel 21:47, 25 September 2012 (EDT)

Other Syntheses of Gold Nanoparticles

Preparation of Gold Nanoparticles Using Tea: A Green Chemistry Experiment

• R. K. Sharma, Shikha Gulati, and Shilpa Mehta, Journal of Chemical Education Article ASAP
• how to synthesis AuNPs using biomaterials that are not mammalian proteins
  • Abigail E. Miller 21:11, 28 August 2012 (EDT):

New, fast and green procedure for the synthesis of gold nanoparticles based on sonocatalysis

• AuNPs are synthesized using sonic vibration, with sodium citrate dihydrate as a stabilizing and reducing agent. Compared to previous protocols, this method takes an extremely short amount of time to prepare AuNPs and does not require the solutions to be heated.
• Melissa Novy 14:07, 5 September 2012 (EDT)

Green synthesis of gold nanoparticles with Zingiber officinale extract: Characterization and blood compatibility

• Extract from Zingiber officinale, a type of ginger, is used as a stabilizing and reducing agent to synthesize AuNPs. According to the literature, ginger extract is more efficient than aspirin in decreasing blood platelet aggregation, so this method of AuNP synthesis is promising for use in medical treatments.
• Melissa Novy 14:15, 5 September 2012 (EDT)

Biological synthesis of silver and gold nanoparticles using apiin as reducing agent

• Apiin, a compound found in parsley, celery, and henna, is used as a stabilizing and reducing agent to synthesize AuNPs. The interaction between apiin and AuNPs was analyzed using FT-IR.
• Melissa Novy 14:19, 5 September 2012 (EDT)

Amino Acids Binding to AuNPs

• Ossi Horovitz, Aurora Mocanu, Gheorghe Tomoaia, Maria Crisan, Liviu-Dorel Bobos, Casaba Racz and Maria Tomoaia-Cotisel, Studia Universitatis Babes-Bolyai, Chemia, Lii, 3, 2007
• AuNP capped with citrate anions
• Discusses which amino acids interact with AuNPs and which have poor interactions with AuNPs.

--Dhea Patel 21:54, 24 September 2012 (EDT)
An Effective Strategy for the Synthesis of Biocompatible Gold Nanoparticles Using Cinnamon Phytochemicals for Phantom CT Imaging and Photoacoustic Detection of Cancerous Cells

• Explored the possibility of coating Gold nano-particles in cinnamon to aid in cancer detection procedures. The alcoholic components of cinnamon reduce NaAuCl₄ to produce gold- nanoparticles. the Cin-AuNPs are biocompatible and can serve as excellent CT/ photoacoustic contrast-enhancement agents to detect tumors.
  • ""Puja Mody 20:48, 22 September 2012 (EDT)""

Non-cross-linking gold nanoparticle aggregation as a detection method for single-base substitutions

• DNA-modified gold nanoparticles were used to detect single-base subsitutions in DNA by colorimetry/spectroscopy. The nanoparticles were stabilized with single-stranded DNA molecules. AuNPs aggregate by crosslinking with DNA molecules but also without crosslinking (NCL). The NCL aggregations were able to detect single-base mutations at very low concentrations.
• Melissa Novy 15:32, 25 September 2012 (EDT)

Functionalization of gold nanoparticles with amino acid, β-amyloid peptides and fragment

• A. Majzik, L. Fülöp, E. Csapó, F. Bogár, T. Martinek, B. Penke, G. Bíró, I. Dékány, Colloids and Sufraces B: Biointerfaces [Elsevier], 2010
• AuNPs functionalized by cysteine, β-amyloid peptides, and pentapeptide fragment.
• No aggregation was observed in the samples containing β-amyloid peptides; however, aggregation was observed in the samples containing cysteine.

--Dhea Patel 21:38, 25 September 2012 (EDT)

Lysine Mediated Assembly of Gold Nanoparticles

• Ossi Horovitz, Aurora Mocanu, Gheorghe Tomoaia, Maria Crisan, Liviu-Dorel Bobos, Casaba Racz and Maria Tomoaia-Cotisel, Studia Universitatis Babes-Bolyai, Chemia, Lii, 1, 2007
• reduced in a citrate aqueous solution
• UV absorption band at 528nm
• TEM: Au size ~14nm
• At high Au/Lys Ratios, a second peak emerged at ~630nm, shifting from a red solution to a blue solution.

--Dhea Patel 22:57, 25 September 2012 (EDT)

Self-assembly characteristics of gold nanoparticles in the presence of cysteine

• Aurora Mocanu, Ileana Cernica, Gheorghe Tomoaia, Liviu-Dorel Bobos, Ossi Horovitz, Maria Tomoaia-Cotisel, Colloids and Surfaces A: Physicochemical and Engineering Aspects, 2009
• reducing agent: sodium citrate
• discusses the differences in average Au size
  • slight UV-vis shift (from 528nm to 522nm) observed with decrease in Au size
  • might help us understand discrepancies in absorbance peaks.

Analysis of Gold Nanoparticles

Determination of Size and Concentration of Gold Nanoparticles from UV−Vis Spectra

• W. Haiss, N. T. K. Thanh, J. Aveyard and D. G. Fernig Analytical Chemistry 2007 79 (11), 4215-4221
• demonstrates how to calculate the size and concentration of the AuNPs from the position of the gold nanoparticle plasmon absorbance peak around 550 nm.
  • Abigail E. Miller 13:54, 4 September 2012 (EDT):

Determination of the Concentration and the Average Number of Gold Atoms in a Gold Nanoparticle by Osmotic Pressure

• Y. Lu, L. Wang, D. Chen, and G. Wang Langmuir 2012 28 (25), 9282-9287
• xx
  • Abigail E. Miller 13:55, 5 September 2012 (EDT):

Fluorescence Dynamics in BSA-Protected Au25 Nanoclusters

• Xiaoming Wen, Pyng Yu, Yon-Rui Toh, An-Chia Hsu, Yu-Chieh Lee, and Jau Tang The Journal of Physical Chemistry C 2012 116 (35), 19032-19038
• fast energy transfer between the singlet and triplet states of a gold cluster.....
  • Abigail E. Miller 15:20, 11 September 2012 (EDT):

[http://ac.els-cdn.com/S0021979712006480/1-s2.0-S0021979712006480-main.pdf?_tid=b569df84-051b-11e2-ae62-00000aab0f01&acdnat=1348362914_63c7484b0014b928f582a79a1e760458 Preparation of controlled gold nanoparticle aggregates using a dendronization strategy]

• Julieta I. Paez, Eduardo A. Coronado,Miriam C. Strumia
• A Dendronization strategy was used to control the interparticle spacing and optical properties of gold nanoparticle aggregates in aqueous solution. Tests how disulfide concentration, temperature, time and nature of the ligand (dendritic vs nondendritic), determine the control exerted over the size and stability of the NP aggregates.
  • ""Puja Mody 20:48, 22 September 2012 (EDT)""

Photoluminescence from water-soluble BSA-protected gold nanoparticles

• Li Liu, Hu-Zhi Zheng, , Zhu-Jun Zhang, Yu-Ming Huang, Su-Ming Chen, Yu-Fei Hu
• Observed the photoluminescence of water-soluble gold nano-particles which were wrapped in BSA protective layer. Alternative to organic fluorophores or semiconductor nanoparticles for biological labeling and imaging.
• The size effects and contributions from surface characteristics of small nano particles.
  • ""Puja Mody 20:48, 22 September 2012 (EDT)""

Isothermal Titration Calorimetry Studies on the Binding of Amino Acids to Gold Nanoparticles [1]

• Hrushikesh Joshi, Pravin S. Shirude, Vipul Bansal, K. N. Ganesh, and Murali Sastry, J. Phys. Chem, 2004
• Contains a gel electrophroesis of differently charge AuNP.
  • Au-Lys pH7, Au-Lus pH 11, and borohydride-reduced AuNP
  • partially capped Au-Asp and fully capped Au-Asp
  • helps determine which combination is most negatively charged or positively charged.
• Isothermal titration calorimetry (ITC) measures the heats of interaction of reactants and therefore can determine strengths of bonds between the reactants and help deduce how the reactants are bonded together.

--Dhea Patel 22:16, 25 September 2012 (EDT)

Protein Aggregation (of Proteins with Nanoparticles)

Buffer and Ionic Strength Effects

The effect of pH on amino acids binding to gold nanoparticles [2]

• Mihailescu, Olenic, Pruneanu, Bratu, Kacso, Journal of Optoelectronics and Advanced Materials, 2007.
• Na₃AU(SO₃)₂ was reduced with sodium citrate.
• pH affects the relationship between amino acids and AuNPs.
• low pH of amino acid solution is a good condidtion for negatively charged AuNP because the COO- and NH₂ groups become protonated and the AuNP can then bind to these functional groups.

--Dhea Patel 18:09, 24 September 2012 (EDT)

Aggregation Stability

Gold nanoparticles can induce the formation of protein-based aggregates at physiological pH

• The study discovered that gold nanoparticles cause BSA proteins to become partially unfolded at the nanoparticle-protein interface. Aggregation of proteins is catalyzed by these misfolded BSA proteins.
• Melissa Novy 14:28, 25 September 2012 (EDT)