S4-01-05: The 28-amino acid form of an APLP1-derived abeta-like peptide is a surrogate marker for Abeta42 production

The X-ray crystal structure of (S)-2,2,5,5-tetramethylthiazolidine-4-carboxylic acid, 1, has been determined. Crystals are monoclinic, P21, with cell dimensions a = 11.351(4) b = 8.303(2), c = 11.969(3) Å, β = 116.69(2)°, and Z = 4. The structure was solved by standard methods and refined to R1 = 0.0774, R2 = 0.0670 for 2388 independent reflections. Compound 1 exists in the amino-acid form as shown by two distinctly different C—O bond lengths, 1.209 and 1.309 Å, typical of the COOH group, and by the positions of the hydrogen atoms. The amino-acid form of 1 found in the solid also exists in solution as shown by infrared and Raman spectra. The mass spectra, and 1H and 13C nmr spectra are reported, as well as detailed infrared and Raman spectra for the title compound and several deuterated species.

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2′-Fluoropyrimidine RNA-based Aptamers to the 165-Amino Acid Form of Vascular Endothelial Growth Factor (VEGF165)

Journal of Biological Chemistry ◽

10.1074/jbc.273.32.20556 ◽

1998 ◽

Vol 273 (32) ◽

pp. 20556-20567 ◽

Cited By ~ 475

Author(s):

Judy Ruckman ◽

Louis S. Green ◽

Jim Beeson ◽

Sheela Waugh ◽

Wendy L. Gillette ◽

...

Keyword(s):

Vascular Endothelial Growth Factor ◽

Amino Acid ◽

Growth Factor ◽

Vascular Endothelial ◽

Acid Form ◽

Amino Acid Form ◽

Endothelial Growth Factor

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38-Amino acid form of pituitary adenylate cyclase activating peptide induces process outgrowth in human neuroblastoma cells

Journal of Neuroscience Research ◽

10.1002/jnr.490350311 ◽

1993 ◽

Vol 35 (3) ◽

pp. 312-320 ◽

Cited By ~ 45

Author(s):

P. J. Deutsch ◽

V. C. Schadlow ◽

N. Barzilai

Keyword(s):

Amino Acid ◽

Adenylate Cyclase ◽

Neuroblastoma Cells ◽

Acid Form ◽

Human Neuroblastoma Cells ◽

Human Neuroblastoma ◽

Pituitary Adenylate Cyclase ◽

Amino Acid Form ◽

Process Outgrowth

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Rules for designing protein fold switches and their implications for the folding code

10.1101/2021.05.18.444643 ◽

2021 ◽

Author(s):

Yingwei Chen ◽

Yanan He ◽

Biao Ruan ◽

Eun Jung Choi ◽

Yihong Chen ◽

...

Keyword(s):

Amino Acid ◽

Single Amino Acid ◽

Acid Form ◽

State Behavior ◽

Amino Acid Region ◽

Highly Sensitive ◽

Amino Acid Form ◽

The Stability ◽

Similar Conformation ◽

Acid Region

We have engineered switches between the three most common small folds, 3a, 4b+a, and a/b plait, referred to here as A, B, and S, respectively. Mutations were introduced into the natural S protein until sequences were created that have a stable S-fold in their longer (~90 amino acid) form and have an alternative fold (either A or B) in their shorter (56 amino acid) form. Five sequence pairs were designed and key structures were determined using NMR spectroscopy. Each protein pair is 100% identical in the 56 amino acid region of overlap. Several rules for engineering switches emerged. First, designing one sequence with good native state interactions in two folds requires care but is feasible. Once this condition is met, fold populations are determined by the stability of the embedded A- or B-fold relative to the S-fold and the conformational propensities of the ends that are generated in the switch to the embedded fold. If the stabilities of the embedded fold and the longer fold are similar, conformation is highly sensitive to mutation so that even a single amino acid substitution can radically shift the population to the alternative fold. The results provide insight into why dimorphic sequences can be engineered and sometimes exist in nature, while most natural protein sequences populate single folds. Proteins may evolve toward unique folds because dimorphic sequences generate interactions that destabilize and can produce aberrant functions. Thus two-state behavior may result from nature's negative design rather than being an inherent property of the folding code.

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The Influence of Free 3-Nitrotyrosine and Saliva on the Quantitative Analysis of Protein-Bound 3-Nitrotyrosine in Sputum

Analytical Chemistry Insights ◽

10.4137/117739010700200006 ◽

2007 ◽

Vol 2 ◽

pp. 117739010700200 ◽

Cited By ~ 4

Author(s):

Kazuhito Ueshima ◽

Yoshiaki Minakata ◽

Hisatoshi Sugiura ◽

Satoru Yanagisawa ◽

Tomohiro Ichikawa ◽

...

Keyword(s):

Amino Acid ◽

Free Amino Acid ◽

Free Amino ◽

High Performance ◽

Nitrosative Stress ◽

Protein Hydrolysate ◽

Streptomyces Griseus ◽

Induced Sputum ◽

Acid Form ◽

Amino Acid Form

Background We have recently developed a new technique for quantitatively measuring protein-bound 3-nitrotyrosine (3-NT), a footprint of nitrosative stress, utilizing high-performance liquid chromatography with an electrochemical detection (HPLC-ECD) system. Using this system, we showed that 3-NT formation was upregulated in the sputum of both COPD and asthmatic patients. However, in order to improve the accuracy of the measurement system, We have to resolve some problems which were the influence of free amino acid form of 3-NT and of salivary contamination. Objectives We initially investigated the amount of the free amino acid form of 3-NT in induced sputum and compared with that of protein-bound 3-NT. Next, we evaluated the concentration of protein-bound 3-NT in saliva and compared with that in induced sputum by means of HPLC-ECD. Methods Five male COPD patients were enrolled. Induced sputum and saliva were obtained from the patients. The free amino acid form of 3-NT in sputum and saliva was measured by HPLC-ECD, and the protein-bound 3-NT and tyrosine in sputum and saliva were enzymatically hydrolyzed by Streptomyces griseus Pronase and measured for the protein hydrolysate by HPLC-ECD. Results The mean value of the amount of protein-bound 3-NT was 65.0 fmol (31.2 to 106.4 fmol). On the other hand, the amount of the free amino acid form of 3-NT was under the detection limit (<10 fmol). The levels of both 3-NT (sputum: 0.55 ± 0.15 pmol/ml, saliva: 0.02 ± 0.01 pmol/ml, p < 0.01) and tyrosine (sputum: 0.81 ± 0.43 μmol/ml, saliva: 0.07 ± 0.04 μmol/ml, p < 0.01) in saliva were significantly lower than in sputum. The percentage of 3-NT in saliva to that in sputum was about 3.1%, and that of tyrosine was about 9.0%. Conclusion The free amino acid form of 3-NT does not affect the measurement of protein-bound 3-NT. Furthermore, the influence of salivary contamination on the measurement of protein-bound 3-NT in induced sputum by means of HPLC-ECD was very small and could be negligible.

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