scholarly journals Multiple Alignment Tensors from a Denatured Protein

2006 ◽  
Vol 128 (29) ◽  
pp. 9310-9311 ◽  
Author(s):  
Erika B. Gebel ◽  
Ke Ruan ◽  
Joel R. Tolman ◽  
David Shortle
Keyword(s):  
Multiple Alignment ◽  
Denatured Protein ◽  
Alignment Tensors

A Heuristic Method Based on Multi-Objective Optimization Concept for Solving RNA Multiple Alignment

2017 ◽  
Vol 10 (5) ◽  
pp. 371
Author(s):  
Arakil Chentoufi ◽  
Abdelhakim El Fatmi ◽  
Molay Ali Bekri ◽  
Said Benhlima ◽  
Mohamed Sabbane
Keyword(s):  
Heuristic Method ◽  
Multiple Alignment ◽  
Multi Objective Optimization ◽  
Multi Objective

scholarly journals PRALINETM: a strategy for improved multiple alignment of transmembrane proteins

2008 ◽  
Vol 24 (4) ◽  
pp. 492-497 ◽  
Author(s):  
W. Pirovano ◽  
K. A. Feenstra ◽  
J. Heringa
Keyword(s):  
Transmembrane Proteins ◽  
Multiple Alignment

scholarly journals CONCENTRATION AND PURIFICATION OF BACTERIOPHAGE

1938 ◽  
Vol 21 (3) ◽  
pp. 335-366 ◽  
Author(s):  
John H. Northrop
Keyword(s):  
Molecular Weight ◽  
Small Molecules ◽  
Specific Activity ◽  
Active Agent ◽  
Pure Substance ◽  
Solubility Curve ◽  
Denatured Protein ◽  
Sedimentation Constant ◽  
Rate Of Sedimentation ◽  
Living Organisms

1. A method for isolating a nucleoprotein from lysed staphylococci culture is described. 2. It is homogeneous in the ultracentrifuge and has a sedimentation constant of 650 x 10–13 cm. dyne–1 sec.–1, corresponding to a molecular weight of about 300,000,000. 3. The diffusion coefficient varies from about 0.001 cm.2/day in solutions containing more than 0.1 mg. protein/ml. to 0.02 in solutions containing less than 0.001 mg. protein/ml. The rate of sedimentation also decreases as the concentration decreases. It is suggested, therefore, that this protein exists in various sized molecules of from 500,000–300,000,000 molecular weight, the proportion of small molecules increasing as the concentration decreases. 4. This protein is very unstable and is denatured by acidity greater than pH 5.0, by temperature over 50°C. for 5 minutes. It is digested by chymo-trypsin but not by trypsin. 5. The loss in activity by heat, acid, and chymo-trypsin digestion is roughly proportional to the amount of denatured protein formed under these conditions. 6. The rate of diffusion of the protein is the same as that of the active agent. 7. The rate of sedimentation of the protein is the same as that of the active agent. 8. The loss in activity when susceptible living or dead bacteria are added to a solution of the protein is proportional to the loss in protein from the solution. Non-susceptible bacteria remove neither protein nor activity. 9. The relative ultraviolet light absorption, as determined directly, agrees with that calculated from Gates' inactivation experiments in the range of 2500–3000 Å. u. but is somewhat greater in the range of 2000–2500 Å. u. 10. Solubility determinations showed that most of the preparations contained at least two proteins, one being probably the denatured form of the other. Two preparations were obtained, however, which had about twice the specific activity of the earlier ones and which gave a solubility curve approximating that of a pure substance. 11. It is suggested that the formation of phage may be more simply explained by analogy with the autocatalytic formation of pepsin and trypsin than by analogy with the far more complicated system of living organisms.

Spectral Diffusion Experiment with a Denatured Protein

2004 ◽  
Vol 108 (3) ◽  
pp. 1109-1114 ◽  
Author(s):  
Vladimir V. Ponkratov ◽  
Josef Friedrich ◽  
Dejan Markovic ◽  
Hugo Scheer ◽  
Jane M. Vanderkooi
Keyword(s):  
Spectral Diffusion ◽  
Diffusion Experiment ◽  
Denatured Protein

scholarly journals Dissociation, unfolding and refolding trials of pig kidney 3,4-dihydroxyphenylalanine (dopa) decarboxylase

1993 ◽  
Vol 295 (2) ◽  
pp. 493-500 ◽  
Author(s):  
P Dominici ◽  
P S Moore ◽  
C Borri Voltattorni
Keyword(s):  
Conformational Changes ◽  
Dopa Decarboxylase ◽  
Experimental Conditions ◽  
High Tendency ◽  
Denatured Protein ◽  
Pig Kidney ◽  
Plausible Model ◽  
Spectroscopic Characteristics ◽  
Equilibrium Transition ◽  
Almost All

The effect of guanidinium chloride (GuCl) on enzyme activity, hydrodynamic volume, circular dichroism, and fluorescence of 3,4-dihydroxyphenylalanine (Dopa) decarboxylase from pig kidney (pkDDC) was studied under equilibrium conditions. Unfolding proceeds in at least three stages. The first transition, occurring between 0 and 1 M GuCl, gives rise to a dimeric inactive species which has lost pyridoxal 5′-phosphate (PLP), and has a high tendency to aggregate, but retains almost all of the native spectroscopic characteristics. The second equilibrium transition, between 1 and 2.2 M GuCl, involves dimer dissociation, with some loss of tertiary and secondary structure. Additionally, gross conformational changes at or near the PLP microenvironment were detected by fluorescence of NaBH4-reduced enzyme. The third step, presumably representing complete unfolding of pkDDC, appears to be complete at 4.5 M GuCl, as indicated by the lack of further substantial changes in any of the signals being studied. Attempts at refolding resulted in the findings that: (1) partial reactivation is observed only starting from enzyme denatured at concentrations below 1.5 M GuCl, and (2) starting from completely denatured protein, the refolding process is apparently reversible down to concentrations of approx. 2 M GuCl. Taken together, this would seem to indicate that the monomer-dimer transition is impaired under the experimental conditions tested. A plausible model is presented for the unfolding/refolding of pkDDC.

scholarly journals BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs

1999 ◽  
Vol 15 (1) ◽  
pp. 87-88 ◽  
Author(s):  
J. Thompson ◽  
F Plewniak ◽  
O Poch
Keyword(s):  
Multiple Alignment
Sign in / Sign up

Export Citation Format

Share Document