Proteins

The nitrogen of the protein precipitate is converted to acid ammonium sulphate by digestion with sulphuric acid and various catalysts. On making the reaction mixture alkaline, ammonia is liberated, which is removed by steam distillation. The ammonia liberated by steam distillation is gathered in acid solution containing an indicator. Change in pH of the acid solution due to addition of ammonia is indicated by the indicator dye. This solution is back-titrated with 0.01 N HCI, and the original acidic condition indicated by the indicator dye, is taken as the end point. The amount of HCl consumed in back titration is proportional to the amount of ammonia liberated. Percentage of nitrogen is calculated from the titre value, which is converted into gm% of protein present in sample by multiplying the percentage nitrogen with a factor 6.2S. The factor 6.25 is used for conversion because in average, protein contains 16% of nitrogen

Why Do Proteins Look Like Proteins?

Protein structures in nature often exhibit a high degree of regularity (secondary structures, tertiary symmetries, etc.) absent in random compact conformations. We demonstrate in a simple lattice model of protein folding that structural regularities are related to high designability and evolutionary stability. We measure the designability of each compact structure by the number of sequences which can design the structure, i.e., which possess the structure as their nondegenerate ground state. We find that compact structures are drastically different in terms of their designability; highly designable structures emerge with a number of associated sequences much larger than the average. These structures are found to have ``protein like'' secondary structure and even tertiary symmetries. In addition, they are also thermodynamically more stable than ordinary structures. These results suggest that protein structures are selected because they are easy to design and stable against mutations, and that such a selection simutaneously leads to thermodynamic stability.Comment: 5 pages, 4 figures, RevTex, some minor changes from the original version, also available at http://www.neci.nj.nec.com/homepages/tang.htm

Proteins Wriggle

We propose an algorithmic strategy for improving the efficiency of Monte Carlo searches for the low-energy states of proteins. Our strategy is motivated by a model of how proteins alter their shapes. In our model when proteins fold under physiological conditions, their backbone dihedral angles change synchronously in groups of four or more so as to avoid steric clashes and respect the kinematic conservation laws. They wriggle; they do not thrash. We describe a simple algorithm that can be used to incorporate wriggling in Monte Carlo simulations of protein folding. We have tested this wriggling algorithm against a code in which the dihedral angles are varied independently (thrashing). Our standard of success is the average root-mean-square distance (rmsd) between the alpha-carbons of the folding protein and those of its native structure. After 100,000 Monte Carlo sweeps, the relative decrease in the mean rmsd, as one switches from thrashing to wriggling, rises from 11% for the protein 3LZM with 164 amino acids (aa) to 40% for the protein 1A1S with 313 aa and 47% for the protein 16PK with 415 aa. These results suggest that wriggling is useful and that its utility increases with the size of the protein. One may implement wriggling on a parallel computer or a computer farm.Comment: 12 pages, 2 figures, JHEP late

Proteins

Uch37 is a de-ubiquitylating enzyme that is functionally linked with the 26S proteasome via Rpn13, and is essential for metazoan development. Here, we report the X-ray crystal structure of full-length human Uch37 at 2.95 \uc5 resolution. Uch37's catalytic domain is similar to those of all UCH enzymes characterized to date. The C-terminal extension is elongated, predominantly helical and contains coiled coil interactions. Additionally, we provide an initial characterization of Uch37's oligomeric state and identify a systematic error in previous analyses of Uch37 activity. Taken together, these data provide a strong foundation for further analysis of Uch37's several functions.T15 LM007359-06/LM/NLM NIH HHS/United StatesR01 LM008796-04/LM/NLM NIH HHS/United StatesS10 RR013790/RR/NCRR NIH HHS/United StatesGM074901/GM/NIGMS NIH HHS/United StatesU54 GM074901-03/GM/NIGMS NIH HHS/United StatesT15 LM007359-06S2/LM/NLM NIH HHS/United StatesT15 LM007359-09/LM/NLM NIH HHS/United StatesS10 RR13790/RR/NCRR NIH HHS/United StatesT15 LM007359-09S1/LM/NLM NIH HHS/United StatesR01 LM008796-03/LM/NLM NIH HHS/United StatesT15-LM007359/LM/NLM NIH HHS/United StatesT15 LM007359/LM/NLM NIH HHS/United StatesU54 GM074901-02S1/GM/NIGMS NIH HHS/United StatesT15 LM007359-08/LM/NLM NIH HHS/United StatesT15 LM007359-06S1/LM/NLM NIH HHS/United StatesT15 LM007359-07/LM/NLM NIH HHS/United StatesU54 GM074901-05/GM/NIGMS NIH HHS/United StatesDE-AC02-06CH11357/CH/OID CDC HHS/United StatesR01 LM008796-02/LM/NLM NIH HHS/United StatesU54 GM074901-01/GM/NIGMS NIH HHS/United StatesU54 GM074901-01S1/GM/NIGMS NIH HHS/United StatesT15 LM007359-10/LM/NLM NIH HHS/United StatesU54 GM074901-02/GM/NIGMS NIH HHS/United StatesR01-LM008796/LM/NLM NIH HHS/United StatesU54 GM074901-03S1/GM/NIGMS NIH HHS/United StatesR01 LM008796-01/LM/NLM NIH HHS/United StatesR01 LM008796/LM/NLM NIH HHS/United StatesU54 GM074901/GM/NIGMS NIH HHS/United StatesU54 GM074901-04/GM/NIGMS NIH HHS/United States2013-02-02T00:00:00Z21953935PMC3251636vault:729

Seminal Plasma Proteins

The ejaculated semen consists of two major components viz. sperm cells (spermatozoa) and the fluid part obtained after centrifugation called seminal plasma. The spermatozoa originate from the semniferous tubule and are suspended in the seminal plasma. The seminal plasma is composed of secretions contributed by the testis, epididymis, seminal vesicles, ampullae, prostate and bulbourethral glands. About 60-80 % of the ejaculated semen of the bull originates from these sources. Seminal plasma is a highly complex biological fluid containing proteins, amino acids, enzymes, fructose and other carbohydrates, lipids, major minerals and trace elements. Seminal plasma proteins partly originates from the blood plasma by exudation through the lumen of the male genital tract and partly are synthesized and secreted by various reproductive organs and are known as seminal plasma specific proteins. Several seminal plasma proteins of blood origin viz. prealbumin, albumin, globulin, transferring, α-antitrypsin, β-lipoprotein, β-glycoprotein, orsomucoid, kininogen, Peptide hormones, IgG, IgA and IgM have been identified and characterized. These proteins are involved in regulation of osmotic pressure and pH of seminal plasma, transport of ions, lipid and hormones. A major part of seminal plasma proteins originate from the testis, epididymis, vas deference, prostate, seminal vesicle and bulbourethral glands. The biosynthesis and secretion of these proteins is regulated by testosterone levels in the blood

Proteins and polymers

Proteins, chain molecules of amino acids, behave in ways which are similar to each other yet quite distinct from standard compact polymers. We demonstrate that the Flory theorem, derived for polymer melts, holds for compact protein native state structures and is not incompatible with the existence of structured building blocks such as $\alpha$-helices and $\beta$-strands. We present a discussion on how the notion of the thickness of a polymer chain, besides being useful in describing a chain molecule in the continuum limit, plays a vital role in interpolating between conventional polymer physics and the phase of matter associated with protein structures.Comment: 7 pages, 6 figure

Precise Similarity of Many Human Proteins to Proteins of Prokarya

	 Proteins originated in early forms of life and have long survived, because they have always been required. Some recognizably similar proteins are found in all sequence comparisons between species, no matter how distant, including prokaryotes and eukaryotes. Reported here are observations on the relationships of human proteins to the proteins of 458 prokaryotes for which protein libraries are available. Each of these libraries includes a protein that matches a human protein with a BLAST score of 573 or more, indicating excellent conservation of certain amino acid sequences. A majority of these proteins also match a yeast protein and other eukaryote proteins with comparable accuracy, indicating that protein conservation is responsible in most cases rather than the horizontal transfer (HGT) between eukaryotes and prokaryotes. Rare examples of HGT are apparently also seen.
	Very many significant matches are seen as the criterion is opened, including 20,596 human proteins that match at least one prokaryote protein with expectation of 10-3 or less. Individual prokaryote proteins accurately match parts of many modern human proteins that have a wide range of functions showing directly that many proteins of different functions have evolved from an ancestral protein by duplication, rearrangement and divergence of function. The implication is that most or all modern proteins derive from the proteins of the last common ancestor with prokaryotes through many such events. 
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Idiosyncratic evolution of conserved eukaryote proteins that are similar in sequence to archaeal or bacterial proteins

	Sequence comparisons have been made between the proteins of 571 prokaryote species including 46 archaea and 525 bacteria and the set of human proteins. Highly conserved eukaryotic proteins are often strikingly similar in sequence to archaeal and bacterial proteins. Yet in many cases similarity to archaeal proteins is not correlated to the similarity to bacterial proteins. In these comparisons there are hundreds of eukaryote proteins that match well archeal proteins, but do not match recognizably to bacterial proteins, while thousands of proteins match well to bacterial proteins but not recognizably to archeal proteins. Forty percent of the 21,440 human proteins that significantly match prokaryote proteins are in this extreme idiosyncratic category. These relationships have been preserved over billions of years since the last common ancestor or sharing of protein genes between prokaryotes and eukaryotes. For each of the 21,440 members of this set of human proteins (that make significant matches to any of the 1.8 million proteins in this set of prokaryote species protein libraries) it is certain that each protein has important functions both in prokaryotes and eukaryotes and the precursor proteins have been important in the precursor species of both. That is the only explanation for the preservation of amino acid sequence similarity for the billions of years since the last common ancestor or period of sharing of proteins. Comparisons were made between the proteins of Arabidopsis thaliana and Saccharomyces cerevisiae to the proteins of the 571 prokaryote species. The results agreed with the human comparisons indicating that the conclusions apply to eukaryotes generally

Transport of Cytoplasmically Synthesized Proteins into the Mitochondria in a Cell Free System from Neurospora crassa

Synthesis and transport of mitochondrial proteins were followed in a cell-free homogenate of Neurospora crassa in which mitochondrial translation was inhibited. Proteins synthesized on cytoplasmic ribosomes are transferred into the mitochondrial fraction. The relative amounts of proteins which are transferred in vitro are comparable to those transferred in whole cells. Cycloheximide and puromycin inhibit the synthesis of mitochondrial proteins but not their transfer into mitochondria. The transfer of immunoprecipitable mitochondrial proteins was demonstrated for matrix proteins, carboxyatractyloside-binding protein and cytochrome c. Import of proteins into mitochondria exhibits a degree of specificity. The transport mechanism differentiates between newly synthesized proteins and preexistent mitochondrial proteins, at least in the case of matrix proteins. In the cell-free homogenate membrane-bound ribosomes are more active in the synthesis of mitochondrial proteins than are free ribosomes. The finished translation products appear to be released from the membrane-bound ribosomes into the cytosol rather than into the membrane vesicles. The results suggest that the transport of cytoplasmically synthesized mitochondrial proteins is essentially independent of cytoplasmic translation; that cytoplasmically synthesized mitochondrial proteins exist in an extramitochondrial pool prior to import; that the site of this pool is the cytosol for at least some of the mitochondrial proteins; and that the precursors in the extramitochondrial pool differ in structure or conformation from the functional proteins in the mitochondria