Protein inference

Nesvizhskii, A.I., Aebersold, R. (2005). Interpretation of shotgun proteomics data the protein inference problem. Mol. Cell. Proteomics 4, 1419-1440. 

Gotoh O. Substrate recognition sites in cytochrome P450 family 2 (CYP2) proteins inferred from comparative analyses of amino acid and coding nucleotide sequences. J Biol Chem 1992 267(1) 83-90. 

D-MS bromobenzene Rat liver DNA array/proteomics IDed proteins infer degradation, oxidative stress... 

Several of the above methods significantly increase the size of proteomic databases. This causes a decrease in peptide identification sensitivity (111,130), complicates protein inference (because of many redundant sequences) (160,161), and leads to longer search times. Although some efforts have been made to optimize search speeds (162), these hurdles remain unsolved. 

Marienhagen J, Kennerknecht N, Sahm H, Eggehng L (2005) Functional analysis of aU aminotransferase proteins inferred from the genome sequence of Corynebacterium glutamicum. J Bacteriol 187 7639-7646... 

Yoo, H.-Y., Boatz, J.A., Helms, V, McCammon, J.A., and Langhoff, RW, Chromophore protonation states and the proton shuttle mechanism in green fluorescent protein inferences drawn from ab initio theoretical studies of chemical structures and vibrational spectra.. Phys. Chem. B., 105, 2450-2457, 2001. 

Female sexual development and behaviour in mammals occurs by default and requires no ovarian secretion, and it is only in genetic males that the testis can secrete hormones which destroy this female pattern and superimpose that of the male. Sexual differentiation is not so well defined in fish, and larval exposure to both synthetic estrogens and androgens is widely used in aquaculture to produce monosex cultures. Endocrine disruption of sexual differentiation in fish may therefore reflect both the complexity and diversity of such processes between different species. Some care is required in use of the terms hermaphrodite and sex-reversal since a true hermaphrodite has both functional testes and ovaries and a sex-reversed fish is fully functional as its final sex—both produce the appropriate viable gametes. Such functional sex-reversal is not possible in mammals, but in some species of fish it is the normal developmental pattern. In most of the cases of hermaphroditism or sex-reversal reported in the non-scientific press, there is evidence only for a few ovarian follicles within a functional testis. This may be considered as feminisation or a form of intersex, and is very clearly endocrine disruption, but it is certainly neither sex-reversal nor hermaphroditism. In some cases the terms have even been used to infer induction of a single female characteristic such as production of yolk-protein by males. 

The goal of any statistical analysis is inference concerning whether on the basis of available data, some hypothesis about the natural world is true. The hypothesis may consist of the value of some parameter or parameters, such as a physical constant or the exact proportion of an allelic variant in a human population, or the hypothesis may be a qualitative statement, such as This protein adopts an a/p barrel fold or I am currently in Philadelphia. The parameters or hypothesis can be unobservable or as yet unobserved. How the data arise from the parameters is called the model for the system under study and may include estimates of experimental error as well as our best understanding of the physical process of the system. 

MO Dayhoff, WC Barker, PJ McLaughlin. Inferences from protein and nucleic acid sequences Early molecular evolution, divergence of kingdoms and rates of change. Orig Life 5 311-330, 1974. 

Recombinant DNA techniques have provided tools for the rapid determination of DNA sequences and, by inference, the amino acid sequences of proteins from structural genes. The number of such sequences is now increasing almost exponentially, but by themselves these sequences tell little more about the biology of the system than a New York City telephone directory tells about the function and marvels of that city. 

Ohlendorf, D.H., et al. The molecular basis of DNA-protein recognition inferred from the structure of Cro repressor. Nature 298 718-723, 1982. 

It can be inferred from the first section of this chapter that many different forces work together in a delicate balance to determine the overall three-dimensional structure of a protein. These forces operate both within the protein structure itself and between the protein and the water solvent. How, then, does nature dictate the manner of protein folding to generate the three-dimensional... 

The hindering potentials must be of importance in the question of the flexibility of long-chain molecules such as synthetic polymers and naturally occurring macromolecules such as proteins and nucleic acids. Again, direct information on barriers in these molecules will be difficult to obtain but inferences can presumably be drawn from experiments on simpler analogues. 

The native luciferase having a molecular weight of 106,000 probably consists of two units of the functional 19 kDa protein and two units of the 35 kDa protein. The value of A28o,icm for a solution containing 1 mg/ml of the native luciferase is calculated to be about 0.9 from the inferred amino acid sequence. The function of the 35 kDa protein remains unclear, although it might have a role in the stabilization of the 19 kDa protein. 

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