Protein using

Prediction of pKaS of Titratable Residues in Proteins Using a Poisson-Boltzmann Model of the Solute-Solvent System... 

Fig. 1. CPU times (in hours) for 1 ps MD runs for various proteins using three different methods, direct velocity Verlet with a time-step 0.5 fs, r-RESPA with direct evaluation of electrostatic forces and an overall time-step of 4.0 fs, and r-RESPA/TFMM with an overall time-step 4.0 fs (combination of (2,2,2,2) in force breakup).The energy conservation parameter log AE for the three methods are comparable. The CPU time (hours) is for RISC6000 /MODEL 590 computer.

Nlng Q and T J Sejnowsld 1988. Predicting the Secondary Structure of Globular Proteins Using Neural Network Models. Journal of Molecular Biology 202 865-888. 

Ortiz A R, A Kolinski and J Skolnick 1998. Fold Assembly of Small Proteins Using Monte C Simulations Driven by Restraints Derived from Multiple Sequence Alignments. Jourru Molecular Biology 277 419-446. 

Pander J W and F M Richards 1987. Tertiary Templates for Proteins. Use of Packing Criteria in Enumeration of Allowed Sequences for Different Structural Classes. Journal of Molecular Bio 193 775-791. 

It affects the metabolisms of glucose and proteins used in rheumatoid arthritis, inflammatory conditions, etc. 

Most potential energy surfaces are extremely complex. Fiber and Karplus analyzed a 300 psec molecular dynamics trajectory of the protein myoglobin. They estimate that 2000 thermally accessible minima exist near the native protein structure. The total number of conformations is even larger. Dill derived a formula to calculate the upper bound of thermally accessible conformations in a protein. Using this formula, a protein of 150 residues (the approx-... 

Most molecular dynamics simulations, and particularly those for proteins, use constant temperature conditions. 

Eor larger molecules, such as proteins, use a switching function to dramatically decrease computing time. 

In the United States, more than 16.3 x 10 kg of human-inedible raw materials are available each year, and the rendering industry is a valuable asset in diverting these into valuable ingredients for use primarily in animal foods (4). The three largest meat packers are responsible for nearly four-fifths of aU red meat production (5) and enormous amounts of rendered meat meal and animal fat. Three broiler producers account for about 40% of the total broiler production. American Proteins, Inc. (RosweU, Georgia), the world s largest processor of poultry by-products, produces more than 450,000 t of poultry meal, feather meal, and poultry fat each year. It also produces more than 100,000 t of fish meal, fish oil, and fish products each year. Pish meal production worldwide in 1986 was estimated at 6.23 x 10 t, which with the 125 x 10 t of meat and bone meal plus 6.67 x 10 t of feather meal and poultry by-product meal (6) is the primary source of animal proteins used by the pet food industry. 

Conversion of Biomass for Fuels. Many predictions for protein uses in the 1970s have already been flilfilled (36). Biomass is being used for fuel, for example (see Fuels frombiomass). Many predictions were again made in 1995 (37). 

To date, a number of simulation studies have been performed on nucleic acids and proteins using both AMBER and CHARMM. A direct comparison of crystal simulations of bovine pancreatic trypsin inliibitor show that the two force fields behave similarly, although differences in solvent-protein interactions are evident [24]. Side-by-side tests have also been performed on a DNA duplex, showing both force fields to be in reasonable agreement with experiment although significant, and different, problems were evident in both cases [25]. It should be noted that as of the writing of this chapter revised versions of both the AMBER and CHARMM nucleic acid force fields had become available. Several simulations of membranes have been performed with the CHARMM force field for both saturated [26] and unsaturated [27] lipids. The availability of both protein and nucleic acid parameters in AMBER and CHARMM allows for protein-nucleic acid complexes to be studied with both force fields (see Chapter 20), whereas protein-lipid (see Chapter 21) and DNA-lipid simulations can also be performed with CHARMM. 

C Wilson, LM Gregoret, DA Agard. Modeling side-chain conformation for homologous proteins using an energy-based rotamer search. J Mol Biol 229 996-1006, 1993. 

AR Ortiz, A Kolinski, J Skolnick. Fold assembly of small proteins using Monte Carlo simulations driven by restraints derived from multiple sequence alignments. J Mol Biol 277 419-448, 1998. 

C Bystroff, D Baker. Prediction of local structure m proteins using a library of sequence-structure motifs. J Mol Biol 281 565-577, 1998. 

N Qian, TJ Sejnowski. Predicting the secondary structure of globular proteins using neural network models. J Mol Biol 202 865-884, 1988. 

JW Ponder, FM Richards. Tertiary templates for proteins Use of packing criteria m the enumeration of allowed sequences for different structural classes. J Mol Biol 193 775-792, 1987. 

Molecular mechanics and electrostatics calculations have both played an important role in studying electron transfer proteins. Molecular mechanics calculations of these proteins use the same techniques (molecular dynamics, energy minimization) as for other proteins, although special consideration must be made in simulation conditions. 

Proteins differ from the other polymers we have discussed in that they may contain up to 20 different monomer units. This means that there are a huge number of possible proteins. Using the amino acids listed in Table 23.3, we could make... 

Deschamps, J. R., Miller, C. E., and Ward, K. B. (1995). Rapid purification of recombinant green fluorescent protein using the hydrophobic properties of an HPLC size-exclusion column. Protein Expression and Purification 6 555-558. 

The list of MoAb or fusion proteins used in treatment of every type of cancer is continually growing as research identifies more cancer-associated antigens. MoAb targeting a tumor-specific antigen is used... 

Computationally deriving a 3D molecular structure of a given protein using a sequence overlay with a related protein of known structure. 

Wallraff, E., Schleicher, M., Modersitzki. M Reiger, D., Isenberg, G., Gerish, G. (1986). Selection of Dictyostelium mutants defective in cytoskeletal protein Use of an antibody that binds to the ends of alpha-actinin rods. EMBO J. 5,61-67. 

Determination of the Amino Acid Sequence of a Novel Protein Using LC-MS Data from an Enzyme Digest 160... 

Figure 5.6 Positive-ion electrospray spectrum obtained from the major component in the LC-MS analysis of a purified recombinant 62 kDa protein using a Cig microbore 50 X 1 mm column and a flow rate of 50 p.lmin . The starting buffer (buffer A ) was 0.1% TEA in water, while the gradient buffer (buffer B ) consisted of 0.1% TEA in acetonitrile-water (9 1 vol/vol). The running conditions consisted of 0% B for 5 min, followed by a linear gradient of 100% B for 55 min. Reprinted from J. Chromatogr., B, 685, McAtee, C. P., Zhang, Y., Yarbough, P. O., Fuerst, T. R., Stone, K. L., Samander, S. and Williams, K. R., Purification and characterization of a recombinant hepatitis E protein vaccine candidate by liquid chromatography-mass spectrometry , 91-104, Copyright (1996), with permission from Elsevier Science.

Attempts were then made, using these data, to identify the proteins by searching against known peptide databases, such as ProFound [14], PepSea [15] and MSFit [16] that contain the molecular weights of theoretically expected polypeptides obtained from a known protein using a specific enzyme. The molecular weights... 

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