Biomacromolecules residues

Alternatively, one interesting drug delivery technique exploits the active transport of certain naturally-occurring and relatively small biomacromolecules across the cellular membrane. For instance, the nuclear transcription activator protein (Tat) from HIV type 1 (HlV-1) is a 101-amino acid protein that must interact with a 59-base RNA stem-loop structure, called the traus-activation region (Tar) at the 5 end of all nascent HlV-1 mRNA molecules, in order for the vims to replicate. HIV-Tat is actively transported across the cell membrane, and localizes to the nucleus [28]. It has been found that the arginine-rich Tar-binding region of the Tat protein, residues 49-57 (Tat+9 57), is primarily responsible for this translocation activity [29]. 

Asakura, T., Ohgo, K., Ishida, T., Taddei, P., Monti, P., and Kishore, R. (2005). Possible implications of serine and tyrosine residues and intermolecular interactions on the appearance of silk I structure of Bombyx mod silk fibroin-derived synthetic peptides High-resolution 13C cross-polarization/magic-angle spinning NMR study. Biomacromolecules 6, 468-474. 

Stjemdahl A, Wistrand AF, Albertsson A-C (2007) Industrial utilization of tin-initiated resorbable polymers synthesis on a large scale with a low amount of initiator residue. Biomacromolecules 8 937-940... 

From a software point of view, it is desirable to have a well-structured hierarchical description for the different biomacromolecules in the simulation system. Such a hierarchy should provide data structures and access functions on the atomic, residue, molecule, and system levels. This allows routines for the evaluation of energy terms to be set up at the level of residue pairs. Experience [14] suggests that this setup is advantageous since it provides a route to easily and intuitively implement the computational algorithms sketched below. 

Fujita K, Macfarlane DR, Forsyth M et al (2007) Solubility and stability of cytochrome c in hydrated ionic liquids effect of oxo acid residues and kosmotropicity. Biomacromolecules 8 2080-2086... 

Ma JH, Goldberg GI, Tjandra N (2008) Weak alignment of biomacromolecules in collagen gels an alternative way to yield residual dipolar couplings for NMR measurements. J Am Chem Soc 130(48) 16148... 

Tertiary structure (3° stracture) describes the global three-dimensional fold or topology of the macromolecule, relating the positions of each atom and residue in three-dimensional space. For biomacromolecules with a single subunit, the functional tertiary structure is its native structure. Thus the tertiary stracture includes a description not only of local symmetric stracture (2° stracture) but also of the spatial location of all residues as possible. 

In the noncooperative model (Figure 9.1), the biomacromolecule converts stepwise from a to b, with an increase in the fraction of b with each transition. Each step j represents a different state j with wy being the statistical weight in which j also represents the total number of residues in b conformation with the probability, s = [h]/[a]. There are N unique combinations, i.e. degeneracy with a single residue b for a chain of N residues, therefore wi = Ns and Wy = gys. The general form of the partition function for N number of residues is the polynomial expression ... 

Therefore rms displacement is dependent on N , i.e. the square root of the number of residues in a biomacromolecular chain. These relationships derived in a one-dimensional random walk can be extended to two and three dimensions, and thus are applicable to the description of the properties of the tertiary structures of biomacromolecules. The rms displacement describes the average absolute distance between the first and the last residues of a macromolecular chain. This is defined as the rms end-to-end distance that... 

The knowledge based structural prediction (Blundell et al, 1987) depends on analogies between a biomacromolecule of known sequence and other biomacromolecules of the same class with known 3D structure at all levels in the hierarchy of biomacromolecular organization. In the numerically based statistical methods, the structural rules and parameters (conformational propensities) for each residue are extracted by statistical analyses of the structural database and used to predict the structure along the sequence of the macromolecule. Examples of the statistical methods that are commonly applied to predict secondary structure and folding preference of proteins will be illustrated. 

Amino acid analogs with a reactive functionality afford cross-linking between the selected (mutated) residue and the adjacent residues. Such study may be used to infer topologies inter- and intra-molecularly within the mutant protein or between the interacting biomacromolecules. 

J. Rieger, H. Freichels, A. Imberty, J.-L. Putaux, T. Delair, C. Jerome, and R. Auzely-Velty, Polyester nanoparticles presenting mannose residues Toward the development of new vaccine dehvery systems combining biodegradability and targeting properties, Biomacromolecules, 10 (2009) 651-657. 

FIGURE 54.3 Introduction of thiol groups into the lysine residues of PEG-PLL. (Reprinted with permission from Biomacromolecules, 2(2), Kakizawa, Y., Harada, A., and Kataoka, K., Glutathione-sensitive stabilization of block copolymer micelles composed of antisense DNA and thiolated poly(ethylene glycol)-block-poly(l-lysine) A potential carrier for systemic delivery of antisense DNA, 491. Copyright 2001 American Chemical Society.)... 

Leontidis E, Aroti A, Belloni L (2009) Liquid expanded monolayers of lipids as model systems to understand the anionic Hofmeister series 1. A tale of model. J Phys Chem B 113 1447-1459 Levitsky VY, Panova AA, Mozhaev VV (1994) Correlation of high-temperamre stability of a-chymotrypsin with salting-in properties of solution. Eur J Biochem 219 231-236 Lipkind GM, Fozzard HA (2008) Voltage-gated Na channel selectivity the role of the conserved domain III lysine residue. J Gen Physiol 131 523-529 Lo Nostro P Fratoni L, Ninham BW, Baglioni P (2002) Water absorbency by wool fibers Hofmeister effect. Biomacromolecules 3 1217-1224... 

Tsuji, H. and Ikarash, K. (2004) In vitro hydrolysis of poly(L-lactide) crystalline residues as extended-chain crystalhtes II. Effects of hydrolysis temperature. Biomacromolecules, 5, 1021-1028. 

T. Izdebski, P. Akhenblit, J.E. Jenkins, J.L. Yarger, G.P. Holland, Structure and dynamics of aromatic residues in spider sHk 2D carbon correlation NMR of dragline fibers. Biomacromolecules 11 (2010) 168-174. 

The adsorption of dh nucleic acids at the mercury electrodes from neutral and acid media is somewhat more complex due to the protonation of bases at the interface. The protonation of base residues in dh nucleic acids results in the surface conformational alternation in this biomacromolecule adsorbed at the mercury electrode polarized to a broad range of potentials around the p.z.c.. This conformational change leads to a more extensive participation of base residues in the adsorption of dh nucleic acids at the mercury electrodes even at short times of the contact of the biomacromolecules with the electrode [110]. 

Salvatore D, Duraffourg N, Favier A et al (2011) Investigation at residue level of the early steps during the assembly of two proteins into supramolecular objects. Biomacromolecules 12(6) 2200-2210... 

---