Protein architecture

Lesk, A. Protein Architecture A Practical Approach. Oxford, UK Oxford University Press, 1991. 

Einkelstein AV, Badretdinov A, Gutin AM. Why do protein architectures have Boltzmann-like statistics Proteins 1995 23 142-50. 

The essential distinction between the approaches used to formulate and evaluate proteins, compared with conventional low molecular weight drugs, lies in the need to maintain several levels of protein structure and the unique chemical and physical properties that these higher-order structures convey. Proteins are condensation polymers of amino acids, joined by peptide bonds. The levels of protein architecture are typically described in terms of the four orders of structure [23,24] depicted in Fig. 2. The primary structure refers to the sequence of amino acids and the location of any disulfide bonds. Secondary structure is derived from the steric relations of amino acid residues that are close to one another. The alpha-helix and beta-pleated sheet are examples of periodic secondary structure. Tertiary... 

Lesk AM, (2001) Introduction to protein architecture the structural biology of proteins,Oxford... 

Kauffmann, S. (1995). At Home in the Universe. Oxford University Press, New York Lesk, A.M. (1991). Protein Architecture. IRL Press, Oxford... 

Y. Lvov, in Protein Architecture Interfacing Molecular Assemblies and Immobilization Biotechnology (Y. Lvov and H. Mohwald, eds), p. 125. Marcel Dekker, New York (2000). 

Entities resulting from self-assembly and self-organization of a number of components may undergo self-correction and adaptation. This might also explain why large multisite protein architectures are formed by the association of several smaller protein subunits rather than from a single long polypeptide. 

Considering the multitude of ubiquitin domains and their cognate recognition modules, the next question to address is how cells make use of these building blocks to form the highly complex ubiquitination system. Before starting with the discussion of some prominent modular protein architectures, we should bear in mind that there are a number of other functional domains participating in this... 

Significant advances have been made in the preparation of discrete macromolecules that include both coenzyme function and a defined polypeptide or protein architecture. Preliminary, but promising, functional studies have been carried out and assay methods developed. While in many cases rather modest effects have been observed, what is significant is that the methodology exists to prepare, characterize, and study defined macromolecular constructs. With new information becoming available on co enzyme-dependent protein catalysts from structural biology and mechanistic enzymology, it should be possible to more fully exploit the remarkable breadth of coenzyme reactivity in tailored synthetic systems. 

Bustin, M. and Reeves, R. (1996) High mobility group chromosomal proteins architectural components that facilitate chromatin function. Progr. Nucl. Acid Res. Mol. Biol. 54, 35-100. 

Crasser, K.D. (1998) HMGl and HU proteins architectural elements in plant chromatin. Trends Plant Sci. 3, 260-265. 

Muller, S., Scaffidi, P., Degryse, B., Bonaldi, T., Ronfani, L., Agresti, A., Beltrame, M. and Bianchi, M.E. (2001) The double life of HMGBl chromatin protein architectural factor and extracellular signal. EMBO J. 20, 4337-4340. 

Since the primary structure of a peptide determines the global fold of any protein, the amino acid sequence of a heme protein not only provides the ligands, but also establishes the heme environmental factors such as solvent and ion accessibility and local dielectric. The prevalent secondary structure element found in heme protein architectures is the a-helix however, it should be noted that p-sheet heme proteins are also known, such as the nitrophorin from Rhodnius prolixus (71) and flavocytochrome cellobiose dehydrogenase from Phanerochaete chrys-osporium (72). However, for the purpose of this review, we focus on the structures of cytochromes 6562 (73) and c (74) shown in Fig. 2, which are four-a-helix bundle protein architectures and lend themselves as resource structures for the development of de novo designs. 

As a first step toward the construction of three-dimensional protein architectures, formation of an avidin monolayer and an avidin plus enzyme double layer was studied. The adsorption behavior of avidin and biotin-labeled enzymes onto a Pt electrode was monitored by means of QCM. Figure 11 illustrates the frequency changes induced by the adsorption of the avidin first layer and the next layer of... 

Protein Architecture—a Helix Pauling and Corey Were aware of the importance of hydrogen bonds in orient-... 

Protein Architecture—Tertiary Structure of Fibrous Proteins... 

Protein Architecture—Tertiary Structure of Large Globular Proteins For the beginning student, the very complex tertiary structures of globular proteins much larger than those shown in Figure 4-18 are best approached by fo-... 

Pan P., Woehl, E., Dunn, M.F. (1997) Protein architecture, dynamics and allostery in tryptophan synthase channeling. Trends Biochem, Sci, 22, 22-27. 

The previous chapter described the types of secondary and tertiary structures that are the bricks-and-mortar of protein architecture. By arranging these fundamental structural elements in different combinations, widely diverse proteins can be constructed that are capable of various specialized functions. This chapter examines the relationship between structure and function for the clinically important globular hemeproteins. Fibrous structural proteins are discussed in Chapter 4. 

Lesk, A M Introduction to Protein Architecture The Structural Biology of Protein, Oxford University Press, Inc., New York, NY. 2000. 

Another very important factor in protein architecture is the disulfide —S—S— link. Remote parts of the polypeptide chain can be held close together through the oxidative coupling of two cysteine thiol groups to form a disulfide bridge ... 

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