scholarly journals Flowering Buds of Globular Proteins: Transpiring Simplicity of Protein Organization

2002 ◽  
Vol 3 (6) ◽  
pp. 525-534 ◽  
Author(s):  
Igor N. Berezovsky ◽  
Edward N. Trifonov
Keyword(s):  
Protein Evolution ◽  
Closed Loop ◽  
Globular Proteins ◽  
Polymer Physics ◽  
Basic Unit ◽  
Amino Acid Residues ◽  
Sequence Motifs ◽  
Closed Loops ◽  
Physical Necessity ◽  
Functional Complexity

Structural and functional complexity of proteins is dramatically reduced to a simple linear picture when the laws of polymer physics are considered. A basic unit of the protein structure is a nearly standard closed loop of 25–35 amino acid residues, and every globular protein is built of consecutively connected closed loops. The physical necessity of the closed loops had been apparently imposed on the early stages of protein evolution. Indeed, the most frequent prototype sequence motifs in prokaryotic proteins have the same sequence size, and their high match representatives are found as closed loops in crystallized proteins. Thus, the linear organization of the closed loop elements is a quintessence of protein evolution, structure and folding.

scholarly journals Identification and Analysis of Novel Amino-Acid Sequence Repeats inBacillus anthracisstr.AmesProteome Using Computational Tools

2007 ◽  
Vol 2007 ◽  
pp. 1-23 ◽  
Author(s):  
G. R. Hemalatha ◽  
D. Satyanarayana Rao ◽  
L. Guruprasad
Keyword(s):  
Amino Acid ◽  
Amino Acid Residue ◽  
Protein Sequence ◽  
Amino Acid Residues ◽  
Sequence Motifs ◽  
Computational Tools ◽  
Conserved Sequence ◽  
Conserved Sequence Motifs ◽  
Multiple Copies ◽  
Domain 3

We have identified four repeats and ten domains that are novel in proteins encoded by theBacillus anthracisstr.Amesproteome using automated in silico methods. A “repeat” corresponds to a region comprising less than 55-amino-acid residues that occur more than once in the protein sequence and sometimes present in tandem. A “domain” corresponds to a conserved region with greater than 55-amino-acid residues and may be present as single or multiple copies in the protein sequence. These correspond to (1) 57-amino-acid-residue PxV domain, (2) 122-amino-acid-residue FxF domain, (3) 111-amino-acid-residue YEFF domain, (4) 109-amino-acid-residue IMxxH domain, (5) 103-amino-acid-residue VxxT domain, (6) 84-amino-acid-residue ExW domain, (7) 104-amino-acid-residue NTGFIG domain, (8) 36-amino-acid-residue NxGK repeat, (9) 95-amino-acid-residue VYV domain, (10) 75-amino-acid-residue KEWE domain, (11) 59-amino-acid-residue AFL domain, (12) 53-amino-acid-residue RIDVK repeat, (13) (a) 41-amino-acid-residue AGQF repeat and (b) 42-amino-acid-residue GSAL repeat. A repeat or domain type is characterized by specific conserved sequence motifs. We discuss the presence of these repeats and domains in proteins from other genomes and their probable secondary structure.

THE GEOMETRIC PHASE AND THE SCHWINGER TERM IN SOME MODELS

1992 ◽  
Vol 07 (21) ◽  
pp. 5045-5083 ◽  
Author(s):  
H. GROSSE ◽  
E. LANGMANN
Keyword(s):  
Parameter Space ◽  
Geometric Phase ◽  
Closed Loop ◽  
Parallel Transport ◽  
Quantum Mechanical System ◽  
Second Quantization ◽  
Closed Loops ◽  
Gauge Transformations ◽  
Canonical Anticommutation Relations ◽  
Inequivalent Representations

We discuss the quantization of fermions interacting with external fields and observe the occurrence of equivalent as well as inequivalent representations of the canonical anticommutation relations. Implementability of gauge and axial gauge transformations leads to generators which fulfil an algebra of current with a Schwinger term. This term can be written as a cocycle and leads to the boson-fermion correspondence. Transport of a quantum-mechanical system along a closed loop of parameter space may yield a geometric phase. We discuss models for which nonintegrable phase factors are obtained from the adiabatic parallel transport. After second quantization, one obtains, in addition, a Schwinger term. Depending on the type of transformation, a subtle relationship between these two obstructions can occur. We indicate finally how we may transport density matrices along closed loops in parameter space.

scholarly journals Insights into the quaternary association of proteins through structure graphs: a case study of lectins

2005 ◽  
Vol 391 (1) ◽  
pp. 1-15 ◽  
Author(s):  
K. V. Brinda ◽  
Avadhesha Surolia ◽  
Sarawathi Vishveshwara
Keyword(s):  
Amino Acid ◽  
Protein Structures ◽  
Present Review ◽  
Dimensional Structure ◽  
Protein Oligomerization ◽  
Amino Acid Residues ◽  
Sequence Motifs ◽  
Structural Determinants ◽  
Legume Lectin ◽  
Quaternary Structures

The unique three-dimensional structure of both monomeric and oligomeric proteins is encoded in their sequence. The biological functions of proteins are dependent on their tertiary and quaternary structures, and hence it is important to understand the determinants of quaternary association in proteins. Although a large number of investigations have been carried out in this direction, the underlying principles of protein oligomerization are yet to be completely understood. Recently, new insights into this problem have been gained from the analysis of structure graphs of proteins belonging to the legume lectin family. The legume lectins are an interesting family of proteins with very similar tertiary structures but varied quaternary structures. Hence they have become a very good model with which to analyse the role of primary structures in determining the modes of quaternary association. The present review summarizes the results of a legume lectin study as well as those obtained from a similar analysis carried out here on the animal lectins, namely galectins, pentraxins, calnexin, calreticulin and rhesus rotavirus Vp4 sialic-acid-binding domain. The lectin structure graphs have been used to obtain clusters of non-covalently interacting amino acid residues at the intersubunit interfaces. The present study, performed along with traditional sequence alignment methods, has provided the signature sequence motifs for different kinds of quaternary association seen in lectins. Furthermore, the network representation of the lectin oligomers has enabled us to detect the residues which make extensive interactions (‘hubs’) across the oligomeric interfaces that can be targetted for interface-destabilizing mutations. The present review also provides an overview of the methodology involved in representing oligomeric protein structures as connected networks of amino acid residues. Further, it illustrates the potential of such a representation in elucidating the structural determinants of protein–protein association in general and will be of significance to protein chemists and structural biologists.

scholarly journals The cyclol hypothesis and the “globular” proteins

1937 ◽  
Vol 161 (907) ◽  
pp. 505-524 ◽  
Keyword(s):  
Amino Acid ◽  
Hydrogen Bonds ◽  
Ad Hoc ◽  
Globular Proteins ◽  
The Body ◽  
Amino Acid Residues ◽  
Native Protein ◽  
Orderly Arrangement

A number of facts relating to proteins suggest that the polypeptides in native protein are in a folded state (Astbury 1933, 1934; Astbury and Street 1930, 1931; Pryde 1931; Wrinch 1936 a , b , c , 1937 a ; Langmuir, Schaefer and Wrinch 1937). The type of folding must be such as to imply the possibility of the regular and orderly arrangement of hundreds 01 amino-acid residues which to some extent at least is independent of the particular residues in question. We propose therefore to formulate all types of folding which are geometrically possible. Each hypothesis in turn can then be tested in two ways. We may consider its plausibility in itself: and having developed its implications to the farthest possible point, we may test it against known facts by ad hoc experiments. At present two types of folding have been suggested—by means of cyclol links (Wrinch 1936 a , b , c , 1937 a ; Langmuir, Schaefer and Wrinch 1937; Astbury 1936 a , b , c ; Frank, 1936) and by means of hydrogen bonds (Jordan Lloyd 1932; Jordan Lloyd and Marriott 1933; Mirsky and Pauling 1936; Wrinch and Jordan Lloyd 1936). The search for other types of folding is being continued. So far it has not proved possible to discard either theory on the grounds that the type of link postulated is out of the question. It is there­ fore very desirable to test these theories by means of their implications. Accordingly, on this occasion we consider (Wrinch 1937 b , c ) whether the cyclol theory can stand the test of the body of facts relating to the “globular” proteins, established by Svedberg and his collaborators (Svedberg and others 1929, 1930 a , b , 1934 a , b , 1935).

Constraint Wrench Formulation for Closed-Loop Systems Using Two-Level Recursions

2007 ◽  
Vol 129 (12) ◽  
pp. 1234-1242 ◽  
Author(s):  
Himanshu Chaudhary ◽  
Subir Kumar Saha
Keyword(s):  
Lagrange Multipliers ◽  
Spanning Tree ◽  
Closed Loop ◽  
Equations Of Motion ◽  
Constraint Forces ◽  
Minimal Set ◽  
Closed Loops ◽  
Closed Loop Systems ◽  
Subsystem Level ◽  
Body Level

In order to compute the constraint moments and forces, together referred here as wrenches, in closed-loop mechanical systems, it is necessary to formulate a dynamics problem in a suitable manner so that the wrenches can be computed efficiently. A new constraint wrench formulation for closed-loop systems is presented in this paper using two-level recursions, namely, subsystem level and body level. A subsystem is referred here as the serial- or tree-type branches of a spanning tree obtained by cutting the appropriate joints of the closed loops of the system at hand. For each subsystem, unconstrained Newton–Euler equations of motion are systematically reduced to a minimal set in terms of the Lagrange multipliers representing the constraint wrenches at the cut joints and the driving torques/forces provided by the actuators. The set of unknown Lagrange multipliers and the driving torques/forces associated to all subsystems are solved in a recursive fashion using the concepts of a determinate subsystem. Next, the constraint forces and moments at the uncut joints of each subsystem are calculated recursively from one body to another. Effectiveness of the proposed algorithm is illustrated using a multiloop planar carpet scraping machine and the spatial RSSR (where R and S stand for revolute and spherical, respectively) mechanism.

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