IN SEARCH OF THE PROTEIN NATIVE STATE WITH A PROBABILISTIC SAMPLING APPROACH

2011 ◽  
Vol 09 (03) ◽  
pp. 383-398 ◽  
Author(s):  
BRIAN OLSON ◽  
KEVIN MOLLOY ◽  
AMARDA SHEHU
Keyword(s):  
Structure Prediction ◽  
Computational Models ◽  
Three Dimensional ◽  
Structural Diversity ◽  
Search Space ◽  
Conformational Space ◽  
Conformational Search ◽  
Dimensional Structure ◽  
Computational Techniques ◽  
Native State

The three-dimensional structure of a protein is a key determinant of its biological function. Given the cost and time required to acquire this structure through experimental means, computational models are necessary to complement wet-lab efforts. Many computational techniques exist for navigating the high-dimensional protein conformational search space, which is explored for low-energy conformations that comprise a protein's native states. This work proposes two strategies to enhance the sampling of conformations near the native state. An enhanced fragment library with greater structural diversity is used to expand the search space in the context of fragment-based assembly. To manage the increased complexity of the search space, only a representative subset of the sampled conformations is retained to further guide the search towards the native state. Our results make the case that these two strategies greatly enhance the sampling of the conformational space near the native state. A detailed comparative analysis shows that our approach performs as well as state-of-the-art ab initio structure prediction protocols.

scholarly journals RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction

RNA ◽  
2012 ◽  
Vol 18 (4) ◽  
pp. 610-625 ◽  
Author(s):  
J. A. Cruz ◽  
M.-F. Blanchet ◽  
M. Boniecki ◽  
J. M. Bujnicki ◽  
S.-J. Chen ◽  
...  
Keyword(s):  
Structure Prediction ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Three Dimensional Structure

scholarly journals Analysis of structural similarities between brain Thy-1 antigen and immunoglobulin domains. Evidence for an evolutionary relationship and a hypothesis for its functional significance

1981 ◽  
Vol 195 (1) ◽  
pp. 31-40 ◽  
Author(s):  
F E Cohen ◽  
J Novotný ◽  
M J E Sternberg ◽  
D G Campbell ◽  
A F Williams
Keyword(s):  
Functional Significance ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Three Dimensional ◽  
Evolutionary Relationship ◽  
Dimensional Structure ◽  
Sequence Homologies ◽  
Beta Structure ◽  
Beta 2 Microglobulin

The Thy-1 membrane glycoprotein from rat brain is shown to have structural and sequence homologies with immunoglobulin (Ig) domains on the basis of the following evidence. 1. The two disulphide bonds of Thy-1 are both consistent with the Ig-fold. 2. The molecule contains extensive beta-structure as shown by the c.d. spectrum. 3. Secondary structure prediction locates beta-strands along the sequence in a manner consistent with the Ig-fold. 4. On the basis of rules derived from known beta-sheet structures, a three-dimensional structure with the Ig-fold is predicted as favourable for Thy-1. 5. Sequences in the proposed beta-strands of Thy-1 and known beta-strands of Ig domains show significant sequence homology. This homology is statistically more significant than for the comparison of proposed beta-strand sequences of beta 2-microglobulin with Ig domains. An hypothesis is presented for the possible functional significance of an evolutionary relationship between Thy-1 and Ig. It is suggested that both Thy-1 and Ig evolved from primitive molecules, with an Ig fold, which mediated cell--cell interactions. The present-day role of Thy-1 may be similar to that of the primitive domain.

scholarly journals Protein Folding: Search for Basic Physical Models

2003 ◽  
Vol 3 ◽  
pp. 623-635 ◽  
Author(s):  
Ivan Y. Torshin ◽  
Robert W. Harrison
Keyword(s):  
Protein Folding ◽  
Tertiary Structure ◽  
Three Dimensional ◽  
Physical Models ◽  
Dimensional Structure ◽  
Computational Techniques ◽  
Linear Sequence ◽  
Physical Forces

How a unique three-dimensional structure is rapidly formed from the linear sequence of a polypeptide is one of the important questions in contemporary science. Apart from biological context ofin vivoprotein folding (which has been studied only for a few proteins), the roles of the fundamental physical forces in thein vitrofolding remain largely unstudied. Despite a degree of success in using descriptions based on statistical and/or thermodynamic approaches, few of the current models explicitly include more basic physical forces (such as electrostatics and Van Der Waals forces). Moreover, the present-day models rarely take into account that the protein folding is, essentially, a rapid process that produces a highly specific architecture. This review considers several physical models that may provide more direct links between sequence and tertiary structure in terms of the physical forces. In particular, elaboration of such simple models is likely to produce extremely effective computational techniques with value for modern genomics.

Prediction of Structural and Functional Aspects of Protein

2014 ◽  
pp. 317-333
Author(s):  
Arun G. Ingale
Keyword(s):  
Protein Structure ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Protein Structures ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Sequence Information ◽  
Predict Protein Structure ◽  
Basic Ideas

To predict the structure of protein from a primary amino acid sequence is computationally difficult. An investigation of the methods and algorithms used to predict protein structure and a thorough knowledge of the function and structure of proteins are critical for the advancement of biology and the life sciences as well as the development of better drugs, higher-yield crops, and even synthetic bio-fuels. To that end, this chapter sheds light on the methods used for protein structure prediction. This chapter covers the applications of modeled protein structures and unravels the relationship between pure sequence information and three-dimensional structure, which continues to be one of the greatest challenges in molecular biology. With this resource, it presents an all-encompassing examination of the problems, methods, tools, servers, databases, and applications of protein structure prediction, giving unique insight into the future applications of the modeled protein structures. In this chapter, current protein structure prediction methods are reviewed for a milieu on structure prediction, the prediction of structural fundamentals, tertiary structure prediction, and functional imminent. The basic ideas and advances of these directions are discussed in detail.

scholarly journals Molecular Cloning, Modeling, and Characterization of Type 2 Metallothionein from Plantago ovata Forsk

Sequencing ◽  
2013 ◽  
Vol 2013 ◽  
pp. 1-10 ◽  
Author(s):  
Amitava Moulick ◽  
Debashis Mukhopadhyay ◽  
Shonima Talapatra ◽  
Nirmalya Ghoshal ◽  
Sarmistha Sen Raychaudhuri
Keyword(s):  
Molecular Cloning ◽  
Structure Prediction ◽  
3D Structure ◽  
Three Dimensional ◽  
Transcript Level ◽  
Copper Stress ◽  
Dimensional Structure ◽  
Functional Study ◽  
Plantago Ovata

Plantago ovata Forsk is a medicinally important plant. Metallothioneins are cysteine rich proteins involved in the detoxification of heavy metals. Molecular cloning and modeling of MT from P. ovata is not reported yet. The present investigation will describe the isolation, structure prediction, characterization, and expression under copper stress of type 2 metallothionein (MT2) from this species. The gene of the protein comprises three exons and two introns. The deduced protein sequence contains 81 amino acids with a calculated molecular weight of about 8.1 kDa and a theoretical pI value of 4.77. The transcript level of this protein was increased in response to copper stress. Homology modeling was used to construct a three-dimensional structure of P. ovata MT2. The 3D structure model of P. ovata MT2 will provide a significant clue for further structural and functional study of this protein.

scholarly journals Structural diversity induced by ligand geometry: From two-dimensional to three-dimensional coordination polymers with pyridine

2020 ◽  
pp. 174751982096816
Author(s):  
Fang-Kuo Wang ◽  
Shi-Yao Yang ◽  
Hua-Ze Dong
Keyword(s):  
Coordination Polymers ◽  
Three Dimensional ◽  
Structural Diversity ◽  
Dimensional Structure ◽  
Layer By Layer ◽  
Two Dimensional ◽  
Guest Molecules ◽  
X Ray ◽  
Benzenedicarboxylic Acid ◽  
Benzenetricarboxylic Acid

Two coordination polymers with two-dimensional and three-dimensional structures are, {[Zn3(bdc)3(py)2]·2NMP}n (1) (H2bdc = 1,4-benzenedicarboxylic acid) and [Zn2(NO3−)(btc)(nmp)2(py)]n (2) (H3btc = 1,3,5-benzenetricarboxylic acid), synthesized by hot-solution reactions of Zn(NO3)2·6H2O, pyridine (py) and two different ligands in N-methylpyrrolidone (NMP). {[Zn3(bdc)3(py)2]·2NMP}n exhibits two-dimensional networks with trizinc subunits [Zn3(COO)6py2] stacking with a layer-by-layer alignment, and there are strong π–π interactions involving py from adjacent layers. [Zn2(NO3−)(btc)(nmp)2(py)]n has a three-dimensional structure containing two independent zinc ions, tetrahedral ZnO4 and octahedral ZnNO5. Based on X-ray studies, the coordination polymers {[Zn3(bdc)3(py)2]·2NMP}n (1) have a porous structure with NMP guest molecules. In contrast, X-ray studies revealed that coordination polymer [Zn2(NO3−)(btc)(nmp)2(py)]n (2) had a larger void that was inhabited by coordinated py and NMP. In addition, the form of the two coordination polymers changed from two-dimensional to three-dimensional with transformation of the ligand geometry.

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