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You searched for +publisher:"Georgia Tech" +contributor:("Stephen Harvey"). Showing records 1 – 3 of 3 total matches.

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1. Pan, Minmin. RNA secondary sturcture prediction using a combined method of thermodynamics and kinetics.

Degree: MS, Biology, 2011, Georgia Tech

Nowadays, RNA is extensively acknowledged an important role in the functions of information transfer, structural components, gene regulation and etc. The secondary structure of RNA becomes a key to understand structure-function relationship. Computational prediction of RNA secondary structure does not only provide possible structures, but also elucidates the mechanism of RNA folding. Conventional prediction programs are either derived from evolutionary perspective, or aimed to achieve minimum free energy. In vivo, RNA folds during transcription, which indicates that native RNA structure is a result from both thermodynamics and kinetics. In this thesis, I first reviewed the current leading kinetic folding programs and demonstrate that these programs are not able to predict secondary structure accurately. Upon that, I proposed a new sequential folding program called GTkinetics. Given an RNA sequence, GTkinetics predicts a secondary structure and a series of RNA folding trajectories. It treats the RNA as a growing chain, and adds stable local structures sequentially. It is featured with a Z-score to evaluate stability of local structures, which is able to locate native local structures with high confidence. Since all stable local structures are captured in GTkinetics, it results in some false positives, which prevents the native structure to form as the chain grows. This suggests a refolding model to melt the false positive hairpins, probable intermediate structures, and to fold the RNA into a new structure with reliable long-range helices. By analyzing suboptimal ensemble along the folding pathway, I suggested a refolding mechanism, with which refolding can be evaluated whether or not to take place. Another way to favor local structures over long-distance structures, we introduced a distance penalty function into the free energy calculation. I used a sigmoidal function to compute the energy penalty according to the distance in the primary sequence between two nucleotides of a base pair. For both the training dataset and the test dataset, the distance function improves the prediction to some extent. In order to characterize the differences between local and long-range helices, I carried out analysis of standardized local nucleotide composition and base pair composition according to the two groups. The results show that adenine accumulates on the 5' side of local structure, but not on that of long-range helices. GU base pairs occur significantly more frequent in the local helices than that in the long-range helices. These indicate that the mechanisms to form local and long range helices are different, which is encoded in the sequence itself. Based on all the results, I will draw conclusions and suggest future directions to enhance the current sequential folding program. Advisors/Committee Members: Stephen Harvey (Committee Chair), Heitsch, Christine (Committee Member), Hud, Nick (Committee Member), Wartell, Roger (Committee Member), Weitz, Joshua (Committee Member).

Subjects/Keywords: MFE; RNA secondary structure prediction; Kinetics; Molecules; Genetic transcription

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APA (6th Edition):

Pan, M. (2011). RNA secondary sturcture prediction using a combined method of thermodynamics and kinetics. (Masters Thesis). Georgia Tech. Retrieved from http://hdl.handle.net/1853/44891

Chicago Manual of Style (16th Edition):

Pan, Minmin. “RNA secondary sturcture prediction using a combined method of thermodynamics and kinetics.” 2011. Masters Thesis, Georgia Tech. Accessed January 18, 2021. http://hdl.handle.net/1853/44891.

MLA Handbook (7th Edition):

Pan, Minmin. “RNA secondary sturcture prediction using a combined method of thermodynamics and kinetics.” 2011. Web. 18 Jan 2021.

Vancouver:

Pan M. RNA secondary sturcture prediction using a combined method of thermodynamics and kinetics. [Internet] [Masters thesis]. Georgia Tech; 2011. [cited 2021 Jan 18]. Available from: http://hdl.handle.net/1853/44891.

Council of Science Editors:

Pan M. RNA secondary sturcture prediction using a combined method of thermodynamics and kinetics. [Masters Thesis]. Georgia Tech; 2011. Available from: http://hdl.handle.net/1853/44891

2. Ozer, Gungor. Understanding protein structure and dynamics: from comparative modeling point of view to dynamical perspectives.

Degree: PhD, Chemistry and Biochemistry, 2011, Georgia Tech

In this thesis, we have advanced a set of distinct bioinformatic and computational tools to address the structure and function of proteins. Using data mining of the protein data bank (PDB), we have collected statistics connecting the propensity between the protein sequence and the secondary structure. This new tool has enabled us to evaluate new structures as well as a family of structures. A comparison of the wild type staphylococcal nuclease to various mutants using the proposed tool has indicated long-range conformational deviations spatially distant from the mutation point. The energetics of protein unfolding has been studied in terms of the forces observed in molecular dynamics simulations. An adaptive integration of the steered molecular dynamics is proposed to reduce ground state dominance by the rare low energy trajectories on the estimated free energy profile. The proposed adaptive algorithm is utilized to reproduce the potential of mean force of the stretching of decaalanine in vacuum at lower computational cost. It is then used to construct the potential of mean force of this transition in solvent for the first time as to observe the hydration effect on the helix-coil transformation. Adaptive steered molecular dynamics is also implemented to obtain the free energy change during the unfolding of neuropeptide Y and to confirm that the monomeric form of neuropeptide Y adopts halical-hairpin like pancreatic-polypeptide fold. Advisors/Committee Members: Rigoberto Hernandez (Committee Chair), C. David Sherrill (Committee Member), Jean-Luc Brédas (Committee Member), Joseph Perry (Committee Member), Stephen Harvey (Committee Member).

Subjects/Keywords: Adaptive steered molecular dynamics; Neuropeptide; Proteins Analysis; Proteins Structure; Algorithms; Proteins Denaturation; Molecular dynamics

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Ozer, G. (2011). Understanding protein structure and dynamics: from comparative modeling point of view to dynamical perspectives. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/39577

Chicago Manual of Style (16th Edition):

Ozer, Gungor. “Understanding protein structure and dynamics: from comparative modeling point of view to dynamical perspectives.” 2011. Doctoral Dissertation, Georgia Tech. Accessed January 18, 2021. http://hdl.handle.net/1853/39577.

MLA Handbook (7th Edition):

Ozer, Gungor. “Understanding protein structure and dynamics: from comparative modeling point of view to dynamical perspectives.” 2011. Web. 18 Jan 2021.

Vancouver:

Ozer G. Understanding protein structure and dynamics: from comparative modeling point of view to dynamical perspectives. [Internet] [Doctoral dissertation]. Georgia Tech; 2011. [cited 2021 Jan 18]. Available from: http://hdl.handle.net/1853/39577.

Council of Science Editors:

Ozer G. Understanding protein structure and dynamics: from comparative modeling point of view to dynamical perspectives. [Doctoral Dissertation]. Georgia Tech; 2011. Available from: http://hdl.handle.net/1853/39577


Georgia Tech

3. Watkins, Jason Derrick. X-ray structures of p22 c2 repressor-dna complexes: the mechansism of direct and indirect readout.

Degree: PhD, Chemistry and Biochemistry, 2008, Georgia Tech

The P22 c2 repressor protein (P22R) binds to DNA sequence-specifically and helps direct the temperate lambdoid bacteriophage P22 to the lysogenic developmental pathway. To gain insight into its DNA binding mechanism, we solved the 1.6 Å x-ray structure of the N-terminal domain (NTD) of P22R in a complex with a DNA fragment containing the synthetic operator sequence [d(ATTTAAGATATCTTAAAT)]2 This operator has an A-T at position 9L and T-A at position 9R and is termed DNA9T. Van der Waals interactions between protein and DNA appear to confer sequence-specificity. The structure of the P22R NTD – NA9T complex suggests that sequence-specificity arises substantially from interaction of a valine with a complementary binding cleft on the major groove surface of DNA9T. The cleft is formed by four methyl groups on sequential base pairs of 5' TTAA 3'. The valine cleft is intrinsic to the DNA sequence and does not arise from protein-induced DNA conformational change. Protein-DNA hydrogen bonding plays a secondary role in specificity. Advisors/Committee Members: Loren D. Williams (Committee Chair), Donald Doyle (Committee Member), Nicholas V. Hud (Committee Member), Roger Wartell (Committee Member), Stephen Harvey (Committee Member).

Subjects/Keywords: P22 repressor; Direct readout; Indirect readout; Protein binding; DNA-protein interactions; Van der Waals forces

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Watkins, J. D. (2008). X-ray structures of p22 c2 repressor-dna complexes: the mechansism of direct and indirect readout. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/26709

Chicago Manual of Style (16th Edition):

Watkins, Jason Derrick. “X-ray structures of p22 c2 repressor-dna complexes: the mechansism of direct and indirect readout.” 2008. Doctoral Dissertation, Georgia Tech. Accessed January 18, 2021. http://hdl.handle.net/1853/26709.

MLA Handbook (7th Edition):

Watkins, Jason Derrick. “X-ray structures of p22 c2 repressor-dna complexes: the mechansism of direct and indirect readout.” 2008. Web. 18 Jan 2021.

Vancouver:

Watkins JD. X-ray structures of p22 c2 repressor-dna complexes: the mechansism of direct and indirect readout. [Internet] [Doctoral dissertation]. Georgia Tech; 2008. [cited 2021 Jan 18]. Available from: http://hdl.handle.net/1853/26709.

Council of Science Editors:

Watkins JD. X-ray structures of p22 c2 repressor-dna complexes: the mechansism of direct and indirect readout. [Doctoral Dissertation]. Georgia Tech; 2008. Available from: http://hdl.handle.net/1853/26709

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