dc.contributor.author	Shieh, Josephine G.
dc.date.accessioned	2018-05-17T18:04:19Z
dc.date.available	2018-05-17T18:04:19Z
dc.date.issued	2018-05
dc.identifier.citation	Shieh, Josephine G., "Effects of Helix Dipole Membrane Field Potential Interactions on Hydrophobic Energies of Transmembrane Proteins." Master's thesis, Valdosta State University. May 2018. https://hdl.handle.net/10428/3069.
dc.identifier.other	13F98AF9-CE15-1ABB-4E45-AF5D644C2C07	UUID
dc.identifier.uri	http://hdl.handle.net/10428/3069
dc.description.abstract	The race to uncover new biological drug targets has led to an emerging field of research on the thermodynamic properties that stabilize transmembrane proteins as well as the role of these stabilizing factors in shaping the evolutionary landscape of drug target populations. When proteins are inserted into the plasma membrane, they fold into three- dimensional secondary protein structures called alpha helices. The electrical interactions within the alpha helix causes the protein to form a macrodipole. As a result of this phenomenon, the energetic stabilities of TM proteins may either be disrupted or enhanced due to the interactions between the surrounding membrane potential and the charged dipole termini of the folded helix. Currently, the relative contributions of compensatory factors to TM protein stability and their population distributions are poorly understood. In this study, two categories of bitopic proteins and the hydrophobic energies of their TM domains were investigated. We hypothesized that Type I TM proteins exhibit lower hydrophobic free energies as a compensatory response to the decreased electrical stabilities of Type I proteins that have incurred an energetic penalty due to the spatial orientations. A Z test showed that Type I proteins exhibit significantly lower hydrophobic free energies than Type II proteins (p = 0.0003, α = 0.05). A Z test of Shannon entropies of both protein types revealed that Type 1 proteins exhibit significantly lower Shannon entropies than those of Type 2 (p = 0.000, α = 0.05). Linear regression analysis showed a weak correlation between Type I Shannon entropies and Type I hydrophobic energies (R2 = 0.221) and Type II Shannon entropies and Type II hydrophobic energies (R2 = 0.232), suggesting that Shannon entropies are not a direct function of hydrophobic free energies and may arise from synergistic interactions among various energetic contributors.	en_US
dc.description.tableofcontents	I. INTRODUCTION.1 \| II. REVIEW OF LITERATURE 6 \| Type I and Type II Proteins 6 \| The Alpha Helix Dipole .7 \| Electrical Properties of Cellular Membranes .11 \| Determinants of Protein Stability 13 \| Hydrophobicity Scales 15 \| Functional Significance of Transmembrane Domains .16 \| III. MATERIALS AND METHODS .18 \| Data Collection. 18 \| Retrieval of Type I and Type II Protein Accession Numbers 18 \| Retrieval of Transmembrane Domain Residue Sequences .18 \| Retrieval of Grand Average of Hydropathicity Values .19 \| Retrieval of Kyte and Doolittle Hydropathy Indices 19 \| Retrieval and Determination of Protein Functional Class 20 \| Mathematical Computation .20 \| Computation of Gibb’s Free Energy .20 \| Computation of Hydrophobic Energies 20 \| Computation of Shannon Entropies 21 \| Statistical Analysis 22 \| Monte Carlo Simulation of Normal Distribution of Hydrophobic Energies 22 \| Shapiro Wilk Test of Gaussian Normality of Hydrophobic Energies .22 \| Levene’s Test of Equality of Variances of Hydrophobic Energies .23 \| Mann-Whitney U Test of Hydrophobic Energies .23 \| Z Test of Hydrophobic Energies .24 \| Monte Carlo Simulation of Normal Distribution of Shannon Entropies 24 \| Shapiro Wilk Test of Gaussian Normality of Shannon Entropies .25 \| Levene’s Test of Equality of Variances of Shannon Entropies .25 \| Mann-Whitney U Test of Shannon Entropies 25 \| Z Test of Shannon Entropies .26 \| Linear Regression of Hydrophobic Energies and Shannon Entropies 27 \| IV. RESULTS28 \| Gibb’s Free Energy Difference 28 \| Frequency Distributions of Hydrophobic Energies .28 \| Mann-Whitney U Test of Hydrophobic Energies 30 \| Z Test of Hydrophobic Energies 32 \| Frequency Distributions of Shannon Entropies .32 \| Mann-Whitney U Test of Shannon Entropies 34 \| Z Test of Shannon Entropies 36 \| Shannon Entropy as a Function of Hydrophobic Energy 36 \| Functional Classification .39 \| V. DISCUSSION. 40 \| Hydrophobic Energy Compensation 40 \| Z Test of Transmembrane Domain Hydrophobic Energies .40 \| Z Test of Transmembrane Domain Shannon Entropies .41 \| Linear Regression Analysis of Shannon Entropy as a Function of Hydrophobic \| Energy 42 \| Functional Classification .43 \| Summary. 43 \| REFERENCES.45 \| APPENDIX A: Kyte and Doolittle Amino Acid Hydrophobicity Indices 49 \| APPENDIX B: Type I Hydrophobic Energies and Shannon Entropies 51\|	en_US
dc.language.iso	en_US	en_US
dc.subject	Entropy	en_US
dc.subject	Proteins	en_US
dc.title	Effects of Helix Dipole Membrane Field Potential Interactions on Hydrophobic Energies of Transmembrane Proteins	en_US
dc.type	Thesis	en_US
dc.contributor.department	Department Of Biology of The College Of Arts & Sciences	en_US
dc.description.advisor	Kang, Jonghoon
dc.description.committee	Grove, Theresa J.
dc.description.committee	Gosnell, Donna
dc.description.committee	LaPlant, James T.
dc.description.degree	M.S.	en_US
dc.description.major	Biology	en_US