We think you have liked this presentation. If you wish to download it, please recommend it to your friends in any social system. Share buttons are a little bit lower. Thank you!
Presentation is loading. Please wait.
Published byEzekiel Askren
Modified about 1 year ago
TEMPLATE DESIGN © 2008 www.PosterPresentations.com Statistical Coupling Analysis of the Photosystem II D1 Protein Janan Zhu 1 ; Nicholas Polizzi 2 ; 1 Department of Mathematics, Duke University; 2 Department of Chemistry, Duke University Abstract Method: Eigenvalue Decomposition of Positional Correlations Description of Sectors Summary and Discussion References Statistical coupling analysis can be applied to alignments of related proteins to examine “sectors” in the sequences that are evolving independently of each other. Our application of this technique to the D1 protein of photosystem II identified 4 significant sectors and we assigned different functions to each of the based on their location within the protein. The resulting sectors appear to be clustered around the cofactors of the protein that are involved in the photosynthetic electron transport pathway. These results suggest that the cofactor binding sites in the D1 protein have evolved independently to some degree, a fact that may contribute to further biochemical and structural studies. Introduction The photosystem II D1 protein is vital to the photosynthetic electron transport pathway as it houses the reaction center chlorophylls in addition to the cofactors that channel the excited electrons to other proteins in the membrane. Studies of protein conservation promote a better understanding of how the protein facilitates the transfer of electrons between cofactors. Sector Definition The photosystem II complex, with the D1 protein highlighted D1 Protein Cofactors in the Electron Transfer Pathway The flow of electrons between the cofactors is shown in green. Plastoquinone B is the final electron acceptor and dissociates from the protein into the thylakoid membrane. Cofactors Water-oxidizing complex Tyrosine Z Chlorophyll pair Pheophytin Plastoquinones A set of 152 representative sequences was generated using a BLAST search for sequences similar to that of the T. vulcanus photosystem II D1 protein (length 344 AA). These sequences were then aligned and the alignments were weighted by the Kullback-Leibler relative entropy, a measure of the degree of conservation at a particular position. These weighted pairwise alignments were used to create the 344 x 344 positional correlation matrix, which indicated the degree of correlated evolution between each pair of positions. A graphical representation of the positional correlation matrix Spectral decomposition of the positional correlation matrix was used to identify statistically independent groups of amino acids (sectors). The eigenvectors (also called eigenmodes) used to represent the matrix contain weights for the significance of the position within the sector. Positions in the eigenmodes with a weight greater than 0.09 were considered to be part of the corresponding sectors. Some of the sectors obtained from the raw eigenmodes contained large regions of overlap with other sectors and were merged to simplify functional description. Figure depicting the merging process for three sectors. The unified sector consisted of the union of the pairwise intersections of the sectors. The number of sectors was determined from empirical observation of their 3D mapping onto the T. vulcanus structure. A defining characteristic of a sector aside from statistical independence is physical connectivity in space (Halabi et al. 2009). Eigenmodes with higher eigenvalues accounts for a greater degree of the variance in the correlation matrix. Therefore, the eigenmodes were considered in order of descending eigenvalues until they yielded sectors with disparate amino acids of low descriptive value. This method resulted in four sectors being defined. SectorProposed function Facilitating proton-coupled electron transfer to plastoquinone B. The amino acids in this sector are colored by element, with green representing carbon. They appear to be largely hydrophobic, which stabilizes the binding of the aliphatic tail of the quinone. Several amino acids known to be involved in proton donation are also present in this sector, including Ser246 and Tyr264. Source: Biochemistry Mathews,Van Holde, Ahern 3E Overview of the sectors in the D1 protein Lowering energetic barrier for electron transfer from tyrosine Z (orange) to chlorophyll special pair (red). Electrons from tyrosine Z replenish excited electrons that leave the reaction center. The amino acids in this sector contain many aromatic rings, which bridge the gap between the tyrosine and the special pair. His198 in this sector is coordinated to the chlorophyll and is directly linked to its electron density. Binding the water oxidizing complex and its substrates. This sector contains several histidines which are directly bonded to the complex. There are also amino acids that are hydrogen bonded to the water molecules shown in green. Structural linkage to antenna pigments. The hydrophobic amino acids in this sector are located in close proximity to chain I (yellow) of photosystem II, which is known to stabilize the pigment-containing light harvesting complex. This sector thus holds these antenna pigments within short distance of the reaction center. The application of statistical coupling analysis to the photosystem II D1 protein yielded independent sectors that appear to have biological relevance. The sectors are clustered around the different cofactors of the photosynthetic electron transport pathway. We conclude that the different steps in electron transport appear to be facilitated by evolutionarily independent parts of the protein. This has important implications, as the overall proton-coupled electron transfer is believed to be a concerted reaction, yet separate sectors were found for each step. It remains to be shown if this is true for electron transfer proteins in general and this study has demonstrated the viability of statistical coupling analysis for this purpose. N. Halabi, O. Rivoire, S. Leibler, R. Ranganathan. Cell, 138: 774-786, 2009
Protein Sectors: Evolutionary Units of Three-Dimensional Structure Cell (2009) Najeeb Halabi, Olivier Rivoire, Stanislas Leibler, and Rama Ranganathan.
Photosynthesis Since only absorbed light can excite molecules and thus deliver its energy, so a photosynthetic pigment can act as absorbers of visible.
Plant Physiology Photosynthesis, the light reaction.
Photosynthesis Light-Dependent Reaction By: Naweed Zamani.
Photosynthesis The Light Dependent Reactions. Formula 6 CO H 2 O + Light Energy [CH 2 O] + 6O 2 Chlorophyll.
Photosynthesis. A. Introduction 1. Location: chloroplasts (in plants and algae) or folds in cell membrane (in photosynthetic prokaryotes, cyanobacteria)
Electron Transfer Process and Membrane Bioenergetics APh/BE161: Physical Biology of the Cell Winter 2009 Electron Transfer Rob Phillips.
Phases of Photosynthesis Photosynthesis occurs in 2 phases, which include 3 main goals: A. The Light Reactions 1. Capturing light energy 2. Using the light.
Chapter 6 Photosynthesis. Section 1: The Light Reactions Autotrophs: use energy from sunlight or chemical bonds of inorganic molecules to make organic.
Chapter 14 Energy Generation in Mitochondria and Chloroplasts.
Ch 8- Photosynthesis Animation Quiz - Calvin Cycle Photosynthesis Visualizing Electron Transport Where do plants get the energy they need to produce food?
7.5 Overview: The two stages of photosynthesis are linked by ATP and NADPH The second stage is the Calvin cycle, which occurs in the stroma of the chloroplast.
Light Reactions Takes place in the Thylakoids of chloroplasts in eukaryotes Captures solar energy and converts it to Energy storage molecules ATP and NADPH.
Photosynthesis Chapter 8. Chapter 8 study guide Review 1.Where does the energy that living things need come from (originally)? The Sun.
THE LIGHT REACTIONS. Begin when photons strike the photosynthetic membrane. The process can be divided into three parts. 1) Photoexcitation: absorption.
THE LIGHT DEPENDENT REACTION. OXIDATION AND REDUCTION Oxidation Is a Loss of electrons (OIL) Reduction Is a Gain of electrons (RIG) © 2010 Paul Billiet.
The role of metal ions in photosynthesis. The green plants produce ~ 1 g glucose every hour per square meter of leaf surface. This means that photosynthesis.
An Overview of Photosynthesis Most of the energy used by almost all living cells ultimately comes from the sun plants, algae, and some bacteria capture.
LG 5 Outline Photosynthesis Photosynthesis: An Overview Role of Electrons – CO 2 Fixation – Water – Chloroplast Structure – Light-Dependent Reactions Pigment.
Forms of stored energy in cells Electrochemical gradients Covalent bonds (ATP) Reducing power (NADH) During photosynthesis, respiration and glycolysis.
Photosynthesis PhotosynthesisPhotosynthesis is the process by which plants, use the energy from sunlight to produce sugar, converts into ATP, the "fuel"
Chapter 6 Photosynthesis Section 6.1. Energy Processes for Life Autotrophs manufacture their own food from inorganic substances Autotrophs manufacture.
Photosynthesis – Process by which some organisms capture light energy and store it in organic compounds (mainly carbohydrates, sugars) Autotrophs – make.
Photosynthesis Chapter 5. Outline I. Photosynthesis A. Introduction B. Reactions.
Similarities between photophosphorylation and oxidative phosphorylation e-e- Proton pump ATP synthase H+H+ H+H+ H+H+ H+H+ H+H+ H+H+ H+H+ ADP+Pi ATP.
PHOTOSYNTHESIS Topics 3.8 and 8.2. State that photosynthesis involves the conversion of light energy into chemical energy State that light from the Sun.
Photosynthesis Chapter 10. What is photosynthesis… Photosynthesis transforms light energy into chemical bond energy stored in sugar and other organic.
Photosynthesis ATP (adenosine triphosphate)- basic energy source of all cells, chemical compound that cells use to store and release energy – Adenine,
Chapter 15 (part1) Photosynthesis. The Sun - Ultimate Energy 1.5 x kJ falls on the earth each day 1% is absorbed by photosynthetic organisms and.
LIGHT & DARK REACTIONS OF PHOTOSYNTHESIS. How photosynthesis works Light Dependent Reactions Sugars “Dark Reactions” Light Independent Reactions Photosystem.
Chapter 15 (part1) Photosynthesis. Implications of Photosynthesis on Evolution.
PHOTOSYNTHESIS Photosynthesis is a process that involves transforming the energy from sunlight along with carbon dioxide and water to form sugar and oxygen.
Where does the energy that living things need come from? Food! You’re not you when you’re hungry!
Chapter 5 Photosynthesis Photosynthesis. Thinking Question #1 Why are we talking about photosynthesis? Why is it important that you understand this.
Photosynthesis. Energy Transformations – TWO TYPES ATP (Adenosine Triphosphate): is the energy molecule used in all living things, so supplies must be.
Katrina Garibotto. Explain how light interacts with pigments. Describe how photosystems help harvest light energy. Identify the chemical products of the.
AP Biology Discussion Notes Tuesday 12/09/2014. Goals for the Day 1.Be able to describe what a photosystem is and how it works. 2.Be able to describe.
WHY ARE PLANTS GREEN? It's not that easy bein' green Having to spend each day the color of the leaves When I think it could be nicer being red or yellow.
The Reactions (I). H 2 O is absorbed by the root epidermal cellsepidermal cells Plants absorb water and carbon dioxide through stoma (a pore surrounded.
METABOLISM The sum of all chemical reactions in an organism.
Light Dependent Reactions IB Topic 8.2.3: Explain the light dependent reactions.
Photosynthesis!!!!. 12 H 2 O The overall reaction in photosynthesis: 6CO Light energy C 6 H 12 O 6 6O 2 6 H 2 O + Photosynthesis is divided into.
Photosynthesis Photosynthesis is the process of converting light energy to chemical energy stored in carbon compounds. – Plants, algae, cyanobacteria,
PhotosynthesisPhotosynthesis A definition: Photosynthesis is the process a plant uses to make food and grow. A definition: Photosynthesis is the process.
Photosynthesis Photosynthesis is the process of converting light energy to chemical energy. Plants, algae, cyanobacteria, and some protists produce organic.
Chapter 3 - Photosynthesis: The Details. Photosynthesis Using the sun to make useful forms of energy Sunlight plays a much larger role in our sustenance.
Photosynthesis Objectives 1.PS converts light energy into chemical energy --- food 2.PS occurs in two stages 1.Light Reactions convert Light to ATP and.
Chapter 8 Light Reactions. Need To Know How photosystems convert light energy into chemical energy. (There will be more on this in the next couple of.
Pathways that Harvest and Store Chemical Energy 6.
© 2017 SlidePlayer.com Inc. All rights reserved.