Structure, function and regulation of integral membrane transport proteins

Integral membrane transport proteins are essential for the transport of a wide variety of substrates such as ions, drugs and metabolites across the membranes of microorganisms. They are found in diverse locations such as outer and inner membranes of archaeal, prokaryotic and eukaryotic cells, as well as the outer layers of the membrane-bound organelles, including chloroplasts, endoplasmic reticulum and mitochondria. These proteins are capable of facilitating the transport of substrates both from outside the cell to inside, and vice versa, and they can be very specific, thereby playing a significant role in substrate selection. Integral membrane transport proteins also play important roles in regulation of transport, defense against drugs and antibiotics, and hemostasis. Thus, understanding the structural framework and detailed functional mechanisms of these proteins will contribute to our knowledge of biological processes. In this study, we have investigated the structure, function and regulation of three different types of integral membrane transport proteins. Chapter 2 focuses on elucidating the structure and function of the transcriptional regulator Rv0678 of Mycobacterium tuberculosis, which negatively regulates the expression of the MmpS4-MmpL4 system, which plays a key role in the biosynthesis and transport of lipids from the cytoplasm towards the periplasm. Lipids play an important role in cell wall remodeling and permeability, thereby functioning in bacterial defense against antibiotics. We crystallized Rv0678 and identified the ligand bound to the protein as 2-stearoylglycerol. We used the structure and functional studies to elucidate a possible DNA binding mechanism for the protein. Chapter 3 discusses the crystal structure of the outer membrane channel, CmeC, of CmeABC efflux system of Campylobacter jejuni. CmeABC is a multidrug efflux system that pumps out quinolones and bile acid derivatives. The crystal structure revealed the structural framework of the channel and captured it in closed conformation. Chapter 4 focuses on understanding the structural basis of nitrite transport into the chloroplast in Chlamydomonas reinhardtii. Formate-nitrite transporter family proteins, NAR1.1 and NAR1.5, were crystallized using hanging drop vapor diffusion. Stopped flow light scattering experiments were carried out to identify nitrite as the substrate for both proteins. Site-directed mutagenesis revealed key residues that form the channel and allowed us to propose a possible nitrite transport mechanism

Accumulator pricing

Accumulator is a highly path dependant derivative structure that has been introduced as a retail financial product in recent years and becomes very popular in some Asian cities with its speculative nature. Despite its popularity, its pricing formula is not well known especially when there is a barrier structure. When the barrier in an accumulator contract is applied continuously, this paper obtains exact analytic pricing formulae for immediate settlement and for delay settlement. For discrete barrier, we also obtain analytic formulae which can approximate the fair price of an accumulator under both settlement methods. Through Monte Carlo simulation, we show that the approximation is highly satisfactory. With price formulae in close forms, this paper further explains how to price the product fairly to fit into its zero-cost structure. The analytic formulae also help in computing the Greeks of an accumulator which are documented in this paper. An asymmetry can be observed here that when the buyer is suffering a loss, risk characteristics like delta and vega are substantially larger than when the buyer is enjoying a profit. This means that losing buyers will be more vulnerable to price changes and volatility changes than winning buyers. This is consistent with another observation in the paper that the value at risk for the buyer can be several times larger than that of the seller. © 2009 IEEE.published_or_final_versionThe IEEE Symposium on Computational Intelligence for Financial Engineering (CIFEr) 2009, Nashville, TN., 30 March-2 April 2009. In Proceedings of the CIFEr, 2009, p. 72-7

Structure, function and regulation of integral membrane transport proteins

Integral membrane transport proteins are essential for the transport of a wide variety of substrates such as ions, drugs and metabolites across the membranes of microorganisms. They are found in diverse locations such as outer and inner membranes of archaeal, prokaryotic and eukaryotic cells, as well as the outer layers of the membrane-bound organelles, including chloroplasts, endoplasmic reticulum and mitochondria. These proteins are capable of facilitating the transport of substrates both from outside the cell to inside, and vice versa, and they can be very specific, thereby playing a significant role in substrate selection. Integral membrane transport proteins also play important roles in regulation of transport, defense against drugs and antibiotics, and hemostasis. Thus, understanding the structural framework and detailed functional mechanisms of these proteins will contribute to our knowledge of biological processes. In this study, we have investigated the structure, function and regulation of three different types of integral membrane transport proteins. Chapter 2 focuses on elucidating the structure and function of the transcriptional regulator Rv0678 of Mycobacterium tuberculosis, which negatively regulates the expression of the MmpS4-MmpL4 system, which plays a key role in the biosynthesis and transport of lipids from the cytoplasm towards the periplasm. Lipids play an important role in cell wall remodeling and permeability, thereby functioning in bacterial defense against antibiotics. We crystallized Rv0678 and identified the ligand bound to the protein as 2-stearoylglycerol. We used the structure and functional studies to elucidate a possible DNA binding mechanism for the protein. Chapter 3 discusses the crystal structure of the outer membrane channel, CmeC, of CmeABC efflux system of Campylobacter jejuni. CmeABC is a multidrug efflux system that pumps out quinolones and bile acid derivatives. The crystal structure revealed the structural framework of the channel and captured it in closed conformation. Chapter 4 focuses on understanding the structural basis of nitrite transport into the chloroplast in Chlamydomonas reinhardtii. Formate-nitrite transporter family proteins, NAR1.1 and NAR1.5, were crystallized using hanging drop vapor diffusion. Stopped flow light scattering experiments were carried out to identify nitrite as the substrate for both proteins. Site-directed mutagenesis revealed key residues that form the channel and allowed us to propose a possible nitrite transport mechanism.</p

Structure and Function of Neisseria gonorrhoeae MtrF Illuminates a Class of Antimetabolite Efflux Pumps

Neisseria gonorrhoeae is an obligate human pathogen and the causative agent of the sexually transmitted disease gonorrhea. The control of this disease has been compromised by the increasing proportion of infections due to antibiotic-resistant strains, which are growing at an alarming rate. N. gonorrhoeae MtrF is an integral membrane protein that belongs to the AbgT family of transporters for which no structural information is available. Here, we describe the crystal structure of MtrF, revealing a dimeric molecule with architecture distinct from all other families of transporters. MtrF is a bowl-shaped dimer with a solvent-filled basin extending from the cytoplasm to halfway across the membrane bilayer. Each subunit of the transporter contains nine transmembrane helices and two hairpins, posing a plausible pathway for substrate transport. A combination of the crystal structure and biochemical functional assays suggests that MtrF is an antibiotic efflux pump mediating bacterial resistance to sulfonamide antimetabolite drugs

Ion pairs in the transmembrane domain viewed from the cytoplasmic side.

<p>Residues D405 and D406 of TM4 and K948 of TM10 that form ion pairs, which may play an important role in proton translocation, are in green sticks.</p

Secondary structural topology of the MtrE monomer.

<p>The topology was constructed based on the crystal structure of MtrE. The α-helices and β-strands are colored cyan and orange, respectively.</p

Structure of the <i>N. gonorrhoeae</i> MtrD efflux pump.

<p>(a) Ribbon diagram of a protomer of MtrD viewed in the membrane plane. The molecule is colored using a rainbow gradient from the N-terminus (blue) to the C-terminus (red). Sub-domains DN, DC, PN2, PC1 and PC2 are labeled. The location of PN1 is behind PN2, PC1 and PC2. (b) Ribbon diagram of the MtrD trimer viewed in the membrane plane. Each subunit of MtrD is labeled with a different color. Residues 917–927 (only found in MtrD) forming the upper portion of TM9 and the loop connecting TM9 and TM10 are in blue color.</p

Structure of the <i>N. gonorrhoeae</i> MtrE channel protein.

<p>(a) Ribbon diagram of a protomer of MtrE viewed in the membrane plane. The molecule is colored using a rainbow gradient from the N-terminus (blue) to the C-terminus (red). (b) Ribbon diagram of the MtrE trimer viewed in the membrane plane. Each subunit of MtrE is labeled with a different color.</p