The central themes of Cell Boundaries concern the structural and organizational principles underlying cell membranes, and how these principles enable function. By building a biological and biophysical foundation for understanding the organization of lipids in bilayers and the folding, assembly, stability, and function of membrane proteins, the book aims to broaden the knowledge of bioscience students to include the basic physics and physical chemistry that inform us about membranes. In doing so, it is hoped that physics students will find familiar territory that will lead them to an interest in biology. Our progress toward understanding membranes and membrane proteins depends strongly upon the concerted use of both biology and physics. It is important for students to know not only what we know, but how we have come to know it, so Cell Boundaries endeavours to bring out the history behind the central discoveries, especially in the early chapters, where the foundation is laid for later chapters. Science is far more interesting if, as students, we can appreciate and share in the adventures—and misadventures—of discovering new scientific knowledge. Cell Boundaries was written with advanced undergraduates and beginning graduate students in the biological and physical sciences in mind, though this textbook will likely have appeal to researchers and other academics as well. Highlights the history of important central discoveries Early chapters lay the foundation for later chapters to build on, so knowledge is amassed High-quality line diagrams illustrate key concepts and illuminate molecular mechanisms Box features and spreads expand on topics in main text, including histories of discoveries, special techniques, and applications
The extramembraneous segments in a large collection of G-protein coupled receptors (GPCRs) have been analysed in terms of amino acid composition and length. It is shown that this family of multi-spanning integral membrane proteins conforms well to the 'positive inside' rule. Further, the extracellular N-terminal tails of GPCRs lacking a cleavable signal peptide are shown to be considerably shorter and to have a reduced content of positively charged amino acids compared with the N-terminal tails of GPCRs endowed with a signal peptide. This suggests that extracellular N-terminal tails of eukaryotic plasma membrane proteins may be translocated by different mechanisms depending on whether or not they are preceded by a signal peptide.
No abstract is provided for this article.
No abstract is provided for this article.
The overall amino acid composition of membrane-penetrating segments of trans-membrane proteins can be well reproduced by computer simulation of 'evolution' of hydrophobic protein segments, with selection operating only on the hydrophobicity of the sequence. This substantiates the idea that the specific amino acid sequence is relatively less important than the preservation of an overall hydrophobic character in such segments, and furnishes an example of macromolecular evolution where the evolutionary process can be quantitatively mimicked on the computer.
No abstract is provided for this article.
Integral membrane proteins are characterized by long apolar segments that cross the lipid bilayer. Polar domains flanking these apolar segments have a more balanced amino acid composition, typical for soluble proteins. We show that the apolar segments from three different kinds of membrane-assembly signals do not differ significantly in amino acid content, but that the inside/outside location of the polar domains correlates strongly with their content of arginyl and lysyl residues, not only for bacterial inner-membrane proteins, but also for eukaryotic.proteins from the endoplasmic reticulum, the plasma membrane, the inner mitochondrial membrane, and the chloroplast thylakoid membrane. A positive-inside rule thus seems to apply universally to all integral membrane proteins, with apolar regions targeting for membrane integration and charged residues providing the topological information.
Mgm1p is a nuclearly encoded GTPase important for mitochondrial fusion. Long and short isoforms of the protein are generated in a unique "alternative topogenesis" process in which the most N-terminal of two hydrophobic segments in the protein is inserted into the inner mitochondrial membrane in about half of the molecules and translocated across the inner membrane in the other half. In the latter population, the second hydrophobic segment is cleaved by the inner membrane protease Pcp1p, generating the short isoform. Here, we show that charged residues in the regions flanking the first segment critically affect the ratio between the two isoforms, providing new insight into the importance of charged residues in the insertion of proteins into the mitochondrial inner membrane.
Helical membrane proteins constitute roughly a quarter of all proteomes and perform diverse biological functions. To avoid aggregation, they undergo cotranslational membrane insertion and are typically assumed to attain stable transmembrane topologies immediately upon insertion. To what extent post-translational changes in topology are possible in-vivo and how they may affect biogenesis is incompletely understood. Here, we show that monomeric forms of Small Multidrug Resistance (SMR) proteins display topological dynamics, where the N-terminal transmembrane helix equilibrates between membrane-inserted and non-inserted states. We characterize the kinetics of the process and show how the composition of the helix regulates the topological dynamics. We further show that topological dynamics is a property of the unassembled monomeric protein, as the N-terminal helix becomes fixed in a transmembrane disposition upon dimerization. Membrane protein topology can thus remain dynamic long after cotranslational membrane insertion, and can be regulated by later assembly processes.
We present a model for calculating the protein production rate as a function of the translation rate. The model takes into account that the elongation rate along an mRNA molecule is non-uniform as a result of different tRNA availabilities for different codons. Initiation of ribosomes on an mRNA is normally the rate-limiting step in the translation process, and blocking of the initiation site can be avoided if the codons closest to this site allow fast translation by the ribosome. Hence, different selective forces may act on the choice of synonymous codons in the initiation region than elsewhere on a given mRNA. We show that the elongation rate along the whole mRNA influences the production rate of abundant proteins, whereas only the elongation rate in the initiation region is of importance for the production rate of rare proteins. We also present an analysis of the codon distribution along known mRNAs coding for abundant and rare proteins.
Signal peptides (SPs) target proteins to the secretory pathway and are cleaved from the nascent chain once the translocase in the ER has been engaged. Signal-anchor (SA) sequences also interact transiently with the ER translocase, but are not cleaved and move laterally out of the translocase to become permanent membrane anchors. One obvious difference between SP and SA sequences is the considerably longer hydrophobic regions (h regions) of the latter. To study the interaction between SP/SA sequences and the ER translocase, we have constructed signal sequences with poly-Leu h regions ranging in length from 8 to 29 residues and have characterized their locations within the translocase using both a new assay that measures the minimum number of amino acids needed to span the distance between the COOH-terminal end of the h region and the active site of the oligosaccharyl transferase enzyme and an assay where the efficiency of signal peptidase catalyzed cleavage is measured. Our results suggest that SP and SA sequences are positioned differently in the ER translocase.
