N-terminal segment side chains


Crick showed that a left-handed supercoil of two right-handed a helices reduces the number of residues per turn in each helix from 3.6 to 3.5 so that the pattern of side-chain interactions between the helices repeats every seven residues, that is, after two turns. This is reflected in the amino acid sequences of polypeptide chains that form a-helical coiled-coils. Such sequences are repetitive with a period of seven residues, the heptad repeat. The amino acid residues within one such heptad repeat are usually labeled a-g (Figure 3.2a), and one of these, the d-residue, is hydrophobic, usually a leucine or an isoleucine. When two a helices form a coiled-coil structure the side chains of these d-residues pack against each other every second turn of the a helices (Figure 3.2b). The hydrophobic region between the a helices is completed by the a-residues, which are frequently hydrophobic and also pack against each other (Figure 3.3). Residues "e" and "g," which border the hydrophobic core (see Figure 3.2b), frequently are charged residues. The side chains of these residues provide ionic interactions (salt bridges) between the a helices that define the relative chain alignment and orientation (Figure 3.4).  [c.36]

Although most of the p53 mutations detected in tumors are located in the DNA-binding domain, a few have also been observed in the oligomerization domain. The structure provides a clear explanation of the effects of two such mutations. One is a mutation of the p-strand residue Leu 330 to His. The side chain of this Leu residue in the wild-type protein is in the center of the hydrophobic core of the dimer replacing it with the hydrophilic histidine side chain of the mutant destabilizes the core, prevents formation of dimers, and therefore inhibits p53 function. The second example is the mutation of a glycine residue in the turn between the p strand and the a helix. The turn comprises only this glycine residue, which adopts an unusual conformation in a region of the Ramachandran plot (see Figure 1.7) that is energetically  [c.167]

In a multiple-effect evaporator, the effects are numbered in the direction of steam flow, the first effect being the one heated by prime steam. Liquor feed sequence through the evaporator maybe forward, backward, parallel, or mixed. Backward feed (to the coolest effect first and then successively through the higher temperature effects) is generally used when the feed is cold, because only a small volume has to be heated to the highest temperature, thereby reducing sensible heating losses and improving steam economy. Forward feed is generally used when feed is hot and when the concentrated product is not too viscous at the last effect temperature. Where necessary, forward feed can be used on a cold feed and can give almost the same steam economy as backward feed if the feed is preheated in stages by vapor extracted from each higher temperature effect of the evaporator in turn. Such an arrangement is used for seawater, which can be concentrated only in small amounts at high temperature without scaling but about threefold at the lowest effect temperature. These preheaters add to the complexity of the evaporator but not necessarily to total heating surface needs because they reduce the heat loads in the effects themselves. Parallel feed is frequendy used in crystallising operations and involves feeding to and withdrawing product from each effect. Mixed feed operation is common if feed is at some temperature intermediate between first and last effect, the finished product is too viscous to handle at low temperature, or Hquor at an intermediate concentration and temperature is desired for further processing. AH such conditions prevail in a kraft-mill hquor evaporator (see Pulp). The evaporators are usually of the LTV type and the feed heaters are an integral part of the evaporator tube bundles. The highest temperature effect is frequently subdivided so that only a part of the tubes must work on Hquor of the highest concentration and viscosity. Other flow-sheet variations include evaporators with several bodies in parallel on steam and vapor but in series on feed. Thus the kraft-mill evaporator might be an eight-body seven effect with two bodies in parallel in the last effect position in order to better handle the very large vapor volumes generated at the lowest temperature. Variations may also involve the steam path eg, a combination double-triple effect, which may have one effect on prime steam with the evolved vapor being spHt, one part to a single effect and the other to a double effect. This variant is used when the Hquor has a high BPR as it approaches final concentration, so high that not all evaporation can be accompHshed, in this example, in a triple effect. Other flow sheets have been developed for specific types of evaporator, such as parallel spHt feed, which is used for desalination evaporators arranged in vertical stacks. In this case, about half the feed goes to the odd-numbered effects in one stack and the other half to the even-numbered effects in a second stack next to the first, with vapor connections crossing from one stack to the other.  [c.476]

Several important physiological responses, including vision, smell, and stress response, involve large metabolic effects produced from a small number of input signals. The receptors that trigger these responses have two things in common. First, their transmembrane regions contain seven helices each spanning the lipid bilayer of the plasma membrane. Second, the signals transmitted to the intracellular domain of these receptors are amplified, and the amplifiers are members of a common family of proteins with homologous amino acid sequences called G proteins. G proteins bind guanine nucleotides (hence the term G protein) and act as molecular switches that are activated by binding GTP and are inactivated when the GTP is hydrolyzed to GDP. The hydrolysis of GTP is catalyzed by the G protein itself, but G proteins on their own are very slow GTPases, and switching off the G protein is normally accelerated by regulatory molecules, known as RGS (regulators of GTP hydrolysis), which bind to the active G protein and increase the rate of GTP hydrolysis. When in the active GTP-bound state, the G protein can activate many downstream effectors, greatly amplifying the signal, before RGS binds and the signal is switched off. The structural basis of this important switch mechanism is now understood.  [c.252]

The second driving force that affects the folding of polypeptide chains is the need to bury the hydrophobic residues of the chain, protecting them from solvent water. From a topological viewpoint, then, all globular proteins must have an inside where the hydrophobic core can be arranged and an outside toward which the hydrophilic groups must be directed. The sequestration of hydrophobic residues away from water is the dominant force in the arrangement of secondary structures and nonrepetitive peptide segments to form a given tertiary structure. Globular proteins can be classified mainly on the basis of the particular kind of core or backbone structure they use to accomplish this goal. The term hydrophobic core, as used here, refers to a region in which hydrophobic side chains cluster together, away from the solvent. Backbone refers to the polypeptide backbone itself, excluding the particular side chains. Globular proteins can be pictured as consisting of layers of backbone, with hydrophobic core regions between them. Over half the known globular protein structures have two layers of backbone (separated by one hydrophobic core). Roughly one-third of the known structures are composed of three backbone layers and two hydrophobic cores. There are also a few known four-layer structures and one known five-layer structure. A few structures are not easily classified in this way, but it is remarkable that most proteins fit into one of these classes. Examples of each are presented in Figure 6.28.  [c.184]

Two essential features are required to stabilize the covalent tetrahedral transition state in serine proteinases—the oxyanion hole, which provides hydrogen bonds to the negatively charged oxygen atom in the transition state, and the histidine residue of the catalytic triad, which provides a positive charge. The charge on this histidine is, in turn, stabilized by the aspartic acid side chain of the catalytic triad (Figure 11.6). The histidine residue also plays a second role in the catalytic mechanism by accepting a proton from the reactive serine residue and then donating that proton to the nitrogen atom of the leaving group. The effects on the catalytic rate of the different side chains involved in the catalytic triad and the oxyanion hole have been examined by P. Carter, J.A. Wells, and D. Estell at Genentech, USA, by analyses of mutants of subtilisin with one or several of these side chains have been changed.  [c.217]

Cells and organelles within them are bounded by membranes, which are extremely thin (4.5 nm) films of lipids and protein molecules. The lipids form a bilayered sheet structure that is hydrophilic on its two outer surfaces and hydrophobic in between. Protein molecules are embedded in this layer, and in the simplest case they are arranged with three distinct regions one hydrophobic transmembrane segment and two hydrophilic regions, one on each side of the membrane. Those proteins whose polypeptide chain traverses the membrane only once usually form functional globular domains on at least one side of the membrane (Figure 12.1a). Often these can be cleaved off by proteolytic enzymes. The hemagglutinin and neuraminidase of influenza virus (discussed in Chapter 5), G-proteins and receptors (discussed in Chapter 13), and HLA proteins (discussed in Chapter 15) are examples of such cleavage products that can be handled as functional soluble globular domains. The polypeptide chain of other transmembrane proteins passes through the membrane several times, usually as a helices but in some cases as p strands (Figure 12.1b,c). In these cases the hydrophilic regions on either side of the membrane are the termini of the chain and the loops between the membrane-spanning parts. Proteolytic cleavage of these hydrophilic regions produces a number of fragments, and function is not preserved. Some proteins do not traverse the membrane but are instead attached to one side either through a helices that lie parallel to the membrane surface (Figure 12. Id) or by fatty acids, covalently linked to the protein, that intercalate in the lipid bilayer of the membrane.  [c.223]

Ilmenite is more abundant than mtile. Ilmenite world suppHes are estimated to meet the requirements of the Ti02 industry into the twenty-second century. The largest sources of ilmenite are in AustraHa, Canada, South Africa, Russia, and the United States. Large, unexplored sources also exist in China. About 9 million metric tons of ilmenite are mined aimuaHy. Long-term atmospheric effects weather ilmenite into leucoxene [1358-95-8], which contains most of its iron as Fe " . The majority of the world s supply of mtile comes from the beach sands of AustraHa, Florida, India, Bra2H, and South Africa. The total worldwide supply is estimated to be about 50 million metric tons. About 0.5 million tons are mined a year. The supply should last at least until the end of the twenty-first century.  [c.7]

Figure 23 illustrates a countercurrent washing system. Either pressure or rotary vacuum filters may be used. The pulp in the blow tank has a consistency between 9 and 11%, depending on whether it came from a continuous or batch digester, respectively. The pulp is diluted in steps to about 1% before entering the first washer vat. It is extracted to about 10% by thickening. Washing Hquid from the showers is displaced through the pulp sheet. The pulp is reextracted and then discharged to the next stage. Pulp consistency on leaving any filter stage varies between 9 and 18%, depending on the equipment used. This procedure is repeated for each step or stage in the countercurrent system. Fresh or process water is appHed in the last, ie, the third, stage. The thick recovered soHds are sent to the evaporator off the first-stage black Hquor tank. Excess water in any stage removed from the pulp is recycled to the showers of the preceding stage. The dilution factor, typically 2—4 1 water to pulp on a weight basis, is the net water that is added to the washing system. The higher the dilution factor is, the cleaner the pulp and the lower the chemical (soda) losses, but also the greater the amount of water to be evaporated from the residual Hquor in the chemical recovery system. Figure 19 shows the diffusion ring washing used in the Kamyr system. Therein fresh wash water is fed to the second stage of washing where it contacts the pulp for an extended period (1—2 h) and then is sent to the top filtrate tank. From there, the wash water goes to the first stage of diffusion washing for another 1—2 h of contact, back to the filtrate tank, and eventually to the bottom washing 2one of the digester via a filtrate tank.  [c.266]

The hairpin motif is a simple and frequently used way to connect two antiparallel p strands, since the connected ends of the p strands are close together at the same edge of the p sheet. How are parallel p strands connected If two adjacent strands are consecutive in the amino acid sequence, the two ends that must be joined are at opposite edges of the p sheet. The polypeptide chain must cross the p sheet from one edge to the other and connect the next p strand close to the point where the first p strand started. Such CTossover connections are frequently made by a helices. The polypeptide chain must turn twice using loop regions, and the motif that is formed is thus a p strand followed by a loop, an a helix, another loop, and, finally, the second p strand.  [c.27]

Health Hazards Information - Recommended Personal Protective Equipment Organic vapor-acid gas type canister mask rubber, neoprene, vinyl, etc. gloves chemical safety goggles, plus face shield where appropriate acid resistant clothing, plus apron for splash protection rubber safety shoes or boots hard hat Symptoms Following Exposure Inhalation causes irritation of nose and throat. Contact of liquid with eyes or skin causes severe burns. Ingestion causes vomiting and severe bums of mouth and stomach. Overexposure by any route can cause bloody stools, slow pulse, low blood pressure, coma, convulsions, cardiac arrest General Treatment for Exposure INHALATION remove to clean air rinse mouth and gargle with water if overexposure is serious, get prompt medical attention. EYES flush eyes and eye-lids thoroughly with large amounts of water get prompt medical attention. SKIN flush thoroughly with water remove contaminated clothing wash affected area with soap and water if overexposure is serious, get prompt medical attention. INGESTION dilute by drinking water if vomiting occurs, administer more water. If overexposure is serious, get prompt medical attention Toxicity by Inhalation (Threshold Limit Value) 0.5 mg/m as antimony Short-Term Exposure Limits Data not available Toxicity by Ingestion Grade 2 oral LD50 1,115 mg/kg (rat), 900 mg/kg (guinea pig) Late Toxicity Antimony poisoning may result Vapor (Gas) Irritant Characteristics Vapors are moderately irritating such that personnel will not usually tolerate moderate or high vapor concentrations Liquid or Solid Irritant Characteristics Severe skin irritant causes second- and third-degree burns on short contact and is very injurious to the eyes Odor Threshold Data not available. Fire Hazards - Flash Point Not flammable Flammable Limits in Air (%) Not flammable Fire Extinguishing Agents Not pertinent Fire Extinguishing Agents Not To Be Used Do not use water or foam on adjacent fires Special Hazards of Combustion Products Not pertinent Behavior in Fire Irritating fumes of hydrogen chloride given off when water or foam is used to extinguish adjacent fire Ignition Temperature Not pertinent Electrical Hazard Not pertinent Burning Rate Not pertinent. Chemical Reactivity - Reactivity with Water Reacts to form hydrogen chloride gas (hydrochloric acid) Reactivity with Common Materials Causes corrosion on metal Stability During Transport Stable Neutralizing Agents for Acids and Caustics Soda ash or soda ash-lime mixture Polymerization Not pertinent Inhibitor of Polymerization Not pertinent.  [c.25]

Physical and Chemical Properties - Physical State at 15 T7 and I atm. Liquid Molecular Weight 62.1 Boiling Point at I atm. 99,37, 310 Freezing Point -144, -98, 175 Critical Temperature 444, 229, 502 Critical Pressure 826, 56.1, 5.69 Spedfic Gravity 0.85 at 20°C (liquid) Vapor (Gas) Density 2.14 Ratio of Specific Heats of Vapor (Gas) 1.1211 at 16°C Latent Heat of Vaporization 194, 108, 4.52 Heat of Combustion -13,200, -7,340, -307 Heat of Decomposition Not pertinent. Health Hazards Information - Recommended Personal Protective Equipment Respirator with organic v or canister rubber or plastic gloves goggles or face shield Symptoms Following Exposure Inhalation causes moderate irritation of upper respiratory system. Contact of liquid with eyes causes moderate irritation. Repeated contact with skin may extract oils and result in irritation. Ingestion causes nausea and irritation of mouth and stomach General Treatment for Exposure INHALATION remove victim to fresh air at once enforce rest, and keep warm get medical attention Immediately. EYES flush with water for at least 15 min. if irritation persists, get medical attention. SKIN flush with plenty of water and wash thoroughly get treatment for any lasting irritation. INGESTION if large amounts are swallowed, induce vomiting by ticking the back of the throat with the finger or by giving an emetic such as two tablespoons of common salt in a glass of warm water get medical attention Toxidty by Inhalation (Thresholdlimit Value) Data not available Short-Term Exposure limits Data not available Toxidty by Ingestion Grade 2 oral LDjo 535 mg/kg (rat) Late Toxidty Data not available Vapor (Gas) Irritant Characteristics Vapors cause severe irritation of eye and throat and can cause eye and lung injury. They cannot be tolerated even at low concentrations Liquid or Solid Irritant Charaderistics Causes smarting of the skin and first-degree bums on short exposure and may cause second-degree burns on long exposure Odor Threshold 0.001 ppm.  [c.138]

Nuclease cleavage at a restriction site opens, or linearizes, the circular plasmid so that a foreign DNA fragment can be inserted. The ends of this linearized plasmid are joined to the ends of the fragment so that the circle is closed again, creating a recombinant plasmid (Figure 13.2). Recombinant plasmids are hybrid DNA molecules consisting of plasmid DNA sequences plus inserted DNA elements (called inserts). Such hybrid molecules are also called chimeric constructs or chimeric plasmids. (The term chimera is borrowed from mythology and refers to a beast composed of the body and head of a lion, the heads of a goat and a snake, and the wings of a bat.) The presence of foreign DNA sequences does not adversely affect replication of the plasmid, so chimeric plasmids can be propagated in bacteriajust like the original plasmid. Bacteria often harbor several hundred copies of common cloning vectors per cell. Hence, large amounts of a cloned DNA sequence can be recovered from bacterial cultures. The enormous power of recombinant DNA technology stems in part from the fact that virtually any DNA sequence can be selectively cloned and amplified in this manner. DNA sequences that are difficult to clone include inverted repeats, origins of replication, centromeres, and telomeres. The only practical limitation is the size of the foreign DNA segment most plasmids with inserts larger than about 10 kbp are not replicated efficiently.  [c.397]


See pages that mention the term N-terminal segment side chains : [c.178]    [c.39]    [c.263]    [c.15]    [c.400]    [c.175]    [c.1243]    [c.89]    [c.118]    [c.376]    [c.175]   
Introduction to protein structure (1999) -- [ c.7 , c.154 ]