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Globular Proteins (globular + protein)
Selected AbstractsPhysical-chemical determinants of turn conformations in globular proteinsPROTEIN SCIENCE, Issue 8 2007Timothy O. Street Abstract Globular proteins are assemblies of ,-helices and ,-strands, interconnected by reverse turns and longer loops. Most short turns can be classified readily into a limited repertoire of discrete backbone conformations, but the physical,chemical determinants of these distinct conformational basins remain an open question. We investigated this question by exhaustive analysis of all backbone conformations accessible to short chain segments bracketed by either an ,-helix or a ,-strand (i.e., ,-segment-,, ,-segment-,, ,-segment-,, and ,-segment-,) in a nine-state model. We find that each of these four secondary structure environments imposes its own unique steric and hydrogen-bonding constraints on the intervening segment, resulting in a limited repertoire of conformations. In greater detail, an exhaustive set of conformations was generated for short backbone segments having reverse-turn chain topology and bracketed between elements of secondary structure. This set was filtered, and only clash-free, hydrogen-bond,satisfied conformers having reverse-turn topology were retained. The filtered set includes authentic turn conformations, observed in proteins of known structure, but little else. In particular, over 99% of the alternative conformations failed to satisfy at least one criterion and were excluded from the filtered set. Furthermore, almost all of the remaining alternative conformations have close tolerances that would be too tight to accommodate side chains longer than a single ,-carbon. These results provide a molecular explanation for the observation that reverse turns between elements of regular secondary can be classified into a small number of discrete conformations. [source] Structural refinement by restrained molecular-dynamics algorithm with small-angle X-ray scattering constraints for a biomoleculeJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 1 2004Masaki Kojima A new algorithm to refine protein structures in solution from small-angle X-ray scattering (SAXS) data was developed based on restrained molecular dynamics (MD). In the method, the sum of squared differences between calculated and observed SAXS intensities was used as a constraint energy function, and the calculation was started from given atomic coordinates, such as those of the crystal. In order to reduce the contribution of the hydration effect to the deviation from the experimental (objective) curve during the dynamics, and purely as an estimate of the efficiency of the algorithm, the calculation was first performed assuming the SAXS curve corresponding to the crystal structure as the objective curve. Next, the calculation was carried out with `real' experimental data, which yielded a structure that satisfied the experimental SAXS curve well. The SAXS data for ribonuclease T1, a single-chain globular protein, were used for the calculation, along with its crystal structure. The results showed that the present algorithm was very effective in the refinement and adjustment of the initial structure so that it could satisfy the objective SAXS data. [source] Applications of time-resolved resonance energy transfer measurements in studies of the molecular crowding effect,JOURNAL OF MOLECULAR RECOGNITION, Issue 5 2004Varda Ittah Abstract The native structures of many globular proteins are only weakly stabilized and form in solution ensembles of multiple conformers. The energy differences between the conformers are assumed to be small. This is the case of flexible multidomain proteins where domain motions were observed. High concentrations of inert macrosolute, which create a crowded or confined environment, can cause shifts of the distribution of the conformers of such proteins towards the more compact structures. This effect may also promote compact structures in partially folded proteins. Time-resolved dynamic non-radiative excitation energy transfer (tr-RET) is suitable for detection of either subtle or major changes in distributions of intramolecular distances in protein molecules in solutions. Two experiments were performed which demonstrated the applicability of tr-RET for detection of the effect of macrosolutes on the conformational ensembles of flexible states of protein molecules. The distribution of distances between residues 203 and 169 in the CORE domain of E. coli adenylate kinase (AK) in the denatured state was determined in the presence of high concentrations of dextran 40. A significant shift of the mean of the distribution was observed without reduction of its width. This was interpreted as a shift to compact structure without change of the degree of disorder of the chain. In a second experiment the distribution of the distance between residues 55 and 169 in AK, which spans the cleft between the CORE and the AMPbind domains, was monitored. No clear effect of high concentrations of dextran 40 was found. These experiments show the strength of the application of tr-RET in investigation of changes in the sub-states of flexible conformations of globular protein. Networks of pairs of labeled sites can be prepared and tr-RET experiments can be performed in order to search for the segments of the protein molecules, which respond to the presence of inert macromolecules in their environment. Copyright © 2004 John Wiley & Sons, Ltd. [source] Structure and Photoreaction of Photoactive Yellow Protein, a Structural Prototype of the PAS Domain Superfamily,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 1 2007Yasushi Imamoto Photoactive yellow protein (PYP) is a water-soluble photosensor protein found in purple photosynthetic bacteria. Unlike bacterial rhodopsins, photosensor proteins composed of seven transmembrane helices and a retinal chromophore in halophilic archaebacteria, PYP is a highly soluble globular protein. The ,/, fold structure of PYP is a structural prototype of the PAS domain superfamily, many members of which function as sensors for various kinds of stimuli. To absorb a photon in the visible region, PYP has a p -coumaric acid chromophore binding to the cysteine residue via a thioester bond. It exists in a deprotonated trans form in the dark. The primary photochemical event is photo-isomerization of the chromophore from trans to cis form. The twisted cis chromophore in early intermediates is relaxed and finally protonated. Consequently, the chromophore becomes electrostatically neutral and rearrangement of the hydrogen-bonding network triggers overall structural change of the protein moiety, in which local conformational change around the chromophore is propagated to the N-terminal region. Thus, it is an ideal model for protein conformational changes that result in functional change, responding to stimuli and expressing physiological activity. In this paper, recent progress in investigation of the photoresponse of PYP is reviewed. [source] Structural comparison of Escherichia colil -asparaginase in two monoclinic space groupsACTA CRYSTALLOGRAPHICA SECTION D, Issue 3 2003Mario Sanches The functional l -asparaginase from Escherichia coli is a homotetramer with a molecular weight of about 142,kDa. The X-ray structure of the enzyme, crystallized in a new form (space group C2) and refined to 1.95,Å resolution, is compared with that of the previously determined crystal form (space group P21). The asymmetric unit of the new crystal form contains an l -asparaginase dimer instead of the tetramer found in the previous crystal form. It is found that crystal contacts practically do not affect the conformation of the protein. It is shown that subunit C of the tetrameric form is in a conformation which is systematically different from that of all other subunits in both crystal forms. Major conformational differences are confined to the lid loop (residues 14,27). In addition, the stability of this globular protein is analyzed in terms of the interactions between hydrophobic parts of the subunits. [source] Synthesis of Gold Microplates Using Bovine Serum Albumin as a Reductant and a StabilizerCHEMISTRY - AN ASIAN JOURNAL, Issue 1 2010Leslie Au Abstract Gold microplates were synthesized in aqueous solutions by reducing HAuCl4 with the hydroxyl groups in both serine and threonine of bovine serum albumin (BSA), which is a globular protein in its native state. In this article, we systematically investigated the effects of temperature, pH value, the concentration of BSA, and ionic species on the reduction kinetics and thus the size and morphology of the final product. The optimal experimental conditions for producing uniform Au microplates include the following: an elevated temperature in the range of 55,65,°C, an acidic solution with pH,3, and the presence of NaCl (0.14,M). We found that if any one of these parameters was deviated from the optimal condition, Au microplates would not be formed in high yields. We also found that the surfaces of the as-synthesized Au microplates were covered by a dense array of BSA bumps. [source] Similarity of permeabilities for Ficoll, pullulan, charge-modified albumin and native albumin across the rat peritoneal membraneACTA PHYSIOLOGICA, Issue 4 2009D. Asgeirsson Abstract Aim:, Compared to neutral globular proteins, neutral polysaccharides, such as dextran, pullulan and Ficoll, appear hyperpermeable across the glomerular filtration barrier. This has been attributed to an increased flexibility and/or asymmetry of polysaccharides. The present study investigates whether polysaccharides are hyperpermeable also across the continuous capillaries in the rat peritoneum. Methods:, In anaesthetized Wistar rats, FITC,Ficoll or FITC,pullulan together with 125I-human serum albumin (RISA) or neutralized 125I-bovine serum albumin (nBSA) were given intravenously, after which peritoneal dialysis (PD) using conventional PD fluid (Gambrosol 1.5%) was performed for 120 min. Concentrations of FITC-polysaccharides and radioactive albumin species in plasma and dialysis fluid were analysed with high-performance size exclusion chromatography and a gamma counter respectively. Transperitoneal clearance values were calculated for polysaccharides in the molecular radius range 36,150 Å, and for RISA and nBSA. Results:, Ficoll and pullulan showed more or less identical permeabilities, compared to RISA and nBSA, across the peritoneal membrane. Although RISA-clearance, 5.50 ± 0.28 (,L min,1; ±SEM), tended to be lower than the clearances of Ficoll36Å (6.55 ± 0.25), pullulan36Å (6.08 ± 0.22) and nBSA (6.56 ± 0.23), the difference was not statistically significant. This is in contrast to the hyperpermeability exhibited by polysaccharides across the glomerular filtration barrier and also contrasts with the charge selectivity of the latter. Conclusion:, The phenomenon of molecular flexibility is more important for a macromolecule's permeability through the glomerular filter than across the continuous peritoneal capillary endothelium. Furthermore, it seems that charge plays a subordinate role in the steady-state transport across the combined peritoneal capillary,interstitial barrier. [source] Abundance of intrinsic disorder in SV-IV, a multifunctional androgen-dependent protein secreted from rat seminal vesicleFEBS JOURNAL, Issue 4 2008Silvia Vilasi The potent immunomodulatory, anti-inflammatory and procoagulant properties of protein no. 4 secreted from the rat seminal vesicle epithelium (SV-IV) have previously been found to be modulated by a supramolecular monomer,trimer equilibrium. More structural details that integrate experimental data into a predictive framework have recently been reported. Unfortunately, homology modelling and fold-recognition strategies were not successful in creating a theoretical model of the structural organization of SV-IV. It was inferred that the global structure of SV-IV is not similar to that of any protein of known three-dimensional structure. Reversing the classical approach to the sequence,structure,function paradigm, in this paper we report novel information obtained by comparing the physicochemical parameters of SV-IV with two datasets composed of intrinsically unfolded and ideally globular proteins. In addition, we analyse the SV-IV sequence by several publicly available disorder-oriented predictors. Overall, disorder predictions and a re-examination of existing experimental data strongly suggest that SV-IV needs large plasticity to efficiently interact with the different targets that characterize its multifaceted biological function, and should therefore be better classified as an intrinsically disordered protein. [source] In Vitro Selection of Self-Interacting Transmembrane Segments--Membrane Proteins Approached from a Different PerspectiveIUBMB LIFE, Issue 3 2002Dieter Langosch Abstract The principles underlying the folding of integral membrane proteins are uncovered in an increasingly detailed way. Experimental determination of high-resolution structures followed by analysis of packing reveal structural similarities as well as differences to soluble globular proteins. At the same time, protein/protein interactions at the level of membrane-embedded domains have been investigated for different model proteins. More recently, self-interacting transmembrane helices have been selected from combinatorial libraries in vitro to study the mechanistic basis of protein/protein interaction in membranes in a systematic way. With an emphasis on the latter approach, this review discusses insights emerging from an integrated view on the recent advances. [source] Phase and Rheological Behavior of High-Concentration Colloidal Hard-Sphere and Protein DispersionsJOURNAL OF FOOD SCIENCE, Issue 7 2007S.M. Loveday ABSTRACT:, Colloidal hard-sphere (HS) particles of narrow-size distribution exhibit crystalline and glassy states beginning at the particle volume fractions ,= 0.494 and ,G= 0.58, respectively. Dynamic rheological data on the dispersions were strongly modified to solid-like behavior as , approached ,G. In addition, cooperative motion in structural relaxation has been observed microscopically in the colloidal dispersions near the glassy state. Very high viscosities and glassy states were also found in high-concentration dispersions of sodium caseinate and the globular proteins: bovine serum albumin and ,-lactoglobulin. Viscosity models developed for HS dispersions predicted accurately the trends but not the absolute values of protein dispersions. Dispersions of food colloidal particles may be employed in studies, in which volume fraction is the thermodynamic variable, for understanding the relaxation and transport processes related to 1st-order and colloidal glass transitions. [source] Applications of time-resolved resonance energy transfer measurements in studies of the molecular crowding effect,JOURNAL OF MOLECULAR RECOGNITION, Issue 5 2004Varda Ittah Abstract The native structures of many globular proteins are only weakly stabilized and form in solution ensembles of multiple conformers. The energy differences between the conformers are assumed to be small. This is the case of flexible multidomain proteins where domain motions were observed. High concentrations of inert macrosolute, which create a crowded or confined environment, can cause shifts of the distribution of the conformers of such proteins towards the more compact structures. This effect may also promote compact structures in partially folded proteins. Time-resolved dynamic non-radiative excitation energy transfer (tr-RET) is suitable for detection of either subtle or major changes in distributions of intramolecular distances in protein molecules in solutions. Two experiments were performed which demonstrated the applicability of tr-RET for detection of the effect of macrosolutes on the conformational ensembles of flexible states of protein molecules. The distribution of distances between residues 203 and 169 in the CORE domain of E. coli adenylate kinase (AK) in the denatured state was determined in the presence of high concentrations of dextran 40. A significant shift of the mean of the distribution was observed without reduction of its width. This was interpreted as a shift to compact structure without change of the degree of disorder of the chain. In a second experiment the distribution of the distance between residues 55 and 169 in AK, which spans the cleft between the CORE and the AMPbind domains, was monitored. No clear effect of high concentrations of dextran 40 was found. These experiments show the strength of the application of tr-RET in investigation of changes in the sub-states of flexible conformations of globular protein. Networks of pairs of labeled sites can be prepared and tr-RET experiments can be performed in order to search for the segments of the protein molecules, which respond to the presence of inert macromolecules in their environment. Copyright © 2004 John Wiley & Sons, Ltd. [source] Protein Sequences as Literature TextMACROMOLECULAR THEORY AND SIMULATIONS, Issue 5 2006Valentina V. Vasilevskaya Abstract Summary: We have performed analysis of protein sequences treating them as texts written in a "protein" language. We have shown that repeating patterns (words) of various lengths can be identified in these sequences. It was found that the maximum word lengths are different for proteins belonging to different classes; therefore, the corresponding values can be used to characterize the protein type. The suggested technique was first applied to analyze (decompose into words) normal (literature) texts written as a gapless symbolic sequence without spaces and punctuation marks. The tests using fiction, scientific, and popular scientific English texts proved the relative efficiency of the technique. Maximum word length for various proteins: ,fibrillar proteins, ,globular proteins, ,membrane proteins. [source] Physical,chemical determinants of coil conformations in globular proteinsPROTEIN SCIENCE, Issue 6 2010Lauren L. Perskie Abstract We present a method with the potential to generate a library of coil segments from first principles. Proteins are built from ,-helices and/or ,-strands interconnected by these coil segments. Here, we investigate the conformational determinants of short coil segments, with particular emphasis on chain turns. Toward this goal, we extracted a comprehensive set of two-, three-, and four-residue turns from X-ray,elucidated proteins and classified them by conformation. A remarkably small number of unique conformers account for most of this experimentally determined set, whereas remaining members span a large number of rare conformers, many occurring only once in the entire protein database. Factors determining conformation were identified via Metropolis Monte Carlo simulations devised to test the effectiveness of various energy terms. Simulated structures were validated by comparison to experimental counterparts. After filtering rare conformers, we found that 98% of the remaining experimentally determined turn population could be reproduced by applying a hydrogen bond energy term to an exhaustively generated ensemble of clash-free conformers in which no backbone polar group lacks a hydrogen-bond partner. Further, at least 90% of longer coil segments, ranging from 5- to 20 residues, were found to be structural composites of these shorter primitives. These results are pertinent to protein structure prediction, where approaches can be divided into either empirical or abinitio methods. Empirical methods use database-derived information; abinitio methods rely on physical,chemical principles exclusively. Replacing the database-derived coil library with one generated from first principles would transform any empirically based method into its corresponding abinitio homologue. [source] Physical-chemical determinants of turn conformations in globular proteinsPROTEIN SCIENCE, Issue 8 2007Timothy O. Street Abstract Globular proteins are assemblies of ,-helices and ,-strands, interconnected by reverse turns and longer loops. Most short turns can be classified readily into a limited repertoire of discrete backbone conformations, but the physical,chemical determinants of these distinct conformational basins remain an open question. We investigated this question by exhaustive analysis of all backbone conformations accessible to short chain segments bracketed by either an ,-helix or a ,-strand (i.e., ,-segment-,, ,-segment-,, ,-segment-,, and ,-segment-,) in a nine-state model. We find that each of these four secondary structure environments imposes its own unique steric and hydrogen-bonding constraints on the intervening segment, resulting in a limited repertoire of conformations. In greater detail, an exhaustive set of conformations was generated for short backbone segments having reverse-turn chain topology and bracketed between elements of secondary structure. This set was filtered, and only clash-free, hydrogen-bond,satisfied conformers having reverse-turn topology were retained. The filtered set includes authentic turn conformations, observed in proteins of known structure, but little else. In particular, over 99% of the alternative conformations failed to satisfy at least one criterion and were excluded from the filtered set. Furthermore, almost all of the remaining alternative conformations have close tolerances that would be too tight to accommodate side chains longer than a single ,-carbon. These results provide a molecular explanation for the observation that reverse turns between elements of regular secondary can be classified into a small number of discrete conformations. [source] Temperature-induced reversible conformational change in the first 100 residues of ,-synucleinPROTEIN SCIENCE, Issue 3 2006Brian C. McNulty Abstract Natively disordered proteins are a growing class of anomalies to the structure,function paradigm. The natively disordered protein ,-synuclein is the primary component of Lewy bodies, the cellular hallmark of Parkinson's disease. We noticed a dramatic difference in dilute solution 1H- 15N Heteronuclear Single Quantum Coherence (HSQC) spectra of wild-type ,-synuclein and two disease-related mutants (A30P and A53T), with spectra collected at 35°C showing fewer cross-peaks than spectra acquired at 10°C. Here, we show the change to be the result of a reversible conformational exchange linked to an increase in hydrodynamic radius and secondary structure as the temperature is raised. Combined with analytical ultracentrifugation data showing ,-synuclein to be monomeric at both temperatures, we conclude that the poor quality of the 1H- 15N HSQC spectra obtained at 35°C is due to conformational fluctuations that occur on the proton chemical shift time scale. Using a truncated variant of ,-synuclein, we show the conformational exchange occurs in the first 100 amino acids of the protein. Our data illustrate a key difference between globular and natively disordered proteins. The properties of globular proteins change little with solution conditions until they denature cooperatively, but the properties of natively disordered proteins can vary dramatically with solution conditions. [source] Structural composition of ,I - and ,II -proteinsPROTEIN SCIENCE, Issue 2 2003Narasimha Sreerama Abstract Circular dichroism spectra of proteins are sensitive to protein secondary structure. The CD spectra of ,-rich proteins are similar to those of model ,-helices, but ,-rich proteins exhibit CD spectra that are reminiscent of CD spectra of either model ,-sheets or unordered polypeptides. The existence of these two types of CD spectra for ,-rich proteins form the basis for their classification as ,I - and ,II -proteins. Although the conformation of ,-sheets is largely responsible for the CD spectra of ,I -proteins, the source of ,II -protein CD, which resembles that of unordered polypeptides, is not completely understood. The CD spectra of unordered polypeptides are similar to that of the poly(Pro)II helix, and the poly(Pro)II-type (P2) structure forms a significant fraction of the unordered conformation in globular proteins. We have compared the ,-sheet and P2 structure contents in ,-rich proteins to understand the origin of ,II -protein CD. We find that ,II -proteins have a ratio of P2 to ,-sheet content greater than 0.4, whereas for ,I -proteins this ratio is less than 0.4. The ,-sheet content in ,I -proteins is generally higher than that in ,II -proteins. The origin of two classes of CD spectra for ,-rich proteins appears to lie in their relative ,-sheet and P2 structure contents. [source] Understanding on the residue contact network using the log-normal cluster model and the multilevel wheel diagram,BIOPOLYMERS, Issue 10 2010Weitao Sun Abstract Residue clusters play essential role in stabilizing protein structures in the form of complex networks. We show that the cluster sizes in a native protein follow the log-normal distribution for a dataset consisting of 424 proteins. To our knowledge, this is the first time of such fitting for the native structures. Based on log-normal model, the asymptotically increasing mean cluster sizes produce a critical protein chain length of about 200 amino acids, beyond which length most globular proteins have nearly the same mean cluster sizes. This suggests that the larger proteins use a different packing mechanism than the smaller proteins. We confirmed the scale-free property of the residue contact network for most of the protein structures in the dataset, although the violations were observed for the tightly packed proteins. Residue cluster network wheel (RCNW) is proposed to visualize the relationship between the multiple properties of the residue network such as the cluster size, the residue types and contacts, and the flexibility of the residue. We noticed that the residues with large cluster size have smaller C, displacement measured using the normal mode analysis. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 904,916, 2010. [source] Physicochemical studies on the biopolymer inulin: A critical evaluation of its self-aggregation, aggregate-morphology, interaction with water, and thermal stabilityBIOPOLYMERS, Issue 9 2009Abhijit Dan Abstract Physicochemical properties viz., aggregation, molar mass, shape, and size of chicory inulin in solution were determined by fluorimetry, DLS, SLS, TEM, and viscometry methods. The thermal stability of the biopolymer was examined by TGA, DTA, and DSC measurements. The water vapor adsorption of desiccated inulin was also studied by the isopiestic method, and the data were analyzed in the light of the BET equation. On the basis of the obstruction to ion conductance by the inulin aggregates in solution and analysis of the data, the extent of hydration of inulin in solution was estimated. The result was coupled with the intrinsic viscosity, [,], of inulin to ascertain the shape of the biopolymer aggregates in aqueous solution. The critical aggregation concentration (cac) of inulin in aqueous as well as in salt solution was assessed by fluorimetry. The weight average molar mass, , of inulin monomer and its aggregate was found to be 4468 and 1.03 × 106 g/mol, respectively, in aqueous solution. This aggregated mass was 2.4 × 106 g/mol in 0.5M NH4SCN solution. The [,] values of the soft supramolecular aggregates in solution (without and with salt) were small and comparable with globular proteins evidencing spherical geometry of the biopolymer aggregates as supported by the TEM results. In DMSO, rod-like aggregates of inulin was found by the TEM study. The [,] of the biopolymer in the DMSO medium was therefore, higher than that in the aqueous medium. Unlike aqueous medium, the aggregation in DMSO was not associated with a cac. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 687,699, 2009. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] The ribbon of hydrogen bonds in globular proteins.BIOPOLYMERS, Issue 2 2004Abstract A study of the role of the hydrogen-bonding side chains in the ribbon of hydrogen bonds in globular proteins, using the papain family as an example, suggests that these side chains may be divided into three categories depending on their position in the molecule. In the first category, they form part of the local ribbon, in the second they form part of the ribbon at a site remote along the main chain, and in the third they play no role in the formation of the ribbon. The second case is particularly interesting because it provides a natural mechanism for the formation of the tertiary structure of the globular proteins. The results suggest that the robustness of the globular proteins towards mutations arises from the fact that many mutations that involve hydrogen-bonding side chains either leave the hydrogen bonding of the ribbon essentially unchanged or their hydrogen bonding plays no part in the formation of the ribbon in the first place. The results show that it is possible to obtain the ribbon of hydrogen bonds for a family of proteins whose data set's are of intermediate quality by studying the ribbons of several members of such a family and then taking an average over the different partial ribbons to create a standard ribbon of hydrogen bonds for the family as a whole. This method is used here to derive the standard ribbon for the papain family with papain itself, actinidin, and human liver cathepsin B as the representatives of the family. All three members of the family fit the standard ribbon with an accuracy of 85,91%. This result opens up the use of this technique for the study of a large number of globular proteins whose recorded data sets are of intermediate quality. © 2003 Wiley Periodicals, Inc. Biopolymers 73: 178,191, 2004 [source] The ribbon of hydrogen bonds and the pseudomolecule in the three-dimensional structure of globular proteins.BIOPOLYMERS, Issue 5 2002Abstract The model of the three-dimensional structure of globular proteins, which is based on a ribbon of hydrogen bonds along the whole of the backbone, is now applied to the comparison between monomeric bovine pancreatic ribonuclease A and dimeric bovine seminal ribonuclease. Some waters are involved in the hydrogen bonding of the ribbon, and the protein molecule plus these waters forms a pseudomolecule. The conformations of the three backbones are essentially identical and the three ribbons of hydrogen bonds are conserved with greater than 90% accuracy. We suggest that the conservation of the backbone conformations of the two molecules is a consequence of the conservation of the ribbons of hydrogen bonds. There are 16 simple mutations between the two molecules, of which 15 involve only side-chain groups with no more than one hydrogen bond to the backbone. Such mutations are not sufficient to change the ribbon of hydrogen bonds and hence there is no change in the backbone conformation. Generalizing this result, we suggest that the conservation of the ribbon is the reason why single point mutations rarely change the conformation of the backbone of the globular proteins. © 2002 Wiley Periodicals, Inc. Biopolymers 65: 347,353, 2002 [source] Crystallization of IgG1 by mapping its liquid,liquid phase separation curvesBIOTECHNOLOGY & BIOENGINEERING, Issue 5 2006Adam Idu Jion Abstract Monoclonal antibody therapeutics is an important and fast expanding market. While production of these molecules has been a major area of research, much less is known regarding the stabilization of these proteins for delivery as drugs. Crystallization of antibodies is one such promising route for protein stabilization at high titers, and here we took a systematic approach to initiate crystallization through nucleation in a simple PEG (polyethylene glycol), protein in water solution. A ternary mixture of globular proteins, PEG, and water will undergo a liquid,liquid phase separation (LLPS) as shown in a phase diagram or a Binodal curve. Of particular interest within the phase diagram is the position of the critical point, which is where nucleation occurs most rapidly. Detailed LLPS maps were created by increasing concentrations of PEG (from 5% to 11%) and IgG (from 1 to 20 mg/mL). By increasing the molecular weight (MW) of PEG (and hence its radius of gyration) from 1,000 to 6,000 g/mol, the temperatures of the critical point of nucleation were shown to increase. Once these curves were determined, nucleation experiments were conducted close to a chosen critical point (10.5 mg/mL IgG in 11% PEG 1000) and after 3 weeks, crystals of IgG of approximately 100 ,m in size were successfully formed. This is the first example of crystallization of an antibody through systematic mapping of LLPS curves, which is a fundamental step towards the scale-up of antibody crystallization. © 2006 Wiley Periodicals, Inc. [source] The Study of Protein Folding and Dynamics by Determination of Intramolecular Distance Distributions and Their Fluctuations Using Ensemble and Single-Molecule FRET Measurements,CHEMPHYSCHEM, Issue 5 2005Elisha Haas Prof. Abstract The folding and dynamics of globular proteins is a multidimensional problem. The structures of the heterogeneous population of refolding protein molecules are characterized by multiple distances and time constants. Deciphering the mechanism of folding depends on studies of the processes rather than the folded structures alone. Spectroscopy is indispensable for these sorts of studies. Herein, it is shown that the determination of intramolecular distance distributions by ensemble and single-molecule FRET experiments enable the exploration of partially folded states of refolding protein molecules. [source] | |||||||||||||||||||||||||