Calculated minimum energy conformations of nonactin

Nonactin is a cyclic actinomycete metabolite which has been implicated as an ion carrier in the passive transport of potassium across certain biological membranes. In order to discover the conformations of the molecule which are involved in its biochemical function, computer calculations were initiated to derive the energetically favored conformations of the nonactin ring. By assuming that all the relevant three-dimensional conformations of nonactin have the same symmetry property as that suggested by the chemical structure of the molecule (S₄) it was possible to generate a representative sample of all sterically allowed conformations of nonactin. The energies of these conformations were calculated by taking into account the nonbonded interactions among the 116 atoms of the molecule and the torsional potential energy of the 20 rotatable backbone bonds of the ring. The initial results reported in this paper indicate that even in the absence of potassium ion the nonactin ring folds into the same compact tennis-ball seam-like conformation that was found by an X-ray crystallographic investigation of the nonactin/KNCS complex.     

Global minimum energy conformations of thyrotropin releasing hormone analogs by simulated annealing. II

Lowest conformational energy structures of seventeen thyrotropin releasing hormone analogs have been studied by simulated annealing. A surprising conformational similarity was observed for the peptide backbone. The possible role of each substituent in its biological activity is inferred. A composite hydrogen-bonding environment is proposed for the TRH with respect to receptor binding.     

Low-frequency infrared bands and chain conformations of polypeptides

Infrared spectra of polypeptides were measured in the region of 1800–400 cm^?1. For the α-helical form, disordered form, and antiparallel-chain β-form, amide V band- arising from N-H out-of-plane bending models were observed at 610–620, around 650, and 700–705 cm^?1, respectively, and amide V′ bands arising from N-D out-of-plane bending modes were observed at 455–465, around 510, and a 515–530 cm^?1, respectively. These correlations are useful for conformation diagnoses, particularly for copolyamino-acids or proteins which are not oriented. The nature of low-frequency amide bands are discussed with reference to potential energy distributions calculated for the α-helical form and β form.     

Sequence-dependent conformations of short polypeptides in a hydrophobic environment

Summary Surfactants, which provide a hydrophobic environment, may induce an ordered conformation in polypeptides and proteins that contain a sequence with helix- or -forming potential. This hypothesis has been illustrated in circular dichroic studies of oligopeptides and short polypeptides. These peptide-surfactant complexes can form (1) a helix, (2) a -form, (3) either form (depending on experimental conditions), or can remain in (4) an ordered form. The induced helix is stable in a surfactant solution below or above its critical micellar concentration, whereas the induced -form is usually converted back to an unordered form when the surfactant used is above its critical micellar concentration, or it is transformed into a helix in excess surfactant solution if the peptide has both the helix- and -forming potential. In most cases the observed conformations agree with those predicted from the amino acid sequences of the peptides. The induced conformation of a peptide can be destabilized by charges on the side groups having the same sign as that of surfactant ions. Disulfide bonds can inhibit the formation of induced conformation because of steric hindrance. The terminal effect can prevent a peptide from forming an ordered conformation near the NH₂- and COOH-terminus.     

13C-NMR chemical shifts and the conformations of rigid polypeptides

¹³C-nmr chemical shifts of backbone carbonyl and side-chain β-carbons in polypeptides provide structural information. Recent utilization of substituent effects on ¹³C-nmr chemical shifts (principally γ-effects) has permitted the rationalization of their sequence and conformation dependence when observed in linear, flexible polypeptides. In this report, we apply the γ-effect method to study the ¹³C-nmr chemical shifts observed in solution and in the solid state for the backbone carbonyl and side-chain β-carbons in conformationally rigid polypeptides, which are usually cyclic. As found previously for flexible, linear polypetides, the relative ¹³C-nmr chemical shifts observed for the backbone carbonyl and side-chain β-carbons in conformationally rigid polypeptides are predictable from knowledge of their peptide residue sequence (primary structure) and conformation (secondary structure) via the γ-effect method.     

Helix geometry of single stranded DNA ''A'' and ''B'' forms from minimum energy conformations of dimeric subunits.

Low energy conformations with dihedral angles similar to those occurring in fibers of the 'A' and 'B' forms of DNAs have been calculated for the deoxydinucleoside phosphates dApdA, dCpdC, dTpdT, dGpdG and dGpdC (1-3). These conformers have been used as building blocks for generating larger single stranded polymers, whose helical parameters we have calculated. We find that single stranded 'A' and 'B' form helices tend to be narrower and more tightly wound than the duplexes obtained in fibers (4,5). This is consistent with experimental observations on single stranded fibers of poly (rC) (6). We also find that the different sequences have different helix geometries. In addition, it is observed that large variations in helix geometry for a given sequence are achievable at little energetic cost.     

Protein threading by recursive dynamic programming.

We present the recursive dynamic programming (RDP) method for the threading approach to three-dimensional protein structure prediction. RDP is based on the divide-and-conquer paradigm and maps the protein sequence whose backbone structure is to be found (the protein target) onto the known backbone structure of a model protein (the protein template) in a stepwise fashion, a technique that is similar to computing local alignments but utilising different cost functions. We begin by mapping parts of the target onto the template that show statistically significant similarity with the template sequence. After mapping, the template structure is modified in order to account for the mapped target residues. Then significant similarities between the yet unmapped parts of the target and the modified template are searched, and the resulting segments of the target are mapped onto the template. This recursive process of identifying segments in the target to be mapped onto the template and modifying the template is continued until no significant similarities between the remaining parts of target and template are found. Those parts which are left unmapped by the procedure are interpreted as gaps.The RDP method is robust in the sense that different local alignment methods can be used, several alternatives of mapping parts of the target onto the template can be handled and compared in the process, and the cost functions can be dynamically adapted to biological needs.Our computer experiments show that the RDP procedure is efficient and effective. We can thread a typical protein sequence against a database of 887 template domains in about 12 hours even on a low-cost workstation (SUN Ultra 5). In statistical evaluations on databases of known protein structures, RDP significantly outperforms competing methods. RDP has been especially valuable in providing accurate alignments for modeling active sites of proteins.RDP is part of the ToPLign system (GMD Toolbox for protein alignment) and can be accessed via the WWW independently or in concert with other ToPLign tools at http://cartan.gmd.de/ToPLign.html.     

Extended conformations of polypeptides and proteins in urea and guanidine hydrochloride

By analyzing the effect of urea and guanidine hydrochloride on the circular dichroism of many polypeptides and proteins, it is concluded that under conditions of high concentration of the perturbant and at low temperatures the resultant state approached is that of a local extended helix structure instead of a completely random coil. Intensification by urea and guanidine hydrochloride of the circular dichroism bands of poly-L -proline II leads to the proof that the mechanism of interaction of urea and guanidine hydrochloride with proteins is through hydrogen bonding to the backbone carbonyl group.     

Different conformations of nascent polypeptides during translocation across the ER membrane

Background  

In eukaryotic cells, proteins are translocated across the ER membrane through a continuous ribosome-translocon channel. It is unclear to what extent proteins can fold already within the ribosome-translocon channel, and previous studies suggest that only a limited degree of folding (such as the formation of isolated α-helices) may be possible within the ribosome.     

Optimization of CSTRs in series by dynamic programming

This article concerns the development of a simple yet effective procedure for optimizing the design of a reactor system employing CSTRs in series. The basic approach used in this work was to translate the problem of reactor design to a mathematical programming model. The resulting model was then solved by dynamic programming. The procedure was tested on an IBM 3033 computer and an IBM PC-compatible machine, the CORONA PC-II microcomputer. The results of this study indicate that the optimization procedure developed is very effective.     

Optimization of fed-batch fermentors by iterative dynamic programming

By using penalty functions to handle state constraints, iterative dynamic programming can be used in a straightforward manner for the optimization of fedbatch fermentors. No computational difficulties were encountered and better results are obtained than previously reported in the literature for a fed-batch fermentor for biosynthesis of penicillin. (c) 1993 Johy Wiley & Sons, Inc.     

Effect of sequence-specific interactions on the stability of helical conformations in polypeptides

A modification of the Zimm–Bragg two-state model for the helix–coil transition in polypeptides, which considers the effect of charge–dipole, charge–charge, and other specific interactions on helix stability, is presented. The new model introduces a series of adjustable parameters whose values are estimated by fitting to recent spectroscopic results on medium-sized peptides. This formalism, based on traditional two-state helix–coil transition models, provides a framework in which data on the helix contents of peptides of specific sequence can be rationalized by a statistical mechanical theory.     

Minimum energy conformations of proline-containing helices.

Proline occurs frequently in transmembrane alpha-helices of transport and receptor proteins even though statistical surveys demonstrate the overwhelming preference of this residue for a non-alpha-helical, hydrophilic environment. As a result, membrane-buried proline has been proposed to be functionally important, with function arising from structural discontinuity or destabilization of the helix. Destabilization may occur by Pro-mediated conformational transitions between discrete states, and may be manifested in membrane protein systems through reversible processes such as channel opening and closing or signal transduction. In this study, computer modeling of a model transmembrane alpha-helix, (Ala)8-Leu-Pro-Phe-(Ala)8, in a medium of low polarity (dielectric = 2), is used to examine the occurrence and energetic accessibility of Pro-mediated conformational interconversions. Leu psi and chi 1, Pro psi, and Phe phi and chi 1 torsion angles were assigned random values so that a data base of 200 conformations for each of the cis and trans states was generated. The conformations were minimized and low-energy structures organized into families. This analysis demonstrated that the most populated lowest energy family is the Trans-I conformation, corresponding to proline in a kinked alpha-helix. Two additional trans structures, Trans-II and Trans-III, as well as a cis conformation, Cis-I, are also energetically competitive. Interconversions between the trans states could thus be mediated by changes at a single torsion angle, accompanied by minor local hydrogen-bonding rearrangements. This work substantiates that membrane-buried proline can provide the basis for conformational transitions between discrete alpha-helix-based structures in a nonpolar environment.     

A model for the single stranded random coil form of polydeoxyadenylic acid from minimum energy conformations of the dimeric subunit.

The minimum energy conformations of dApdA have been examined for their suitability as buildings blocks of the single stranded coil form of polynucleotides. Calculations of the characteristic ratio C difference = less than ro greater than 2/n liter2 were made for a polymer generated from all the low energy conformers, as well as for selected combinations. A polymer composed of a conformer with omega', omega = t*,g+,(skewed) psi = t, C-(2)-endo type pucker, in combination with the 'B' form, has a C difference equal to that observed in coils of apurinic acid (6) when the fraction of 'B' form conformers is approximately 25% and approximately 91%. The t*,g+ conformer is the second lowest energy form in the C-(2)-endo puckering domain, following the 'B' form.     

Protein elasticity based on conformations of sequential polypeptides: The biological elastic fiber

Fibrous elastin of the biological elastic fiber is a cross-linked condensed state in which there is roughly one-half polypeptide and one-half water. The precursor protein tropoelastin, a chemical fragmentation product -elastin, and a sequential polypeptide (l·Val¹-l·Pro²-Gly³-l·Val⁴-Gly⁵) _n , which is a prominent primary structural feature of tropoelastin, are each soluble in all proportions in water at 20°C. On heating to physiological temperatures, each undergoes aggregation and forms a dense viscoelastic phase, which as the fiber itself, is about 60% water. This reversible heat-elicited condensed phase is called the coacervate. Circular dichroism studies show coacervation to be a process of increasing intramolecular order. Electron microscopy (light, scanning, and transmission) shows coacervation to be a process of increasing order intermolecularly. Thus a rise in temperature between 20 and 40°C results in an increase in order of the polypeptide. Coacervation is an inverse temperature transition, and the condensed state is anisotropic at the molecular level. Thermoelasticity studies in water on bovine ligamentum nuchae fibrous elastin and on -irradiation cross-linked polypentapeptide coacervates show increases in elastomeric force,f, over the same 20–40°C temperature range in which the inverse temperature transition gives rise to the coacervate, and the constancy off/T with temperature, once the transition is effectively completed, suggests a high-entropy component to the elastomeric force. Thus the data argue for an anisotropic-entropic elastomer.Detailed conformational studies on the polypentapeptide result in the development of a -spiral conformation in which there are regularly recurring -turns in loose helical array (a structure that forms on raising the temperature) and in which there are recurring dynamic suspended segments that are the focal point of large, low-energy oscillatory motions called librations. The structure gives rise to a librational entropy mechanism of elasticity wherein the amplitudes of the rocking motions become damped on stretching. This perspective is substantiated by dielectric relaxation studies on the coacervate state and by characterization of synthetic analogs of the polypentapeptide. Dielectric relaxation studies on a concentrated state of about 60% water show the development of a regular structure over the same temperature range as for the development of the coacervate state, and the development of the regular structure with increasing temperature is seen to parallel the development of elastomeric force with increasing temperature. Increasing elastomeric force coincides with increasing regularity of structure! Synthetic analogs of the polypentapeptide, designed to interfere with the librational processes of the suspended segment, impair elastic function, and an analog that makes the -turn more rigid results in increased elastic modulus. This development of a librational entropy mechanism for protein elasticity is a departure from the kinetic theory of rubber elasticity, the random network perspective that has dominated the traditional view of biological elasticity for the past several decades. The new perspective opens the way to insightful consideration of new elastomeric biomaterials with numerous biomedical applications.