Psi-angle dependence of geminal proton–carbonyl-13C coupling constants in peptides. A theoretical investigation†

Theoretical calculations of the geminal carbonyl-13C- proton coupling constant, 2J(C′H), in α-amino acids have been carried out using Dirac Vector model and Penney-Dirac bond order formulations. The results indicate that the couplings are dependent on the backbone torsion angle psi (ψ) of the amino acid residues in peptides. The meagre available experimental data seem to support the theoretical findings.

Visualisation of a 2′-5′ parallel stranded double helix at atomic resolution: crystal structure of cytidylyl-2′,5′-adenosine

X-ray crystallographlc studies on 3′–5′ ollgomers have provided a great deal of information on the stereochemistry and conformational flexibility of nucleic acids and polynucleotides. In contrast, there is very little Information available on 2′–5′ polynucleotides. We have now obtained the crystal structure of Cytidylyl-2′,5′-Adenoslne (C2′p5′A) at atomic resolution to establish the conformational differences between these two classes of polymers. The dlnucleoside phosphate crystallises in the monocllnlc space group C2, with a = 33.912(4)Å, b =16.824(4)Å, c = 12.898(2)Å and 0 = 112.35(1) with two molecules in the asymmetric unit. Spectacularly, the two independent C2′p5′A molecules in the asymmetric unit form right handed miniature parallel stranded double helices with their respective crystallographic two fold (b axis) symmetry mates. Remarkably, the two mini duplexes are almost indistinguishable. The cytosines and adenines form self-pairs with three and two hydrogen bonds respectively. The conformation of the C and A residues about the glycosyl bond is anti same as in the 3′–5′ analog but contrasts the anti and syn geometry of C and A residues in A2′p5′C. The furanose ring conformation is C3′endo, C2′endo mixed puckering as in the C3′p5′A-proflavine complex. A comparison of the backbone torsion angles with other 2′–5′ dinucleoside structures reveals that the major deviations occur in the torsion angles about the C3′–C2′ and C4′-C3′ bonds. A right-handed 2′–5′ parallel stranded double helix having eight base pairs per turn and 45° turn angle between them has been constructed using this dinucleoside phosphate as repeat unit. A discussion on 2′–5′ parallel stranded double helix and its relevance to biological systems is presented.

A Hydraulic Micromanipulator

For biological experiments requiring manipulations under a microscope, it is necessary to have remote control for the manipulator. Available systems offer the required accuracy at a high cost. Passive micromanipulators are economical but are deficient in performance, the most serious defects being the inability to attenuate operator-induced vibrations and lack of speed control The manipulator described in this paper provides versatile remote control and may be constructed economically.

A Hydraulic Micromanipulator

For biological experiments requiring manipulations under a microscope, it is necessary to have remote control for the manipulator. Available systems offer the required accuracy at a high cost. Passive micromanipulators are economical but are deficient in performance, the most serious defects being the inability to attenuate operator-induced vibrations and lack of speed control The manipulator described in this paper provides versatile remote control and may be constructed economically.

Structural features of B-DNA dodecamer crystal structures: Influence of crystal packing versus base sequence

We have analyzed the set of inter and intra base pair parameters for each dinucleotide step in single crystal structures of dodecamers, solved at high and medium resolution and all crystallized in P2(1)2(1)2(1) space group. The objective was to identify whether all the structures which have either the Drew-Dickerson (DD) sequence d[CGCGAATTCGCG] with some base modification or related sequence (non-DD), would display the same sequence dependent structural variability about its palindromic sequence, despite the molecule being bent at one end because of similar crystal lattice packing effect. Most of the local doublet parameters for base pairs steps G2-C3 and G10-C11 positions, symmetrically situated about the lateral twofold, were significantly correlated between themselves. In non-DD sequences, significant correlations between these positional parameters were absent. The different range of local step parameter values at each sequence position contributed to the gross feature of smooth helix axis bending in all structures. The base pair parameters in some of the positions, for medium resolution DD sequence, were quite unlike the high-resolution set and encompassed a higher range of values. Twist and slide are the two main parameters that show wider conformational range for the middle region of non-DD sequence structures in comparison to DD sequence structures. On the contrary, the minor and major groove features bear good resemblance between DD and non-DD sequence crystal structure datasets. The sugar-phosphate backbone torsion angles are similar in all structures, in sharp contrast to base pair parameter variation for high and low resolution DD and non-DD sequence structures, consisting of unusual (epsilon =g(-), xi =t) B-II conformation at the 10(th) position of the dodecamer sequence. Thus examining DD and non-DD sequence structures packed in the same crystal lattice arrangement, we infer that inter and intra base pair parameters are as symmetrically equivalent in its value as the symmetry related step for the palindromic DD sequence about lateral two-fold axis. This feature would lead us to agree with the conclusion that DNA conformation is not substantially affected by end-to-end or lateral inter-molecular interaction due to crystal lattice packing effect. Non-DD sequence structures acquire step parameter values which reflect the altered sequence at each of the dodecamer sequence position in the orthorhombic lattice while showing similar gross features of DD sequence structures

HELANAL: A program to characterise helix geometry in proteins,

A detailed analysis of structural and position dependent characteristic features of helices will give a better understanding of the secondary structure formation in globular proteins. Here we describe an algorithm that quantifies the geometry of helices in proteins on the basis of their C-alpha atoms alone. The Fortran program HELANAL can extract the helices from the PDB files and then characterises the overall geometry of each helix as being linear, curved or kinked, in terms of its local structural features, viz. local helical twist and rise, virtual torsion angle, local helix origins and bending angles between successive local helix axes. Even helices with large radius of curvature are unambiguously identified as being linear or curved. The program can also be used to differentiate a kinked helix and other motifs, such as helix-loop-helix or a helix-turn-helix (with a single residue linker) with the help of local bending angles. In addition to these, the program can also be used to characterise the helix start and end as well as other types of secondary structures.

Conformation of substituted polyacetylenes in solution : relationship between electronic properties and local order

A study of the chain conformation in solutions of polyphenylacetylene and poly(2-octyne) has been performed. The two polymers differ in many ways : polyphenylacetylene gives a red solution while poly(2-octyne) is transparent and, a marked difference on the chain rigidity is observed : the statistical length are 45 Å and 135 Å respectively. From the study of these two systems, one deduces that curvature fluctuations play a minor role on the π electrons localization, and that the torsion between monomer units is the pertinent parameter to understand the chain conformation and the π electrons localization.

Molecular Mechanics Studies of Homopolymeric and Mixed Sequence Py.Pu*Pu Triple Helices,

DNA triple helices containing two purine strands and one pyrimidine strand (C.G*G and T.A*A) have been studied, using model building followed by energy minimisation, for different orientations of the third strand resulting from variation in the hydrogen bonding between the Watson-Crick duplex and the third strand and the glycosidic torsion angle in the third strand. Our results show that in the C.G*G case the structure with a parallel orientation of the third strand, resulting from Hoogsteen hydrogen bonds between the third strand and the Watson-Crick duplex, is energetically the most favourable while in the T.A*A case the antiparallel orientation of the third strand, resulting from reverse Hoogsteen hydrogen bonds, is energetically the most favourable. These studies when extended to the mixed sequence triplexes, in which the second strand is a mixture of G and A, correspondingly the third strand is a mixture of G and APT, show that though the parallel orientation is still energetically more favourable, the antiparallel orientation becomes energetically comparable with an increasing number of thymines in the third strand. Structurally, for the mixed triplexes containing G and T in the third strand, it is seen that the basepair non-isomorphism between the C.G*G and the T.A*T triplets can be overcome with some changes in the base pair parameters without much distortion of either the backbone or the hydrogen bonds.

Structural Polymorphism in d(T).d(A)*d(T) Triple Helices

DNA triple helices containing two thymine strands and one adenine strand have been studied, using model building followed by energy minimisation, for different orientations of the third strand resulting from variation in the hydrogen bonding between the Watson-Crick duplex and the third strand and the glycosidic torsion angle in the third strand. Our results show that the structure with a parallel orientation of the third strand, in which the third strand base forms Hoogsteen hydrogen bonds with the adenine base in the Watson-Crick duplex, is energetically the most favourable. An antiparallel orientation of the third strand is also possible, in which the third strand base hydrogen bonds to both the bases in the Watson-Crick duplex. This structure is energetically comparable to the parallel structure. For the parallel triplex a 200ps molecular dynamics simulation starting from two different starting structures indicates that at 300K significant structural heterogeneity exists in this tripler structure. The results are compared with existing structural data on this class of triplexes derived from theoretical and NMR techniques.

(2E)-3-(4-Ethoxyphenyl)-1-(2-methyl-4-phenylquinolin-3-yl)prop-2-en-1-on e monohydrate

The title hydrate, C27H23NO2 center dot H2O, features an almost planar quinoline residue (r.m.s. deviation = 0.015 angstrom) with the benzene dihedral angle = 63.80 (7)degrees] and chalcone C-C-C-O torsion angle = -103.38 (18)degrees] substituents twisted significantly out of its plane. The configuration about the C=C bond 1.340 (2) angstrom] is E. In the crystal, molecules related by the 21 symmetry operation are linked along the b axis via water molecules that form O-H center dot center dot center dot O-c and O-H center dot center dot center dot N-q hydrogen bonds (c = carbonyl and q = quinoline). A C-H center dot center dot center dot O interaction also occurs.

A parity-violatingU4-gravitation theory

The general structure of a metric-torsion theory of gravitation allows a parity-violating contribution to the complete action which is linear in the curvature tensor and vanishes identically in the absence of torsion. The resulting action involves, apart from the constant ¯K E =8pgr/c4, a coupling (B) which governs the strength of the parity interaction mediated by torsion. In this model the Brans-Dicke scalar field generates the torsion field, even though it has zero spin. The interesting consequence of the theory is that its results for the solar-system differ very little from those obtained from Brans-Dicke (BD) theory. Therefore the theory is indistinguishable from BD theory in solar-system experiments.

Computer modelling studies of ribonuclease A-pyrimidine nucleotide complexes

Different modes of binding of pyrimidine monophosphates 2'-UMP, 3'-UMP, 2'-CMP and 3'-CMP to ribonuclease (RNase) A are studied by energy minimization in torsion angle and subsequently in Cartesian coordinate space. The results are analysed in the light of primary binding sites. The hydrogen bonding pattern brings out roles for amino acids such as Asn44 and Ser123 apart from the well known active site residues viz., His12,Lys41,Thr45 and His119. Amino acid segments 43-45 and 119-121 seem to be guiding the ligand binding by forming a pocket. Many of the active site charged residues display considerable movement upon nucleotide binding.

1H NMR Study of Molecular Motions and Phase Transitions in Methyl Ammonium Hexabromo Selenate [(CH3NH3)2SeBr6]

The temperature dependence of 1H spin-lattice relaxation time, T1, and that of the second moment, M2, are analysed in the temperature range 390 K to 77 K. A plot of T1 vs inverse temperature shows three phase transitions at 250 K, 167 K and 111 K. At 167 K, T1 displays a large jump while it shows changes in slope at 250 K and 111 K. In the high temperature phase (> 167 K), the correlated motion of CH3 and NH3 groups is found to cause the relaxation while their uncorrelated motion takes over in the low temperature phases (< 167 K). The unusual T1 behaviour in phase II (250 K-167 K) is ascribed to the small angle torsion of the cation. A constant M2 value of ∼ 9.7 G2, throughout the range of temperature studied, indicates the presence of reorientation of CH3 and NH3 groups.

Processing map for hot working of stainless steel type AISI 316L

Processing and instability maps using a dynamic materials model have been developed for stainless steel type AISI 316L in the temperature range 600-1250-degrees-C and strain rate range 0.001-100 s-1 with a view to optimising its hot workability. Stainless steel type AISI 316L undergoes dynamic recrystallisation, with a peak efficiency of 35% at 1250-degrees-C and 0.05 s-1, which are the optimum parameters for hot working this material. The material undergoes dynamic recovery at 900-degrees-C and 0.001 s-1. The increase in the dynamic recrystallisation and dynamic recovery temperatures in comparison with stainless steel type AISI 304L is attributed to the presence of a backstress caused by the molybdenum additions. These results are in general agreement with those reported elsewhere on stainless steel type 316 deformed in hot extrusion and hot torsion. At temperatures < 850-degrees-C and strain rates > 10 s-1, the material exhibits flow localisation owing to adiabatic shear band formation, whereas at higher temperatures (> 850-degrees-C) and strain rates (> 10 s-1) mechanical twinning and wavy slip bands are observed. (C) 1993 The Institute of Materials.

Pressure-induced band gap reduction, orientational ordering and reversible amorphization in single crystals of C70: Photoluminescence and Raman studies

Photoluminescence and Raman scattering experiments have been carried out on single crystals of C70 up to 31 GPa to investigate the effect of pressure on the optical band gap, vibrational modes and stability of the molecule. The photoluminescence band shifts to lower energies and the pressure dependence of the band maxima yields the hydrostatic deformation potential to be 2.15 eV. The slope changes in the pressure dependence of peak positions and linewidths of the Raman modes associated with the intramolecular vibrations at 1 GPa mark the known face-centred cubic-->rhombohedral orientational ordering transition. The reversible amorphization in C70 at P > 20 GPa has been compared with the irreversible amorphization in C60 at P > 22 GPa in terms of carbon-carbon distance between the neighbouring molecules at the threshold transition pressures, in conjunction with the interplay between the intermolecular and intramolecular interactions.