The hydrogen bond is the most important of all directional intermolecular interactions. It is operative in determining molecular conformation, molecular aggregation, and the function of a vast number of chemical systems ranging from inorganic to biological. Research into hydrogen bonds experienced a stagnant period in the 1980s, but re-opened around 1990, and has been in rapid development since then. In terms of modern concepts, the hydrogen bond is understood as a very broad phenomenon, and it is accepted that there are open borders to other effects. There are dozens of different types of X-H.A hydrogen bonds that occur commonly in the condensed phases, and in addition there are innumerable less common ones. Dissociation energies span more than two orders of magnitude (about 0.2-40 kcal mol(-1)). Within this range, the nature of the interaction is not constant, but its electrostatic, covalent, and dispersion contributions vary in their relative weights. The hydrogen bond has broad transition regions that merge continuously with the covalent bond, the van der Waals interaction, the ionic interaction, and also the cation-pi interaction. All hydrogen bonds can be considered as incipient proton transfer reactions, and for strong hydrogen bonds, this reaction can be in a very advanced state. In this review, a coherent survey is given on all these matters.

The hydrogen bond in the solid state.

Infrared spectroscopy of proteins.

We have used the pH-induced self-assembly of a peptide-amphiphile to make a nanostructured fibrous scaffold reminiscent of extracellular matrix. The design of this peptide-amphiphile allows the nanofibers to be reversibly cross-linked to enhance or decrease their structural integrity. After cross-linking, the fibers are able to direct mineralization of hydroxyapatite to form a composite material in which the crystallographic c axes of hydroxyapatite are aligned with the long axes of the fibers. This alignment is the same as that observed between collagen fibrils and hydroxyapatite crystals in bone.

http://science.sciencemag.org/content/sci/294/5547/1684.full.pdf

Self-assembly and mineralization of peptide-amphiphile nanofibers

Fourier transform ir (FTIR) spectra of 21 globular proteins have been obtained at 2 cm−1 resolution from 1600 to 1700 cm−1 in deuterium oxide solution. Fourier self-deconvolution was applied to all spectra, revealing that the amide I band of each protein except casein consists of six to nine components. The components are observed at 11 well-defined frequencies, although all proteins do not exhibit components at every characteristic frequency. The root mean square (RMS) deviation of 124 individual values from the 11 average characteristic frequencies is 1.9 cm−1. The observed components are assigned to helical segments, extended beta-segments, unordered segments, and turns. Segments with similar structures do not necessarily exhibit band components with identical frequencies. For instance, the lower frequency beta-structure band can vary within a range of approximately 15 cm−1. The relative areas of the individual components of the deconvolved spectra were determined by a Gauss–Newton, iterative curve-fitting procedure that assumed Gaussian band envelopes for the deconvolved components. The measured areas were used to estimate the percentage of helix and beta-structure for each of 21 globular proteins. The results are in good general agreement with values derived from x-ray data by Levitt and Greer. The RMS deviation between 22 values (alpha- and beta-content of 11 beta-rich proteins measured by both techniques) is 2.5 percentage points; the maximum absolute deviation is 4 percentage points.

Examination of the secondary structure of proteins by deconvolved FTIR spectra.

Infrared spectroscopy is one of the oldest and well established experimental techniques for the analysis of secondary structure of polypeptides and proteins. It is convenient, non-destructive, requires less sample preparation, and can be used under a wide variety of conditions. This review introduces the recent developments in Fourier transform infrared (FTIR) spectroscopy technique and its applications to protein structural studies. The experimental skills, data analysis, and correlations between the FTIR spectroscopic bands and protein secondary structure components are discussed. The applications of FTIR to the secondary structure analysis, conformational changes, structural dynamics and stability studies of proteins are also discussed.

/pdf/fourier-transform-infrared-spectroscopic-analysis-of-protein-1q1ipm94ib.pdf

Fourier Transform Infrared Spectroscopic Analysis of Protein Secondary Structures

Publisher Summary The vibrational spectrum of a molecule is determined by its three-dimensional structure and its vibrational force field. An analysis of this (usually infrared (IR) and Raman) spectrum can therefore provide information on the structure and on intramolecular and intermolecular interactions. The more probing the analysis, the more detailed is the information that can be obtained. Detailed analyses of the vibrational spectra of macromolecules, however, have provided a deeper understanding of structure and interactions in these systems. An important advance in this direction for proteins came with the determination of the normal modes of vibration of the peptide group in N-methylacetamide, and the characterization of several specific amide vibrations in polypeptide systems. Extensive use has been made of spectra-structure correlations based on some of these amide modes, including attempts to determine secondary structure composition in proteins. Polypeptide molecules exhibit many more vibrational frequencies than the amide modes. Over the years, some normal-mode calculations have provided greater insight into the spectra of particular molecules. However, these have often been based on approximate structures or have employed limited force fields. These force fields can now serve as a basis for detailed analyses of spectral and structural questions in other polypeptide molecules. The aim of this chapter is to present these recent developments in the vibrational spectroscopy of peptides, polypeptides, and proteins.

Vibrational spectroscopy and conformation of peptides, polypeptides, and proteins.

Attempts have been made to understand the nature and significance of hydrogen bonds of the type X-H-C
(X = 0, N) . These unusual interactions have been discussed recently. Crystallographic studies on 17a-ethynylandrosta-
2,4-dieno[2,3-d]dihydroxazol1-7 8-01 (donazole) provide direct evidence of such an 0-H.0-C interaction. Ab initio
computations, IR spectroscopy, and database studies show that these hydrogen bonds, while uncommon, are energetically
and structurally significant.

Evidence for O-H.cntdot..cntdot..cntdot.C and N-H.cntdot..cntdot..cntdot.C hydrogen bonding in crystalline alkynes, alkenes, and aromatics

modes are given for the latter three structures. Calculations have been done for structures with standard dihedral angles, as well as for structures whose dihedral angles differ from these by amounts found in protein structures. The force field was that refined in our previous work on polypeptides. Transition dipole coupling was included, and is crucial to predicting frequency splittings in the amide I and amide I1 modes. The results show that in the amide I region, P-turn frequencies can overlap with those of the cu-helix and @-sheet structures, and therefore caution must be exercised in the interpretation of protein bands in this region. The amide I11 modes of 0-turns are predicted at significantly higher frequencies than those of (?-helix and 0-sheet structures, and this region therefore provides the hest possibility of identifying 0-turn structures. Amide V frequencies of fl-turns may also he distinctive for such structures.

/pdf/vibrational-analysis-of-peptides-polypeptides-and-proteins-v-1ivukcgkmg.pdf

Vibrational analysis of peptides, polypeptides, and proteins. V. Normal vibrations of β‐turns

Normal vibration calculations have been done for a type I beta-turn of CH(3)-CO-(Ala)(4)-NH-CH(3) and a type II beta-turn of CH(3)-CO-(Ala)(2)-Gly-Ala-NH-CH(3) The force field was the one we refined for beta-sheet and alpha-helical structures A calculation was also done for CH(3)-O-CO-Gly-(Ala)(2)-Gly-O-CH(3), which is an appropriate model for two tetrapeptides for which infrared data are available The agreement between observed and calculated frequencies in this case is good, thus supporting the conclusions drawn from the above beta-turn calculations The most important result of the calculations is the prediction of bands near 1690 cm(-1), a region heretofore associated only with the antiparallel-chain pleated sheet structure This means that bands observed in proteins near 1690 cm(-1) should be associated with the presence of beta-turns as well as of beta-sheets We also find that a band near 1665 cm(-1) is characteristic of type II turns

https://www.pnas.org/content/pnas/76/2/774.full.pdf

Vibrational analysis of peptides, polypeptides, and proteins: Characteristic amide bands of β-turns

The normal modes have been calculated for structures having the dihedral angles of the four β-turns of insulin. Frequencies are predicted in the amide I region near 1652 and 1680 cm−1. The former overlaps the α-helix band at 1658 cm−1 in the Raman spectrum, while the latter accounts for the hitherto unassignable band at 1681 cm−1. Calculated amide III frequencies extend above 1300 cm−1, providing a compelling assignment of the 1303-cm−1 band in insulin and similar bands in other globular proteins.

/pdf/vibrational-analysis-of-peptides-polypeptides-and-proteins-25td0n2kir.pdf

Jagdeesh Bandekar

Papers

Vibrational spectroscopy and conformation of peptides, polypeptides, and proteins.

Evidence for O-H.cntdot..cntdot..cntdot.C and N-H.cntdot..cntdot..cntdot.C hydrogen bonding in crystalline alkynes, alkenes, and aromatics

Vibrational analysis of peptides, polypeptides, and proteins. V. Normal vibrations of β‐turns

Vibrational analysis of peptides, polypeptides, and proteins: Characteristic amide bands of β-turns

Vibrational analysis of peptides, polypeptides, and proteins. VI. Assignment of beta-turn modes in insulin and other proteins.