Vibrational studies of the disulfide group in proteins. VII. Normal mode analysis of the Raman spectra of erabutoxin, γ‐II crystallin and immunoglobulin

Normal mode calculations have been made on the known structures of disulfide bridges in erabutoxin b, a form of γ‐II crystallin, and fragments (Fab, variable‐domain of Bence‐Jones proteins) of immunoglobulins. Previously obtained Raman spectra of these molecules are analyzed in terms of general correlations derived from normal mode calculations and also the results of calculations on these particular structures. This results in more specific conclusions about these disulfide bridge structures and their changes than was possible on the basis of previous empirical correlations.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/91092/1/1250231003_ftp.pd

Weak Lensing from Space III: Cosmological Parameters

Weak gravitational lensing provides a unique method to directly map the dark matter in the universe and measure cosmological parameters. Current weak lensing surveys are limited by the atmospheric seeing from the ground and by the small field of view of existing space telescopes. We study how a future wide-field space telescope can measure the lensing power spectrum and skewness, and set constraints on cosmological parameters. The lensing sensitivity was calculated using detailed image simulations and instrumental specifications studied in earlier papers in this series. For instance, the planned SuperNova/Acceleration Probe (SNAP) mission will be able to measure the matter density parameter Omega_m and the dark energy equation of state parameter w with precisions comparable and nearly orthogonal to those derived with SNAP from supernovae. The constraints degrade by a factor of about 2 if redshift tomography is not used, but are little affected if the skewness only is dropped. We also study how the constraints on these parameters depend upon the survey geometry and define an optimal observing strategy.Comment: 12 pages, 11 figures. Accepted versio

DATABASE OF HOMOLOGY-DERIVED PROTEIN STRUCTURES AND THE STRUCTURAL MEANING OF SEQUENCE ALIGNMENT

The database of known protein three-dimensional structures can be significantly increased by the use of sequence homology, based on the following observations. (1) The database of known sequences, currently at more than 12,000 proteins, is two orders of magnitude larger than the database of known structures. (2) The currently most powerful method of predicting protein structures is model building by homology. (3) Structural homology can be inferred from the level of sequence similarity. (4) The threshold of sequence similarity sufficient for structural homology depends strongly on the length of the alignment. Here, we first quantify the relation between sequence similarity, structure similarity, and alignment length by an exhaustive survey of alignments between proteins of known structure and report a homology threshold curve as a function of alignment length. We then produce a database of homology-derived secondary structure of proteins (HSSP) by aligning to each protein of known structure all sequences deemed homologous on the basis of the threshold curve. For each known protein structure, the derived database contains the aligned sequences, secondary structure, sequence variability, and sequence profile. Tertiary structures of the aligned sequences are implied, but not modeled explicitly. The database effectively increases the number of known protein structures by a factor of five to more than 1800. The results may be useful in assessing the structural significance of matches in sequence database searches, in deriving preferences and patterns for structure prediction, in elucidating the structural role of conserved residues, and in modeling three-dimensional detail by homology

Psychoneuroimmunology: application to ocular diseases

Psychoneuroimmunology (PNI) is a relatively new discipline within the field of neuroscience which researches the relationship between emotional states, the central and peripheral nervous systems, and the endocrine and immune systems. Negative psychological states, such as stress, anxiety, and depression, may alter immune system regulation and modulation of peripheral cytokines. A plethora of PNI studies have shown that increased psychological stress and depression are associated with an alteration of immune functioning and worsened health outcomes for many conditions. To date, application of PNI methodology has not been reported for ocular diseases. This article provides an historical perspective on the origins of the rift between the emotional and spiritual from physical aspects of disease. A review of how stress is mediated through sympathetic adrenomedullary and hypothalamic pituitary axis activation with shifts in immunity is provided. The literature which supports spirituality in healing is presented. Finally, ocular diseases which would be most amenable to a PNI approach are discussed