Biophysics Reports

2016 Vol. 2, No. 1

Cover Story

COVER Although near-atomic resolutions have been routinely achieved for structural determination of many icosahedral viral capsids, structures of genomes and associated proteins within the capsids are still less characterized because the genome information is overlapped by the highly symmetric capsid information in the virus particle images. A software package was developed for symmetry-mismatch structural reconstruction and determined the structures of the genome and RNA polymerases within an icosahedral virus for the ??irst time. Here, the protocol used for this structural determination was described, which may facilitate structural biologists in investigating the structures of viral genome and associated proteins.

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Radiolabeled cyclic RGD peptides as radiotracers for tumor imaging

Jiyun Shi, Fan Wang, Shuang Liu

2016, 2(1): 1-20. doi: 10.1007/s41048-016-0021-8

Abstract(90)

PDF(155)

Abstract:
The integrin family comprises 24 transmembrane receptors, each a heterodimeric combination of one of 18α and one of 8β subunits. Their main function is to integrate the cell adhesion and interaction with the extracellular microenvironment with the intracellular signaling and cytoskeletal rearrangement through transmitting signals across the cell membrane upon ligand binding. Integrin α_vβ₃ is a receptor for the extracellular matrix proteins containing arginine-glycine-aspartic (RGD) tripeptide sequence. The α_vβ₃ is generally expressed in low levels on the epithelial cells and mature endothelial cells, but it is highly expressed in many solid tumors. The α_vβ₃ levels correlate well with the potential for tumor metastasis and aggressiveness, which make it an important biological target for development of antiangiogenic drugs, and molecular imaging probes for early tumor diagnosis. Over the last decade, many radiolabeled cyclic RGD peptides have been evaluated as radiotracers for imaging tumors by SPECT or PET. Even though they are called "α_vβ₃-targeted" radiotracers, the radiolabeled cyclic RGD peptides are also able to bind α_vβ₅, α₅β₁, α₆β₄, α₄β₁, and α_vβ₆ integrins, which may help enhance their tumor uptake due to the "increased receptor population." This article will use the multimeric cyclic RGD peptides as examples to illustrate basic principles for development of integrin-targeted radiotracers and focus on different approaches to maximize their tumor uptake and T/B ratios. It will also discuss important assays for pre-clinical evaluations of the integrin-targeted radiotracers, and their potential applications as molecular imaging tools for noninvasive monitoring of tumor metastasis and early detection of the tumor response to antiangiogenic therapy.

Exploring the inside details of virions by electron microscopy

Zheng Liu, Jingqiang Zhang

2016, 2(1): 21-24. doi: 10.1007/s41048-016-0022-7

Abstract(59)

PDF(223)

Abstract:

Symmetry-mismatch reconstruction of genomes and associated proteins within icosahedral viruses using cryo-EM

Xiaowu Li, Hongrong Liu, Lingpeng Cheng

2016, 2(1): 25-32. doi: 10.1007/s41048-016-0024-5

Abstract(60)

PDF(119)

Abstract:
Although near-atomic resolutions have been routinely achieved for structural determination of many icosahedral viral capsids, structures of genomes and associated proteins within the capsids are still less characterized because the genome information is overlapped by the highly symmetric capsid information in the virus particle images. We recently developed a software package for symmetry-mismatch structural reconstruction and determined the structures of the genome and RNA polymerases within an icosahedral virus for the first time. Here, we describe the protocol used for this structural determination, which may facilitate structural biologists in investigating the structures of viral genome and associated proteins.

Combining biophysical methods to analyze the disulfide bond in SH2 domain of C-terminal Src kinase

Dongsheng Liu, David Cowburn

2016, 2(1): 33-43. doi: 10.1007/s41048-016-0025-4

Abstract(77)

PDF(149)

Abstract:
The Src Homology 2 (SH2) domain is a structurally conserved protein domain that typically binds to a phosphorylated tyrosine in a peptide motif from the target protein. The SH2 domain of C-terminal Src kinase (Csk) contains a single disulfide bond, which is unusual for most SH2 domains. Although the global motion of SH2 domain regulates Csk function, little is known about the relationship between the disulfide bond and binding of the ligand. In this study, we combined X-ray crystallography, solution NMR, and other biophysical methods to reveal the interaction network in Csk. Denaturation studies have shown that disulfide bond contributes significantly to the stability of SH2 domain, and crystal structures of the oxidized and C122S mutant showed minor conformational changes. We further investigated the binding of SH2 domain to a phosphorylated peptide from Csk-binding protein upon reduction and oxidation using both NMR and fluorescence approaches. This work employed NMR, X-ray cryptography, and other biophysical methods to study a disulfide bond in Csk SH2 domain. In addition, this work provides in-depth understanding of the structural dynamics of Csk SH2 domain.