https://www.seas.upenn.edu/%7Edischer/pdfs/Cell_on_Gel-CELLpaper.pdf

Matrix elasticity directs stem cell lineage specification.

Publisher Summary This chapter provides an insight of the findings of past significant papers with the current knowledge of the recently determined high resolution X-ray structure of serum albumin. The most outstanding property of albumin is its ability to bind reversibly an incredible variety of ligands. The sequences of all albumins are characterized by a unique arrangement of disulfide double loops that repeat as a series of triplets. Albumin belongs to a multigene family of proteins that includes α- fetoprotein (AFP) and vitamin D-binding protein (VDP), also known as G complement (Gc) protein. Although AFP is considered the fetal counterpart of albumin, its binding properties are distinct and it is suggested that AFP may have a higher affinity for some unknown ligands important for fetal development. Domain structure and the arrangement of the disulfides, the surface charge distribution, and the conformational flexibility of the albumin molecule are described. The nature of ligand binding, including small organics, long-chain fatty acids, and metals, to multiple sites on the albumin molecule is clearly depicted. The chapter concludes with the perceptive comments on future directions being taken to explore the structure and function of this fascinating protein.

Structure of serum albumin.

The ability to control the size, shape, and material of a surface has reinvigorated the field of surface-enhanced Raman spectroscopy (SERS). Because excitation of the localized surface plasmon resonance of a nanostructured surface or nanoparticle lies at the heart of SERS, the ability to reliably control the surface characteristics has taken SERS from an interesting surface phenomenon to a rapidly developing analytical tool. This article first explains many fundamental features of SERS and then describes the use of nanosphere lithography for the fabrication of highly reproducible and robust SERS substrates. In particular, we review metal film over nanosphere surfaces as excellent candidates for several experiments that were once impossible with more primitive SERS substrates (e.g., metal island films). The article also describes progress in applying SERS to the detection of chemical warfare agents and several biological molecules.

Surface-Enhanced Raman Spectroscopy

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Principles Of Fluorescence Spectroscopy

Nanomaterials, such as metal or semiconductor nanoparticles and nanorods, exhibit similar dimensions to those of biomolecules, such as proteins (enzymes, antigens, antibodies) or DNA. The integration of nanoparticles, which exhibit unique electronic, photonic, and catalytic properties, with biomaterials, which display unique recognition, catalytic, and inhibition properties, yields novel hybrid nanobiomaterials of synergetic properties and functions. This review describes recent advances in the synthesis of biomolecule-nanoparticle/nanorod hybrid systems and the application of such assemblies in the generation of 2D and 3D ordered structures in solutions and on surfaces. Particular emphasis is directed to the use of biomolecule-nanoparticle (metallic or semiconductive) assemblies for bioanalytical applications and for the fabrication of bioelectronic devices.

Integrated Nanoparticle–Biomolecule Hybrid Systems: Synthesis, Properties, and Applications

The use of molecular dynamics simulation to investigate the properties of hydration water around proteins is outlined. A variety of structural and dynamical properties of the protein hydration water are reviewed and compared with those of bulk and with the corresponding experimental results. In particular, the accessibility to the protein medium, the hydrogen bond networking capability, the residence times, the diffusive mobility, the relaxation behavior, and the inelastic vibrational features of hydration water are analyzed in framework of the peculiar interactions of water at the protein surface. All these features, which can be traced back to the complexity of the overall protein−solvent energy landscape, are discussed in connection with the role played by hydration water in the biological functionality.

Molecular Dynamics of Water at the Protein-Solvent Interface

We present a computer simulation picture of the dynamical behavior, at room temperature, of water in the region close to a protein surface. We analyzed the probability distribution of water molecules diffusing near the surface, and we found that it deviates from a Gaussian, which is predicted for Brownian particles. Consistently, the mean square displacements of water oxygens show a sublinear trend with time. Moreover, the relaxation of hydration layers around the whole protein is found to follow a stretched exponential decay, typical of complex systems, which could as well be ascribed to the non-Gaussian shape of the propagator. In agreement with such findings, the analysis of water translational and reorientational diffusion showed that not only are the solvent molecule motions hindered in the region close to the protein surface, but also the very nature of the particle diffusive processes, both translational and rotational, is affected. The deviations from the bulk water properties, which put into evidence a deep influence exerted by the protein on the solvent molecule motion, are discussed in connection with the presence of spatial ~protein surface roughness! and temporal ~distribution of water residence times! disorder inherent in the system. @S1063-651X~98!07003-2#

Water dynamical anomalies evidenced by molecular-dynamics simulations at the solvent-protein interface

Atomic force spectroscopy (AFS) is one of the most promising and powerful tools to get information on biorecognition processes at single molecule resolution. AFS allows to measure forces acting between biomolecules undergoing biorecognition process with a picoNewton sensitivity in near-physiological conditions and without any labelling. The capability of AFS to provide detailed information about the kinetics and thermodynamics of a single pair of interacting biomolecules, besides complementing traditional biochemical approaches, offers the possibility to elucidate non-conventional aspects of biorecognition processes, such as rare events, transient phenomena, conformational changes and molecular heterogeneity. Despite its enormous capabilities and potentialities, AFS as applied to biomolecular interactions, has provided some ambiguous and controversial results in different experimental contexts. The present critical review describes, after an in-depth introduction to AFS and to the most used experimental and data analysis procedures, the more recent and rewarding ideas and advancements to overcome the main critical aspects faced in the investigation of biorecognition processes. Possible developments of AFS in applicative fields are briefly addressed (150 references).

The application of atomic force spectroscopy to the study of biological complexes undergoing a biorecognition process.

Nanostructured enzymatic biosensor based on fullerene and gold nanoparticles: Preparation, characterization and analytical applications

The extremely large cross-section available from metallic surface enhancement has been exploited to investigate the Raman spectrum of heme myoglobin adsorbed on silver colloidal nanoparticles at very low concentrations. The study has been performed on particles both in solution and immobilized onto a polymer-coated glass surface. In both the cases, we have observed striking temporal fluctuations in the surface-enhanced resonance Raman spectroscopy (SERRS) spectra collected at short times. A statistical analysis of the temporal intensity fluctuations and of the associated correlations of the Raman signals has allowed us to verify that the single molecule limit is approached. The possible connections of these fluctuations with the entanglement of the biomolecule within the local minima of its rough energy landscape is discussed.

Salvatore Cannistraro

Papers

Molecular Dynamics of Water at the Protein-Solvent Interface

Water dynamical anomalies evidenced by molecular-dynamics simulations at the solvent-protein interface

The application of atomic force spectroscopy to the study of biological complexes undergoing a biorecognition process.

Nanostructured enzymatic biosensor based on fullerene and gold nanoparticles: Preparation, characterization and analytical applications

Surface-Enhanced Resonance Raman Spectroscopy Signals from Single Myoglobin Molecules