1. Introduction 3702. Infrared (IR) spectroscopy – general principles 3722.1 Vibrations 3722.2 Information that can be derived from the vibrational spectrum 3722.3 Absorption of IR light 3753. Protein IR absorption 3763.1 Amino-acid side-chain absorption 3763.2 Normal modes of the amide group 3814. Interactions that shape the amide I band 3824.1 Overview 3824.2 Through-bond coupling 3834.3 Hydrogen bonding 3834.4 Transition dipole coupling (TDC) 3835. The polarization and IR activity of amide I modes 3875.1 The coupled oscillator system 3875.2 Optically allowed transitions 3885.3 The infinite parallel β-sheet 3885.4 The infinite antiparallel β-sheet 3895.5 The infinite α-helix 3906. Calculation of the amide I band 3916.1 Overview 3916.2 Perturbation treatment by Miyazawa 3936.3 The parallel β-sheet 3946.4 The antiparallel β-sheet 3956.5 The α-helix 3966.6 Other secondary structures 3987. Experimental analysis of protein secondary structure 3987.1 Band fitting 3987.2 Methods using calibration sets 4017.3 Prediction quality 4038. Protein stability 4048.1 Thermal stability 4048.2 ¹H/²H exchange 4069. Molecular reaction mechanisms of proteins 4089.1 Reaction-induced IR difference spectroscopy 4089.2 The origin of difference bands 4099.3 The difference spectrum seen as a fingerprint of conformational change 4109.4 Molecular interpretation: strategies of band assignment 41610. Outlook 41911. Acknowledgements 42012. References 420This review deals with current concepts of vibrational spectroscopy for the investigation of protein structure and function. While the focus is on infrared (IR) spectroscopy, some of the general aspects also apply to Raman spectroscopy. Special emphasis is on the amide I vibration of the polypeptide backbone that is used for secondary-structure analysis. Theoretical as well as experimental aspects are covered including transition dipole coupling. Further topics are discussed, namely the absorption of amino-acid side-chains, ¹H/²H exchange to study the conformational flexibility and reaction-induced difference spectroscopy for the investigation of reaction mechanisms with a focus on interpretation tools.

We collected plastic debris in the Stockholm Archipelago using a manta trawl, and additionally along a transect in the Baltic Sea from the island of Gotland to Stockholm in a citizen science study. The samples were concentrated by filtration and organic material was digested using hydrogen peroxide. Suspected plastic material was isolated by visual sorting and 59 of these were selected to be characterized with Fourier transform infrared spectroscopy. Polypropylene and polyethylene were the most abundant plastics identified among the samples (53% and 24% respectively). We found nearly ten times higher abundance of plastics near central Stockholm than in offshore areas (4.2×105plastics km-2 compared to 4.7×104plastics km-2). The abundance of plastic debris near Stockholm was similar to urban areas in California, USA, and the overall abundance in the Stockholm Archipelago was similar to plastic abundance reported in the northwestern Mediterranean Sea.

Risk assessment of microplastic (MP) pollution requires understanding biodegradation processes and related changes in polymer properties. In the environment, there are two-way interactions between the MP properties and biofilm communities: (i) microorganisms may prefer some surfaces, and (ii) MP surface properties change during the colonization and weathering. In a 2-week experiment, we studied these interactions using three model plastic beads (polyethylene [PE], polypropylene [PP], and polystyrene [PS]) exposed to ambient bacterioplankton assemblage from the Baltic Sea; the control beads were exposed to bacteria-free water. For each polymer, the physicochemical properties (compression, crystallinity, surface chemistry, hydrophobicity, and surface topography) were compared before and after exposure under controlled laboratory conditions. Furthermore, we characterized the bacterial communities on the MP surfaces using 16S rRNA gene sequencing and correlated community diversity to the physicochemical properties of the MP. Significant changes in PE crystallinity, PP stiffness, and PS maximum compression were observed as a result of exposure to bacteria. Moreover, there were significant correlations between bacterial diversity and some physicochemical characteristics (crystallinity, stiffness, and surface roughness). These changes coincided with variation in the relative abundance of unique OTUs, mostly related to the PE samples having significantly higher contribution of Sphingobium, Novosphingobium, and uncultured Planctomycetaceae compared to the other test materials, whereas PP and PS samples had significantly higher abundance of Sphingobacteriales and Alphaproteobacteria, indicating possible involvement of these taxa in the initial biodegradation steps. Our findings demonstrate measurable signs of MP weathering under short-term exposure to environmentally relevant microbial communities at conditions resembling those in the water column. A systematic approach for the characterization of the biodegrading capacity in different systems will improve the risk assessment of plastic litter in aquatic environments.