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Can One Define the Conductance of Amino Acids?

ABSTRACT: We studied the electron-transport properties of ten different amino acids and one dimer (di-methionine) using the mechanically controlled break-junction (MCBJ) technique. For methionine and cysteine, additional measurements were performed with the scanning tunneling microscope break-junction (STM-BJ) technique. By means of a statistical clustering technique, we identified several conductance groups for each of the molecules considered. Ab initio calculations revealed that the observed broad conductance distribution stems from the possibility of various binding geometries which can be formed during stretching combined with a multitude of possible conformational changes. The results suggest that it would be helpful to explore different experimental techniques such as recognition tunneling and conditions to help identify the nature of amino-acid-based junctions even further, for example, with the goal to establish a firm platform for their unambiguous recognition by tunneling break-junction experiments.

SUBMITTER: Zotti LA

PROVIDER: S-EPMC6843363 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

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Can One Define the Conductance of Amino Acids?

Zotti Linda A LA Bednarz Beatrice B Hurtado-Gallego Juan J Cabosart Damien D Rubio-Bollinger Gabino G Agrait Nicolas N van der Zant Herre S J HSJ

Biomolecules 20191007 10

We studied the electron-transport properties of ten different amino acids and one dimer (di-methionine) using the mechanically controlled break-junction (MCBJ) technique. For methionine and cysteine, additional measurements were performed with the scanning tunneling microscope break-junction (STM-BJ) technique. By means of a statistical clustering technique, we identified several conductance groups for each of the molecules considered. Ab initio calculations revealed that the observed broad cond ...[more]

PMID: 31591358

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Project description:UnlabelledNoroviruses (NoV) are members of the family Caliciviridae. The human NoV open reading frame 1 (ORF1) encodes a 200-kDa polyprotein which is cleaved by the viral 20-kDa 3C-like protease (Pro, NS6) into 6 nonstructural proteins that are necessary for viral replication. The NoV ORF1 polyprotein is processed in a specific order, with "early" sites (NS1/2-3 and NS3-4) being cleaved rapidly and three "late" sites (NS4-5, NS5-6, and NS6-7) processed subsequently and less efficiently. Previously, we demonstrated that the NoV polyprotein processing order is directly correlated with the efficiency of the enzyme, which is regulated by the primary amino acid sequences surrounding ORF1 cleavage sites. Using fluorescence resonance energy transfer (FRET) peptides representing the NS2-3 and NS6-7 ORF1 cleavage sites, we now demonstrate that the amino acids spanning positions P4 to P2' (P4-P2') surrounding each site comprise the core sequence controlling NoV protease enzyme efficiency. Furthermore, the NoV polyprotein self-processing order can be altered by interchanging this core sequence between NS2-3 and any of the three late sites in in vitro transcription-translation assays. We also demonstrate that the nature of the side chain at the P3 position for the NS1/2-3 (Nterm/NTPase) site confers significant influence on enzyme catalysis (kcat and kcat/Km), a feature overlooked in previous structural studies. Molecular modeling provides possible explanations for the P3 interactions with NoV protease.ImportanceNoroviruses (NoV) are the prevailing cause of nonbacterial acute gastroenteritis worldwide and pose a significant financial burden on health care systems. Proteolytic processing of the viral nonstructural polyprotein is required for norovirus replication. Previously, the core sequence of amino acids surrounding the scissile bonds responsible for governing the relative processing order had not been determined. Using both FRET-based peptides and full-length NoV polyprotein, we have successfully demonstrated that the core sequences spanning positions P4-P2' surrounding the NS2-3, NS4-5, NS5-6, and NS6-7 cleavage sites contain all of the structural information necessary to control processing order. We also provide insight into a previously overlooked role for the NS2-3 P3 residue in enzyme efficiency. This article builds upon our previous studies on NoV protease enzymatic activities and polyprotein processing order. Our work provides significant additional insight into understanding viral polyprotein processing and has important implications for improving the design of inhibitors targeting the NoV protease.

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Can One Define the Conductance of Amino Acids?

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Can One Define the Conductance of Amino Acids?

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