Quasi-equivalence in site-specific recombinase structure and function: crystal structure and activity of trimeric cre recombinase bound to a three-way lox DNA junction 1 1Edited by K. Morikawa

2001 ◽  
Vol 313 (1) ◽  
pp. 49-69 ◽  
Author(s):  
Kevin C. Woods ◽  
Shelley S. Martin ◽  
Victor C. Chu ◽  
Enoch P. Baldwin
Keyword(s):  
Crystal Structure ◽  
Cre Recombinase ◽  
Structure And Function ◽  
Site Specific ◽  
And Function ◽  
Structure And Activity

scholarly journals Synaptic transmission induces site-specific changes in sialylation on N-linked glycoproteins in rat nerve terminals

2020 ◽  
Author(s):  
Inga Boll ◽  
Pia Jensen ◽  
Veit Schwämmle ◽  
Martin R. Larsen
Keyword(s):  
Synaptic Transmission ◽  
Structure And Function ◽  
Synaptic Proteins ◽  
Nerve Terminals ◽  
Membrane Glycoproteins ◽  
Site Specific ◽  
Specific Alteration ◽  
And Function ◽  
Rat Nerve ◽  
Stimulation Of

AbstractSynaptic transmission leading to release of neurotransmitters in the nervous system is a fast and highly dynamic process. Previously, protein interaction and phosphorylation have been thought to be the main regulators of synaptic transmission. Here we show a novel potential modulator of synaptic transmission, sialylation of N-linked glycosylation. The negatively charged sialic acids can be modulated, similarly to phosphorylation, by the action of sialyltransferases and sialidases thereby changing local structure and function of membrane glycoproteins. We characterized site-specific alteration in sialylation on N-linked glycoproteins in isolated rat nerve terminals after brief depolarization using quantitative sialiomics. We identified 1965 formerly sialylated N-linked glycosites in synaptic proteins and found that the abundances of 430 glycosites changed after five seconds depolarization. We observed changes on essential synaptic proteins such as synaptic vesicle proteins, ion channels and transporters, neurotransmitter receptors and cell adhesion molecules. This study is to our knowledge the first to describe ultra-fast site-specific modulation of the sialiome after brief stimulation of a biological system.

scholarly journals Regional, watershed, and site-specific environmental influences on fish assemblage structure and function in western Lake Superior tributaries

2005 ◽  
Vol 62 (6) ◽  
pp. 1254-1270 ◽  
Author(s):  
John C Brazner ◽  
Danny K Tanner ◽  
Naomi E Detenbeck ◽  
Sharon L Batterman ◽  
Stacey L Stark ◽  
...  
Keyword(s):  
Fish Assemblage ◽  
Brook Trout ◽  
Fish Assemblages ◽  
Lake Superior ◽  
Structure And Function ◽  
Assemblage Structure ◽  
Fish Assemblage Structure ◽  
Site Specific ◽  
Western Lake ◽  
And Function

The relative importance of regional, watershed, and in-stream environmental factors on fish assemblage structure and function was investigated in western Lake Superior tributaries. We selected 48 second- and third-order watersheds from two hydrogeomorphic regions to examine fish assemblage response to differences in forest fragmentation, watershed storage, and a number of other watershed, riparian, and in-stream habitat conditions. Although a variety of regional, fragmentation, and storage-related factors had significant influences on the fish assemblages, water temperature appeared to be the single most important environmental factor. We found lower water temperatures and trout–sculpin assemblages at lower fragmentation sites and higher temperatures and minnow–sucker–darter assemblages as storage increased. Factors related to riparian shading and flow separated brook trout streams from brown trout (Salmo trutta) – rainbow trout (Oncorhynchus mykiss) streams. Functionally, fish assemblages at lower fragmentation sites were dominated by cold-water fishes that had low silt tolerance and preferred moderate current speeds, while fishes with higher silt tolerances, warmer temperature preferences, and weaker sustained swimming capabilities were most common at higher storage sites. Our results suggest that site-specific environmental conditions are highly dependent on regional- and watershed-scale characters and that a combination of these factors operates in concert to influence the structure and function of stream fish assemblages.

scholarly journals Structure and biogenesis of small nucleolar RNAs acting as guides for ribosomal RNA modification.

1999 ◽  
Vol 46 (2) ◽  
pp. 377-389 ◽  
Author(s):  
W Filipowicz ◽  
P Pelczar ◽  
V Pogacic ◽  
F Dragon
Keyword(s):  
Ribosomal Rna ◽  
Structure And Function ◽  
Hydroxyl Group ◽  
Rna Modification ◽  
Small Nucleolar Rnas ◽  
Yeast Saccharomyces Cerevisiae ◽  
Site Specific ◽  
Alternative Pathways ◽  
And Function ◽  
Nucleolar Rnas

Maturation of pre-ribosomal RNA (pre-rRNA) in eukaryotic cells takes place in the nucleolus and involves a large number of cleavage events, which frequently follow alternative pathways. In addition, rRNAs are extensively modified, with the methylation of the 2'-hydroxyl group of sugar residues and conversion of uridines to pseudouridines being the most frequent modifications. Both cleavage and modification reactions of pre-rRNAs are assisted by a variety of small nucleolar RNAs (snoRNAs), which function in the form of ribonucleoprotein particles (snoRNPs). The majority of snoRNAs acts as guides directing site-specific 2'-O-ribose methylation or pseudouridine formation. Over one hundred RNAs of this type have been identified to date in vertebrates and the yeast Saccharomyces cerevisiae. This number is readily explained by the findings that one snoRNA acts as a guide usually for one or at most two modifications, and human rRNAs contain 91 pseudouridines and 106 2'-O-methyl residues. In this article we review information about the biogenesis, structure and function of guide snoRNAs.

scholarly journals The Contribution of Ribosomal Protein S1 to the Structure and Function of Qβ Replicase

Acta Naturae ◽  
2017 ◽  
Vol 9 (4) ◽  
pp. 26-30
Author(s):  
Z. Sh. Kutlubaeva ◽  
Е. V. Chetverina ◽  
A. B. Chetverin
Keyword(s):  
Crystal Structure ◽  
Ribosomal Protein ◽  
Rna Binding ◽  
Structure And Function ◽  
Ribosomal Protein S1 ◽  
Bacterial Ribosome ◽  
New Findings ◽  
Replicase Complex ◽  
And Function ◽  
Fixed Structure

The high resolution crystal structure of bacterial ribosome was determined more than 10 years ago; however, it contains no information on the structure of the largest ribosomal protein, S1. This unusual protein comprises six flexibly linked domains; therefore, it lacks a fixed structure and this prevents the formation of crystals. Besides being a component of the ribosome, protein S1 also serves as one of the four subunits of Q replicase, the RNA-directed RNA polymerase of bacteriophage Q. In each case, the role of this RNA-binding protein has been thought to consist in holding the template close to the active site of the enzyme. In recent years, a breakthrough was made in studies of protein S1 within Q replicase. This includes the discovery of its paradoxical ability to displace RNA from the replicase complex and determining the crystal structure of its fragment capable of performing this function. The new findings call for a re-examination of the contribution of protein S1 to the structure and function of the ribosome.

scholarly journals Structure of nonstructural protein 1 from SARS-CoV-2.

2020 ◽  
Author(s):  
Lauren K. Clark ◽  
Todd J. Green ◽  
Chad M. Petit
Keyword(s):  
Crystal Structure ◽  
Life Cycle ◽  
High Resolution ◽  
Nonstructural Protein ◽  
Critical Role ◽  
Viral Life Cycle ◽  
Structure And Function ◽  
Future Studies ◽  
Nonstructural Protein 1 ◽  
And Function

The periodic emergence of novel coronaviruses (CoVs) represents an ongoing public health concern with significant health and financial burden worldwide. The most recent occurrence originated in the city of Wuhan, China where a novel coronavirus (SARS-CoV-2) emerged causing severe respiratory illness and pneumonia. The continual emergence of novel coronaviruses underscores the importance of developing effective vaccines as well as novel therapeutic options that target either viral functions or host factors recruited to support coronavirus replication. The CoV nonstructural protein 1 (nsp1) has been shown to promote cellular mRNA degradation, block host cell translation, and inhibit the innate immune response to virus infection. Interestingly, deletion of the nsp1-coding region in infectious clones prevented the virus from productively infecting cultured cells. Because of nsp1’s importance in the CoV life cycle, it has been highlighted as a viable target for both antiviral therapy and vaccine development. However, the fundamental molecular and structural mechanisms that underlie nsp1 function remain poorly understood, despite its critical role in the viral life cycle. Here we report the high-resolution crystal structure of the amino, globular portion of SARS-CoV-2 nsp1 (residues 10 – 127) at 1.77 Å resolution. A comparison of our structure with the SARS-CoV-1 nsp1 structure reveals how mutations alter the conformation of flexible loops, inducing the formation of novel secondary structural elements and new surface features. Paired with the recently published structure of the carboxyl end of nsp1 (residues 148 – 180), our results provide the groundwork for future studies focusing on SARS-CoV-2 nsp1 structure and function during the viral life cycle. IMPORTANCE The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the causative agent for the COVID-19 pandemic. One protein known to play a critical role in the coronavirus life cycle is nonstructural protein1 (nsp1). As such, it has been highlighted in numerous studies as a target for both the development of antivirals and for the design of live-attenuated vaccines. Here we report the high-resolution crystal structure of nsp1 derived from SARS-CoV-2 at 1.77 Å resolution. This structure will facilitate future studies focusing on understanding the relationship between structure and function for nsp1. In turn, understanding these structure-function relationships will allow nsp1 to be fully exploited as a target for both antiviral development and vaccine design.

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