Pub Date : 2023-04-03DOI: 10.1080/0889311X.2023.2208518
G. Zanotti
The structure–function paradigm, i.e. the concept that it is the three-dimensional structure of a protein that determines its function, has been partially modified by the discovery that a significant portion of the eukaryotic proteome is disordered and that this disorder is often functional. The presence of disorder is the origin of several issues, but the most relevant, at least from the biomedical point of view, is the difficulty of designing drugs in absence of a well-defined conformation of the target. To make the problem worse, we have to consider that often the disorder concerns proteins involved in diseases very relevant for human health, as cancer or neurodegenerative disorders. This review tries to summarize the state of the art of our knowledge on the subject and to describe the tools used to detect disorder and how drug design techniques used for well-folded proteins have been adjusted to this more challenging situation. Abbreviations: AD: Alzheimer’s disease; CAID: Critical assessment of intrinsic protein disorder; CASP: Critical assessment of protein structure prediction; CD: circular dichroism; Cryo-EM: cryo-electron microscopy; DIBS: differential binding score; FRET: Förster resonance energy transfer; HD: Huntington’s disease; IDR: Intrinsically disordered regions; IDP: intrinsically disordered proteins; LDR: long intrinsically disordered regions; MG: Molten globule; MoRF: Molecular recognition feature; NMR: Nuclear magnetic resonance; PDB: Protein Data Bank; PD: Parkinson’s disease; POMS: polyoxometalates; SAXS: Small-angle X-ray scattering; SLiMS: short linear motifs; TFs: Transcription factors.
{"title":"Intrinsic disorder and flexibility in proteins: a challenge for structural biology and drug design","authors":"G. Zanotti","doi":"10.1080/0889311X.2023.2208518","DOIUrl":"https://doi.org/10.1080/0889311X.2023.2208518","url":null,"abstract":"The structure–function paradigm, i.e. the concept that it is the three-dimensional structure of a protein that determines its function, has been partially modified by the discovery that a significant portion of the eukaryotic proteome is disordered and that this disorder is often functional. The presence of disorder is the origin of several issues, but the most relevant, at least from the biomedical point of view, is the difficulty of designing drugs in absence of a well-defined conformation of the target. To make the problem worse, we have to consider that often the disorder concerns proteins involved in diseases very relevant for human health, as cancer or neurodegenerative disorders. This review tries to summarize the state of the art of our knowledge on the subject and to describe the tools used to detect disorder and how drug design techniques used for well-folded proteins have been adjusted to this more challenging situation. Abbreviations: AD: Alzheimer’s disease; CAID: Critical assessment of intrinsic protein disorder; CASP: Critical assessment of protein structure prediction; CD: circular dichroism; Cryo-EM: cryo-electron microscopy; DIBS: differential binding score; FRET: Förster resonance energy transfer; HD: Huntington’s disease; IDR: Intrinsically disordered regions; IDP: intrinsically disordered proteins; LDR: long intrinsically disordered regions; MG: Molten globule; MoRF: Molecular recognition feature; NMR: Nuclear magnetic resonance; PDB: Protein Data Bank; PD: Parkinson’s disease; POMS: polyoxometalates; SAXS: Small-angle X-ray scattering; SLiMS: short linear motifs; TFs: Transcription factors.","PeriodicalId":54385,"journal":{"name":"Crystallography Reviews","volume":"29 1","pages":"48 - 75"},"PeriodicalIF":3.0,"publicationDate":"2023-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44319553","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-01-02DOI: 10.1080/0889311x.2023.2197304
P. Bombicz
{"title":"Various structures from thin films via hydrogels to viruses – what the discovery of diffraction by Max von Laue offers in present times","authors":"P. Bombicz","doi":"10.1080/0889311x.2023.2197304","DOIUrl":"https://doi.org/10.1080/0889311x.2023.2197304","url":null,"abstract":"","PeriodicalId":54385,"journal":{"name":"Crystallography Reviews","volume":"29 1","pages":"1 - 2"},"PeriodicalIF":3.0,"publicationDate":"2023-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44647157","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-01-02DOI: 10.1080/0889311X.2023.2173744
D. C. Briggs, Luise Kandler, Lisa Schmidt, G. Santoni, A. Thorn
ABSTRACT The coronavirus SARS-CoV-2 is the causative agent for the COVID-19 pandemic. Its proteome is typically separated into three classes of proteins: (1) Structural proteins which facilitate the transport and host cell infiltration of the viral RNA, (2) non-structural proteins which are thought to be essential for the viral life cycle and are all produced from open reading frame 1ab (ORF1ab) on the RNA, and (3) everything else, called accessory proteins. Although it was originally thought that these accessory proteins are non-essential for viral replication, a growing body of evidence suggests that these diverse proteins have crucial roles in virus-host interactions, in particular in the way they interfere with the signalling pathways that modulate the host cell’s response to infection and viral pathogenicity. Here, we summarize efforts to structurally characterize the accessory proteins from SARS-CoV-2.
{"title":"Structural biology of SARS-CoV-2 accessory proteins","authors":"D. C. Briggs, Luise Kandler, Lisa Schmidt, G. Santoni, A. Thorn","doi":"10.1080/0889311X.2023.2173744","DOIUrl":"https://doi.org/10.1080/0889311X.2023.2173744","url":null,"abstract":"ABSTRACT The coronavirus SARS-CoV-2 is the causative agent for the COVID-19 pandemic. Its proteome is typically separated into three classes of proteins: (1) Structural proteins which facilitate the transport and host cell infiltration of the viral RNA, (2) non-structural proteins which are thought to be essential for the viral life cycle and are all produced from open reading frame 1ab (ORF1ab) on the RNA, and (3) everything else, called accessory proteins. Although it was originally thought that these accessory proteins are non-essential for viral replication, a growing body of evidence suggests that these diverse proteins have crucial roles in virus-host interactions, in particular in the way they interfere with the signalling pathways that modulate the host cell’s response to infection and viral pathogenicity. Here, we summarize efforts to structurally characterize the accessory proteins from SARS-CoV-2.","PeriodicalId":54385,"journal":{"name":"Crystallography Reviews","volume":"29 1","pages":"3 - 18"},"PeriodicalIF":3.0,"publicationDate":"2023-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45095488","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-01-02DOI: 10.1080/0889311X.2023.2185613
M. Moore
{"title":"Max von Laue – intrepid and true: a biography of the physics Nobel laureate","authors":"M. Moore","doi":"10.1080/0889311X.2023.2185613","DOIUrl":"https://doi.org/10.1080/0889311X.2023.2185613","url":null,"abstract":"","PeriodicalId":54385,"journal":{"name":"Crystallography Reviews","volume":"29 1","pages":"38 - 41"},"PeriodicalIF":3.0,"publicationDate":"2023-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45589805","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-01-02DOI: 10.1080/0889311X.2023.2187051
Josef Simbrunner, I. Salzmann, R. Resel
ABSTRACT Grazing Incidence X-ray Diffraction (GIXD) has been established as a powerful tool for the structural characterization of thin films. However, indexing of the experimentally observed diffraction peaks without prior knowledge of the involved crystal lattices has turned out as a challenging task. During the last years a series of works were published which introduce indexing methods for different methods of GIXD experiments. Static GIXD measurements are performed at fixed sample positions for thin films with preferred orientation of the crystallites relative to the substrate surface but without any in-plane order. Rotated GIXD measurements use rotation of the thin film sample about the substrate normal and collect for each rotation angle a single detector image. This method is used for crystals with azimuthal alignments within the thin film. A comprehensive mathematical framework is developed which provides the assignment of Laue indices to the individual diffraction peaks. The algorithms are even reduced from the three-dimensional case to two-dimensional representation of the experimental results. Despite the fact that GIXD experiments provide only a limited number of diffraction peaks, indexing became possible even for thin film crystals with low symmetry, different preferred orientations and multiple azimuthal alignments.
{"title":"Indexing of grazing-incidence X-ray diffraction patterns","authors":"Josef Simbrunner, I. Salzmann, R. Resel","doi":"10.1080/0889311X.2023.2187051","DOIUrl":"https://doi.org/10.1080/0889311X.2023.2187051","url":null,"abstract":"ABSTRACT Grazing Incidence X-ray Diffraction (GIXD) has been established as a powerful tool for the structural characterization of thin films. However, indexing of the experimentally observed diffraction peaks without prior knowledge of the involved crystal lattices has turned out as a challenging task. During the last years a series of works were published which introduce indexing methods for different methods of GIXD experiments. Static GIXD measurements are performed at fixed sample positions for thin films with preferred orientation of the crystallites relative to the substrate surface but without any in-plane order. Rotated GIXD measurements use rotation of the thin film sample about the substrate normal and collect for each rotation angle a single detector image. This method is used for crystals with azimuthal alignments within the thin film. A comprehensive mathematical framework is developed which provides the assignment of Laue indices to the individual diffraction peaks. The algorithms are even reduced from the three-dimensional case to two-dimensional representation of the experimental results. Despite the fact that GIXD experiments provide only a limited number of diffraction peaks, indexing became possible even for thin film crystals with low symmetry, different preferred orientations and multiple azimuthal alignments.","PeriodicalId":54385,"journal":{"name":"Crystallography Reviews","volume":"29 1","pages":"19 - 37"},"PeriodicalIF":3.0,"publicationDate":"2023-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42468816","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-10-02DOI: 10.1080/0889311X.2022.2131154
P. Bombicz
Why is it interesting to study ice? The book reviewed in this issue 4 of Volume 28 of Crystallography Reviews boosts the reader’s amazement, enthusiasm and curiosity about the wonder and science of ice and snowflakes. While the review article gives a comprehensive overview of all the known twenty polymorphic forms of ice with an outlook to further predictable forms. Hydrogen is the most common element in the Universe, around 75% of all atoms in our galaxy is hydrogen. Oxygen is the third most common element in space, making up about 1% of all the atoms. Water, made of these two elements, plays a key role in the formation and evolution of our planetary system and it is essential in the life on Earth. The planet Earth is formed in the warm part of the sun’s protoplanetary disk, at a location well within the ‘snow line’. The presence of water is vital in the search for extraterrestrial life. Brighter regions observed by an optical telescope could indicate reflections of frozen water. Landers and rovers can collect samples from the surface of a planet to be placed in an analysis chamber. There is water-ice on the surface of the moon near the poles [1]. A subglacial lake on Mars, 1.5 km below the southern polar ice cap was detected [2]. Asteroids in the asteroid belt also contain large amounts of water-ice that could be harvested if humans ever regularly travel beyond the inner Solar System. Europa, a moon of Jupiter, and Enceladus, a moon of Saturn, have huge subsurface oceans with a layer of tens or hundreds of kilometres of ice covering their surfaces. Other moons of Jupiter and Saturn such as Ganymede and Titan may have subsurface oceans as well. There are very likely still millions of other icy bodies out there, just waiting to be explored. The varying conditions on the myriads of planets, moons, asteroids in space provide the opportunity of the probable formation of different ice polymorphs. Although ice may be one of the most studied crystalline solids in human history, new discoveries on ice are still being reported on a regular basis. The full review article ‘Neutrons meet ice polymorphs’ by Kazuki Komatsu from the Geochemical Research Center, Graduate School of Science, The University of Tokyo, Japan, gives an extensive review of the discovery and crystallographic characterization of ice polymorphs formed in different conditions. The presented historical background elucidates the experimental difficulties in ice research. The current epoch described by the author is the ‘age of ice-rush’, as the rate of discovery of ice polymorphs has accelerated in the last two decades owing to the advances in neutron diffraction studies of ice under pressure. The most extreme conditions, of both high-temperature and high-pressure, led to a new ice polymorph being created (namely XVIII) at 100GPa and 2000K. The transition between hydrogen-ordered and hydrogen-disordered phases is a common problem for many ice polymorphs. Ice polymorphs may exist in fully or
{"title":"Crystallography of ice","authors":"P. Bombicz","doi":"10.1080/0889311X.2022.2131154","DOIUrl":"https://doi.org/10.1080/0889311X.2022.2131154","url":null,"abstract":"Why is it interesting to study ice? The book reviewed in this issue 4 of Volume 28 of Crystallography Reviews boosts the reader’s amazement, enthusiasm and curiosity about the wonder and science of ice and snowflakes. While the review article gives a comprehensive overview of all the known twenty polymorphic forms of ice with an outlook to further predictable forms. Hydrogen is the most common element in the Universe, around 75% of all atoms in our galaxy is hydrogen. Oxygen is the third most common element in space, making up about 1% of all the atoms. Water, made of these two elements, plays a key role in the formation and evolution of our planetary system and it is essential in the life on Earth. The planet Earth is formed in the warm part of the sun’s protoplanetary disk, at a location well within the ‘snow line’. The presence of water is vital in the search for extraterrestrial life. Brighter regions observed by an optical telescope could indicate reflections of frozen water. Landers and rovers can collect samples from the surface of a planet to be placed in an analysis chamber. There is water-ice on the surface of the moon near the poles [1]. A subglacial lake on Mars, 1.5 km below the southern polar ice cap was detected [2]. Asteroids in the asteroid belt also contain large amounts of water-ice that could be harvested if humans ever regularly travel beyond the inner Solar System. Europa, a moon of Jupiter, and Enceladus, a moon of Saturn, have huge subsurface oceans with a layer of tens or hundreds of kilometres of ice covering their surfaces. Other moons of Jupiter and Saturn such as Ganymede and Titan may have subsurface oceans as well. There are very likely still millions of other icy bodies out there, just waiting to be explored. The varying conditions on the myriads of planets, moons, asteroids in space provide the opportunity of the probable formation of different ice polymorphs. Although ice may be one of the most studied crystalline solids in human history, new discoveries on ice are still being reported on a regular basis. The full review article ‘Neutrons meet ice polymorphs’ by Kazuki Komatsu from the Geochemical Research Center, Graduate School of Science, The University of Tokyo, Japan, gives an extensive review of the discovery and crystallographic characterization of ice polymorphs formed in different conditions. The presented historical background elucidates the experimental difficulties in ice research. The current epoch described by the author is the ‘age of ice-rush’, as the rate of discovery of ice polymorphs has accelerated in the last two decades owing to the advances in neutron diffraction studies of ice under pressure. The most extreme conditions, of both high-temperature and high-pressure, led to a new ice polymorph being created (namely XVIII) at 100GPa and 2000K. The transition between hydrogen-ordered and hydrogen-disordered phases is a common problem for many ice polymorphs. Ice polymorphs may exist in fully or","PeriodicalId":54385,"journal":{"name":"Crystallography Reviews","volume":"28 1","pages":"221 - 223"},"PeriodicalIF":3.0,"publicationDate":"2022-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45202281","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-10-02DOI: 10.1080/0889311X.2022.2127148
K. Komatsu
The current epoch can be described as the ‘age of ice-rush’, as the rate of discovery of ice polymorphs, of which there are currently 20 known, has accelerated, particularly since the end of the last century. This is largely owing to advances in neutron diffraction under pressure. Neutrons can interact with light elements such as hydrogen as well as heavy elements, making neutron diffraction essential for full structural analyses of newly discovered ice polymorphs. It is especially useful for detecting crystallographic symmetry breaking due to hydrogen ordering. This review will go over the most recent technical advances in neutron-diffraction experiments and how they contribute to our understanding of ice polymorphs.
{"title":"Neutrons meet ice polymorphs","authors":"K. Komatsu","doi":"10.1080/0889311X.2022.2127148","DOIUrl":"https://doi.org/10.1080/0889311X.2022.2127148","url":null,"abstract":"The current epoch can be described as the ‘age of ice-rush’, as the rate of discovery of ice polymorphs, of which there are currently 20 known, has accelerated, particularly since the end of the last century. This is largely owing to advances in neutron diffraction under pressure. Neutrons can interact with light elements such as hydrogen as well as heavy elements, making neutron diffraction essential for full structural analyses of newly discovered ice polymorphs. It is especially useful for detecting crystallographic symmetry breaking due to hydrogen ordering. This review will go over the most recent technical advances in neutron-diffraction experiments and how they contribute to our understanding of ice polymorphs.","PeriodicalId":54385,"journal":{"name":"Crystallography Reviews","volume":"28 1","pages":"224 - 297"},"PeriodicalIF":3.0,"publicationDate":"2022-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47125482","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-07-27DOI: 10.1080/0889311x.2022.2104839
Vesselin Dimitrov Tonchev, V. Stoyanova
{"title":"Snow crystals: a case study in spontaneous structure formation","authors":"Vesselin Dimitrov Tonchev, V. Stoyanova","doi":"10.1080/0889311x.2022.2104839","DOIUrl":"https://doi.org/10.1080/0889311x.2022.2104839","url":null,"abstract":"","PeriodicalId":54385,"journal":{"name":"Crystallography Reviews","volume":"28 1","pages":"298 - 300"},"PeriodicalIF":3.0,"publicationDate":"2022-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48242186","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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