Quarterly Reviews of Biophysics

1. Introduction 370

2. Infrared (IR) spectroscopy – general principles 372

2.1 Vibrations 372

2.2 Information that can be derived from the vibrational spectrum 372

2.3 Absorption of IR light 375

3. Protein IR absorption 376

3.1 Amino-acid side-chain absorption 376

3.2 Normal modes of the amide group 381

4. Interactions that shape the amide I band 382

4.1 Overview 382

4.2 Through-bond coupling 383

4.3 Hydrogen bonding 383

4.4 Transition dipole coupling (TDC) 383

5. The polarization and IR activity of amide I modes 387

5.1 The coupled oscillator system 387

5.2 Optically allowed transitions 388

5.3 The infinite parallel β-sheet 388

5.4 The infinite antiparallel β-sheet 389

5.5 The infinite α-helix 390

6. Calculation of the amide I band 391

6.1 Overview 391

6.2 Perturbation treatment by Miyazawa 393

6.3 The parallel β-sheet 394

6.4 The antiparallel β-sheet 395

6.5 The α-helix 396

6.6 Other secondary structures 398

7. Experimental analysis of protein secondary structure 398

7.1 Band fitting 398

7.2 Methods using calibration sets 401

7.3 Prediction quality 403

8. Protein stability 404

8.1 Thermal stability 404

8.2 ¹H/²H exchange 406

9. Molecular reaction mechanisms of proteins 408

9.1 Reaction-induced IR difference spectroscopy 408

9.2 The origin of difference bands 409

9.3 The difference spectrum seen as a fingerprint of conformational change 410

9.4 Molecular interpretation: strategies of band assignment 416

10. Outlook 419

11. Acknowledgements 420

12. References 420

This 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.

Single unit recordings have provided us with a basis for understanding the auditory system, especially about how it behaves under stimulation with simple sounds such as clicks and tones. The experimental as well as the theoretical approach to single unit studies has been dichotomous. One approach, the more familiar, gives a representation of nervous system activity in the form of peri-stimulus-time (PST) histograms, period histograms, iso-intensity rate curves and frequency tuning curves. This approach observes the neural output of units in the various nuclei in the auditory nervous system, and, faced with the random way in which the neurons respond to sound, proceeds by repeatedly presenting the same stimulus in order to obtain averaged results. These are the various histogram procedures (Gerstein & Kiang, 1960; Kiang et al. 1965).

Means to cause an immunogenic cell death could lead to significant insight into how cancer escapes immune control. In this study, we screened a library of five pyrrole–imidazole polyamides coding for different DNA sequences in a model of B-cell lymphoma for the upregulation of surface calreticulin, a pro-phagocytosis signal implicated in immunogenic cell death. We found that hairpin polyamide 1 triggers the release of the damage-associated molecular patterns calreticulin, ATP and HMGB1 in a slow necrotic-type cell death. Consistent with this signaling, we observed an increase in the rate of phagocytosis by macrophages after the cancer cells were exposed to polyamide 1. The DNA sequence preference of polyamide 1 is 5′-WGGGTW-3′ (where W = A/T), indicated by the pairing rules and confirmed by the Bind-n-Seq method. The close correspondence of this sequence with the telomere-repeat sequence suggests a potential mechanism of action through ligand binding at the telomere. This study reveals a chemical means to trigger an inflammatory necrotic cell death in cancer cells.

Alcohol based cosolvents, such as trifluoroethanol (TFE) have been used for many decades to denature proteins and to stabilize structures in peptides. Nuclear magnetic resonance spectroscopy and site directed mutagenesis have recently made it possible to characterize the effects of TFE and of other alcohols on polypeptide structure and dynamics at high resolution. This review examines such studies, particularly of hen lysozyme and β-lactoglobulin. It presents an overview of what has been learnt about conformational preferences of the polypeptide chain, the interactions that stabilize structures and the nature of the denatured states. The effect of TFE on transition states and on the pathways of protein folding and unfolding are also reviewed. Despite considerable progress there is as yet no single mechanism that accounts for all of the effects TFE and related cosolvents have on polypeptide conformation. However, a number of critical questions are beginning to be answered. Studies with alcohols such as TFE, and ‘cosolvent engineering’ in general, have become valuable tools for probing biomolecular structure, function and dynamics.

1. COSOLVENTS: OLD HAT? 298

2. HOW DOES TFE WORK? 299

2.1 Effect on hydrogen bonding 300

2.2 Effect on non-polar sidechains 301

2.3 Effect on solvent structure 302

3. EFFECTS OF TFE ON (UN-)FOLDING TRANSITIONS 303

3.1 Pretransition 303

3.2 Transition 304

3.3 Posttransition 305

3.4 Far UV CD spectroscopic detection of structure 306

3.5 Effect with temperature 306

3.6 Effect with additional denaturants 306

4. THERMODYNAMIC PARAMETERS FROM STRUCTURAL TRANSITIONS OF PEPTIDES AND PROTEINS IN TFE 307

5. ADVANCES IN NMR SPECTROSCOPY 310

5.1 Chemical shifts 310

5.2 ³[Jscr ]_HNHαcoupling constants 311

5.3 Amide hydrogen exchange 312

5.4 Nuclear Overhauser Effects (NOEs) 312

6. α-HELIX – EVERYWHERE? 313

6.1 Intrinsic helix propensity equals helix content? 313

6.2 A helix propensity scale for the amino acids in TFE 314

6.3 Capping motifs and stop signals 315

6.4 Limits and population of helices as seen by CD and NMR 316

7. TURNS 317

8. β-HAIRPINS AND SHEETS 317

9. ‘CLUSTERS’ OF SIDECHAINS 320

10. THE TFE DENATURED STATE OF β-LACTOGLOBULIN 321

11. THE TFE DENATURED STATE OF HEN LYSOZYME 324

12. TERTIARY STRUCTURE, DISULPHIDES, DYNAMICS AND COMPACTNESS 327

13. PROSPECTS FOR STRUCTURE CALCULATION 328

14. EFFECT OF TFE ON QUATERNARY STRUCTURE 329

15. EFFECT ON TFE ON UN- AND REFOLDING KINETICS 330

16. OTHER USES 336

16.1 Mimicking membranes and protein receptors 336

16.2 Solubilizing peptides and proteins 336

16.3 Cosolvents as helpers for protein folding? 338

16.4 Modifying protein dynamics and catalysis 338

16.5 Effects on nucleic acids 339

16.6 Effects on lipid bilayers and micelles 339

16.7 Future applications 339

17. CONCLUSIONS: TFE – WHAT IS IT GOOD FOR? 340

18. ACKNOWLEDGMENTS 340

19. REFERENCES 340

Introduction 351

Part I. A succession of concepts 352

1. Cooperativity 352

2. Cosolvent interaction 352

3. Linearity 354

4. Solvent exchange 354

5. Excluded volume 356

6. Summation 357

Part II

1. The Kirkwood–Buff approach 357

Acknowledgments 360

References 360

In Part I the history of progress in the stabilization and destabilization of protein conformations by means of cosolvents is outlined in terms of distinct conceptual steps. In Part II it is shown that a straightforward application of the Kirkwood–Buff theory of solutions leads to formulas for the preferential interaction and the free energy of unfolding, which confirm and generalize the results of Part I.

Proteins and other biomolecules contain acidic and basic titratable groups that give rise to intricate charge distributions and control electrostatic interactions. ‘Charge regulation’ concerns how the proton equilibria of these sites are perturbed when approached by alien molecular matter such as other proteins, surfaces and membranes, DNA, polyelectrolytes etc. Importantly, this perturbation generates a charge response that leads to attractive intermolecular interactions that can be conveniently described by a single molecular property – the charge capacitance. The capacitance quantifies molecular charge fluctuations, i.e. it is the variance of the mean charge and is anintrinsicproperty on par with the net charge and the dipole moment. It directly enters the free energy expression for intermolecular interactions and can be obtained experimentally from the derivative of the titration curve or theoretically from simulations. In this review, we focus on the capacitance concept as a predictive parameter for charge regulation and demonstrate how it can be used to estimate the interaction of a protein with other proteins, polyelectrolytes, membranes as well as with ligands.

It is generally acknowledged that geometrical and conformational properties of biopolymers have an important effect on their biochemical behaviour. It is less easily recognized that these properties depend also on their macromolecular electronic characteristics.

The aim of this review is to demonstrate the significance of such macromolecular electronic effects. Particularly useful for this sake is the recently much developed concept of ‘molecular electrostatic potential’ (MEP) (Scrocco & Tomasi, 1973, 1978) by which is defined the electrostatic (Coulomb) potential created in the neighbouring space by the nuclear charges and the eletronic distribution of a molecule.

1. Giới thiệu 2

2. Ý nghĩa của các đặc tính cấu trúc chung của các sợi amyloid liên quan đến bệnh? 3

2.1 Cơ chế hình thành sợi amyloid in vitro 6

2.1.1 Quá trình hình thành sợi in vitro bao gồm sự tập hợp tạm thời của các chất kết tập có độ ổn định trung gian, hoặc protofibrils 6

3. Các đặc tính độc hại của protofibrils 7

3.1 Các protofibrils, chứ không phải sợi fibrils, có khả năng là chất gây bệnh 7

3.2 Protofibrils độc hại có thể là một hỗn hợp của các loài liên quan 8

3.3 Các đặc điểm hình thái của protofibrils gợi ý một cơ chế độc tính chung 9

3.4 Liệu các bệnh amyloid có phải là một tập hợp con của một lớp bệnh protofibrils lớn hơn chưa được công nhận? 9

3.5 Sợi fibrils, dưới dạng aggresomes, có thể hoạt động để cô lại các protofibrils độc hại 9

4. Lỗ amyloid, một liên kết cấu trúc chung giữa các bệnh thoái hóa thần kinh do kết tập protein 10

4.1 Các nghiên cứu cơ chế về sự hình thành sợi amyloid tiết lộ các đặc điểm chung, bao gồm protofibrils giống như lỗ 10

4.1.1 Amyloid-β (Aβ) (bệnh Alzheimer) 10

4.1.2 α-Synuclein (bệnh Parkinson và bệnh thể Lewy lan tỏa) 12

4.1.3 ABri (bệnh mất trí nhớ gia đình Anh) 13

4.1.4 Superoxide dismutase-1 (bệnh xơ cứng teo cơ một bên - ALS) 13

4.1.5 Protein Prion (bệnh Creutzfeldt–Jakob, bệnh bò điên, v.v.) 14

4.1.6 Huntingtin (bệnh Huntington) 14

4.2 Các protein amyloidogenic không liên quan đến bệnh cũng hình thành protofibrils giống lỗ 15

4.3 Các protein amyloid hình thành các chất kết tập không theo dạng sợi có đặc tính của kênh protein hoặc lỗ 15

4.3.1 Kênh Aβ 15

4.3.2 Lỗ α-Synuclein 16

4.3.3 Kênh PrP 16

4.3.4 Kênh Polyglutamine 17

4.4 Tự nhiên sử dụng dây β để tạo độc tố tạo lỗ protein bằng cách liên kết các phân tử protein 17

5. Cơ chế độc tính gây ra bởi protofibrils trong các bệnh kết tập protein 19

5.1 Lỗ amyloid có thể giải thích sự liên quan đến tuổi và tính chọn lọc của các bệnh thoái hóa thần kinh 19

5.2 Protofibrils có thể thúc đẩy sự tích lũy của chính nó bằng cách ức chế proteasome 20

6. Kiểm tra giả thuyết lỗ amyloid bằng cách cố thử chứng minh nó sai 21

7. Lời cảm ơn 22

8. Tài liệu tham khảo 22

Sự kết tụ protein có liên quan đến cơ chế bệnh sinh của hầu hết, nếu không muốn nói là tất cả, các bệnh thoái hóa thần kinh gắn với tuổi tác. Tuy nhiên, cơ chế mà bằng cách nào nó kích hoạt cái chết của tế bào thần kinh vẫn chưa được biết. Các nghiên cứu in vitro theo hướng làm giảm các yếu tố gợi ý rằng protofibril amyloid có thể là loài độc hại và nó có thể tự khuếch đại bằng cách ức chế sự phân giải protein phụ thuộc vào proteasome. Mặc dù mục tiêu gây bệnh của nó vẫn chưa được xác định, các đặc tính của protofibril gợi ý rằng các tế bào thần kinh có thể bị tiêu diệt bởi sự thấm màng mà không được kiểm soát, có thể do một loại protofibril được gọi là “lỗ amyloid". Mục đích của bài đánh giá này là tóm tắt bằng chứng hỗ trợ hiện có và khuyến khích các nghiên cứu tiếp theo nhằm kiểm tra tính hợp lý của giả thuyết này.

Calcium ion plays an essential role in many biological processes. The environment about Ca²⁺may be probed by substitution of tripositive lanthanide ions, Ln³⁺. Ca²⁺proteins fall into two broad classes: those that are inhibited by Ln³⁺substitution and those that are not. It is suggested that although Ca²⁺undertakes a primarily structural role in the Ln³⁺non-inhibited proteins, Ca²⁺may be near the active site or participate in the mechanism of action of Ln³⁺inhibited proteins. Ca²⁺and Ln³⁺radii are similar; most Ln³⁺are slightly larger than Ca²⁺in complexes of the same coordination number, and substitution of Ln³⁺for Ca²⁺is accommodated by a slight decrease in bond distance or by an increase in coordination number. Luminescence from Tb³⁺has been demonstrated to be a sensitive environmental probe of Ca²⁺binding sites in proteins.

Fluorescence turn-on aptamers,in vitroevolved RNA molecules that bind conditional fluorophores and activate their fluorescence, have emerged as RNA counterparts of the fluorescent proteins. Turn-on aptamers have been selected to bind diverse fluorophores, and they achieve varying degrees of specificity and affinity. These RNA–fluorophore complexes, many of which exceed the brightness of green fluorescent protein and their variants, can be used as tags for visualizing RNA localization and transport in live cells. Structure determination of several fluorescent RNAs revealed that they have diverse, unrelated overall architectures. As most of these RNAs activate the fluorescence of their ligands by restraining their photoexcited states into a planar conformation, their fluorophore binding sites have in common a planar arrangement of several nucleobases, most commonly a G-quartet. Nonetheless, each turn-on aptamer has developed idiosyncratic structural solutions to achieve specificity and efficient fluorescence turn-on. The combined structural diversity of fluorophores and turn-on RNA aptamers has already produced combinations that cover the visual spectrum. Further molecular evolution and structure-guided engineering is likely to produce fluorescent tags custom-tailored to specific applications.